Starting phenix.real_space_refine on Wed Feb 4 12:02:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dor_47089/02_2026/9dor_47089.map" } resolution = 3.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6598 2.51 5 N 1794 2.21 5 O 1865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10295 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "A" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1841 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "G" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2763 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain: "F" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2844 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 17, 'TRANS': 344} Chain: "C" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1006 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 124} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 1.87, per 1000 atoms: 0.18 Number of scatterers: 10295 At special positions: 0 Unit cell: (70.2, 99.36, 160.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1865 8.00 N 1794 7.00 C 6598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 462.5 milliseconds 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 10 sheets defined 51.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 41 through 51 Processing helix chain 'B' and resid 71 through 79 Processing helix chain 'B' and resid 94 through 104 removed outlier: 4.377A pdb=" N ILE B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.676A pdb=" N PHE B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 154 Processing helix chain 'B' and resid 169 through 187 removed outlier: 4.237A pdb=" N GLY B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 204 removed outlier: 3.805A pdb=" N THR B 200 " --> pdb=" O ASN B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.566A pdb=" N LYS B 231 " --> pdb=" O ASN B 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 71 through 79 Processing helix chain 'A' and resid 94 through 106 removed outlier: 3.819A pdb=" N ILE A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 139 through 154 removed outlier: 3.825A pdb=" N SER A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 removed outlier: 3.525A pdb=" N LYS A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.799A pdb=" N THR A 200 " --> pdb=" O ASN A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'G' and resid 2 through 36 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 44 through 82 Proline residue: G 57 - end of helix Proline residue: G 65 - end of helix Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 94 through 138 Proline residue: G 105 - end of helix Proline residue: G 122 - end of helix removed outlier: 3.913A pdb=" N GLY G 138 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 239 removed outlier: 3.761A pdb=" N THR G 236 " --> pdb=" O GLN G 232 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET G 239 " --> pdb=" O ASN G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 245 through 260 removed outlier: 3.591A pdb=" N GLN G 259 " --> pdb=" O TYR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 275 Processing helix chain 'G' and resid 275 through 292 Processing helix chain 'G' and resid 299 through 328 removed outlier: 3.522A pdb=" N GLY G 322 " --> pdb=" O GLN G 318 " (cutoff:3.500A) Proline residue: G 323 - end of helix removed outlier: 3.841A pdb=" N LEU G 326 " --> pdb=" O GLY G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 331 through 353 removed outlier: 3.879A pdb=" N ALA G 335 " --> pdb=" O PRO G 331 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL G 336 " --> pdb=" O PRO G 332 " (cutoff:3.500A) Proline residue: G 339 - end of helix Processing helix chain 'F' and resid 2 through 41 removed outlier: 4.116A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 47 through 82 Proline residue: F 57 - end of helix Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 83 through 90 Processing helix chain 'F' and resid 94 through 119 removed outlier: 4.263A pdb=" N ALA F 104 " --> pdb=" O GLY F 100 " (cutoff:3.500A) Proline residue: F 105 - end of helix Processing helix chain 'F' and resid 119 through 136 Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'F' and resid 241 through 248 removed outlier: 3.875A pdb=" N SER F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER F 246 " --> pdb=" O PRO F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 275 Processing helix chain 'F' and resid 275 through 292 removed outlier: 4.431A pdb=" N LEU F 279 " --> pdb=" O LEU F 275 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 289 " --> pdb=" O THR F 285 " (cutoff:3.500A) Proline residue: F 290 - end of helix Processing helix chain 'F' and resid 304 through 327 Processing helix chain 'F' and resid 336 through 352 removed outlier: 4.146A pdb=" N HIS F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 361 Processing helix chain 'C' and resid 112 through 115 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 27 removed outlier: 6.109A pdb=" N VAL B 18 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N SER B 12 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG B 20 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA B 10 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL B 22 " --> pdb=" O HIS B 8 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 8 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 9 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 57 " --> pdb=" O LEU B 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.629A pdb=" N LEU B 83 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 31 " --> pdb=" O THR B 206 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N TYR B 208 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY B 33 " --> pdb=" O TYR B 208 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 210 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU B 35 " --> pdb=" O VAL B 210 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 207 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU B 218 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE B 209 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 17 through 27 removed outlier: 6.214A pdb=" N VAL A 18 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N SER A 12 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A 20 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 10 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N VAL A 22 " --> pdb=" O HIS A 8 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 9 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLN A 57 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 83 removed outlier: 3.838A pdb=" N ASP A 162 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 191 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE A 31 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N TYR A 208 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 33 " --> pdb=" O TYR A 208 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 210 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 35 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 217 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASN A 211 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 148 through 152 removed outlier: 6.955A pdb=" N GLU G 155 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG G 175 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE G 157 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG G 173 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE G 159 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 171 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS G 189 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR G 172 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE G 187 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR G 174 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA G 185 " --> pdb=" O TYR G 174 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA G 188 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL G 203 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG G 190 " --> pdb=" O GLU G 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 148 through 152 removed outlier: 6.955A pdb=" N GLU G 155 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG G 175 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE G 157 " --> pdb=" O ARG G 173 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ARG G 173 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE G 159 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL G 171 " --> pdb=" O ILE G 159 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS G 189 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR G 172 " --> pdb=" O PHE G 187 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE G 187 " --> pdb=" O THR G 172 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR G 174 " --> pdb=" O ALA G 185 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA G 185 " --> pdb=" O TYR G 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.555A pdb=" N SER F 191 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 190 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 68 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 92 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 150 through 152 removed outlier: 3.555A pdb=" N SER F 191 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE F 190 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR C 68 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 92 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL C 117 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE C 145 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N LEU C 119 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N THR C 143 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ASP C 121 " --> pdb=" O ARG C 141 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ARG C 141 " --> pdb=" O ASP C 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 199 through 202 Processing sheet with id=AB1, first strand: chain 'C' and resid 50 through 53 628 hydrogen bonds defined for protein. 1794 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3401 1.34 - 1.46: 2050 1.46 - 1.58: 4967 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 10488 Sorted by residual: bond pdb=" C GLN G 163 " pdb=" N PRO G 164 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.66e+00 bond pdb=" C THR C 88 " pdb=" N PRO C 89 " ideal model delta sigma weight residual 1.328 1.351 -0.023 1.25e-02 6.40e+03 3.46e+00 bond pdb=" CA GLU C 69 " pdb=" C GLU C 69 " ideal model delta sigma weight residual 1.526 1.509 0.017 1.08e-02 8.57e+03 2.46e+00 bond pdb=" CA PHE F 69 " pdb=" C PHE F 69 " ideal model delta sigma weight residual 1.524 1.505 0.019 1.24e-02 6.50e+03 2.41e+00 bond pdb=" CB GLN F 37 " pdb=" CG GLN F 37 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 ... (remaining 10483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 13898 2.22 - 4.44: 259 4.44 - 6.65: 50 6.65 - 8.87: 8 8.87 - 11.09: 3 Bond angle restraints: 14218 Sorted by residual: angle pdb=" C GLN G 163 " pdb=" N PRO G 164 " pdb=" CA PRO G 164 " ideal model delta sigma weight residual 120.83 115.74 5.09 1.02e+00 9.61e-01 2.49e+01 angle pdb=" CB MET F 238 " pdb=" CG MET F 238 " pdb=" SD MET F 238 " ideal model delta sigma weight residual 112.70 123.79 -11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA GLN F 37 " pdb=" CB GLN F 37 " pdb=" CG GLN F 37 " ideal model delta sigma weight residual 114.10 121.40 -7.30 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA ASN G 82 " pdb=" CB ASN G 82 " pdb=" CG ASN G 82 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.00e+00 1.00e+00 1.30e+01 angle pdb=" N GLY G 166 " pdb=" CA GLY G 166 " pdb=" C GLY G 166 " ideal model delta sigma weight residual 115.30 110.47 4.83 1.39e+00 5.18e-01 1.21e+01 ... (remaining 14213 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5396 17.39 - 34.78: 681 34.78 - 52.17: 175 52.17 - 69.56: 20 69.56 - 86.95: 9 Dihedral angle restraints: 6281 sinusoidal: 2492 harmonic: 3789 Sorted by residual: dihedral pdb=" CA ALA C 80 " pdb=" C ALA C 80 " pdb=" N THR C 81 " pdb=" CA THR C 81 " ideal model delta harmonic sigma weight residual 180.00 160.88 19.12 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA ASP F 326 " pdb=" CB ASP F 326 " pdb=" CG ASP F 326 " pdb=" OD1 ASP F 326 " ideal model delta sinusoidal sigma weight residual -30.00 -87.56 57.56 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP A 21 " pdb=" CB ASP A 21 " pdb=" CG ASP A 21 " pdb=" OD1 ASP A 21 " ideal model delta sinusoidal sigma weight residual -30.00 -86.90 56.90 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 6278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1332 0.052 - 0.104: 269 0.104 - 0.156: 44 0.156 - 0.207: 1 0.207 - 0.259: 2 Chirality restraints: 1648 Sorted by residual: chirality pdb=" CG LEU F 239 " pdb=" CB LEU F 239 " pdb=" CD1 LEU F 239 " pdb=" CD2 LEU F 239 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CG LEU A 118 " pdb=" CB LEU A 118 " pdb=" CD1 LEU A 118 " pdb=" CD2 LEU A 118 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 62 " pdb=" CA ILE A 62 " pdb=" CG1 ILE A 62 " pdb=" CG2 ILE A 62 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.62e-01 ... (remaining 1645 not shown) Planarity restraints: 1817 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 117 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C GLY G 117 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY G 117 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU G 118 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 82 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ASN G 82 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN G 82 " 0.013 2.00e-02 2.50e+03 pdb=" N SER G 83 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 132 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.37e+00 pdb=" C LEU F 132 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU F 132 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN F 133 " -0.011 2.00e-02 2.50e+03 ... (remaining 1814 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 161 2.68 - 3.23: 10232 3.23 - 3.79: 16093 3.79 - 4.34: 20838 4.34 - 4.90: 34346 Nonbonded interactions: 81670 Sorted by model distance: nonbonded pdb=" OE2 GLU G 35 " pdb=" OH TYR G 43 " model vdw 2.124 3.040 nonbonded pdb=" OD1 ASP G 177 " pdb=" N GLU G 178 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR C 143 " pdb=" OE1 GLN C 152 " model vdw 2.251 3.040 nonbonded pdb=" OG SER G 141 " pdb=" OE1 GLN G 142 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR C 138 " pdb=" O LYS C 158 " model vdw 2.272 3.040 ... (remaining 81665 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' selection = chain 'B' } 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 group one per residue 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: 2.580 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 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 0.044 10488 Z= 0.168 Angle : 0.754 11.088 14218 Z= 0.409 Chirality : 0.043 0.259 1648 Planarity : 0.004 0.044 1817 Dihedral : 16.074 86.951 3853 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.09 % Allowed : 25.41 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1314 helix: 1.81 (0.21), residues: 642 sheet: -0.21 (0.37), residues: 205 loop : -1.41 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 173 TYR 0.024 0.002 TYR G 61 PHE 0.017 0.001 PHE G 330 TRP 0.030 0.001 TRP G 225 HIS 0.004 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00317 (10488) covalent geometry : angle 0.75421 (14218) hydrogen bonds : bond 0.16737 ( 575) hydrogen bonds : angle 6.71902 ( 1794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 208 TYR cc_start: 0.8908 (m-80) cc_final: 0.8494 (m-80) REVERT: G 1 MET cc_start: 0.6328 (ttm) cc_final: 0.5947 (ttm) REVERT: G 38 ASP cc_start: 0.8674 (m-30) cc_final: 0.8450 (m-30) REVERT: G 286 MET cc_start: 0.8045 (tmm) cc_final: 0.7498 (tmm) REVERT: F 152 MET cc_start: 0.8885 (tpp) cc_final: 0.8649 (tpp) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.0926 time to fit residues: 27.3243 Evaluate side-chains 184 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 167 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 129 optimal weight: 30.0000 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 ASN F 268 GLN C 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.106732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.080095 restraints weight = 28996.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082457 restraints weight = 13627.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083975 restraints weight = 8326.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084927 restraints weight = 6052.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085420 restraints weight = 4975.193| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10488 Z= 0.127 Angle : 0.622 7.849 14218 Z= 0.317 Chirality : 0.043 0.178 1648 Planarity : 0.004 0.067 1817 Dihedral : 4.485 25.837 1445 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.30 % Allowed : 23.21 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.24), residues: 1314 helix: 1.97 (0.21), residues: 645 sheet: -0.02 (0.34), residues: 229 loop : -1.39 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 190 TYR 0.021 0.002 TYR B 82 PHE 0.014 0.001 PHE F 128 TRP 0.022 0.001 TRP G 225 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00272 (10488) covalent geometry : angle 0.62197 (14218) hydrogen bonds : bond 0.04517 ( 575) hydrogen bonds : angle 5.03109 ( 1794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.309 Fit side-chains REVERT: B 158 PHE cc_start: 0.8625 (m-80) cc_final: 0.8323 (m-80) REVERT: B 208 TYR cc_start: 0.8982 (m-80) cc_final: 0.8484 (m-80) REVERT: B 212 ASP cc_start: 0.7936 (m-30) cc_final: 0.7715 (t0) REVERT: G 173 ARG cc_start: 0.7090 (mtm-85) cc_final: 0.6593 (mtm-85) REVERT: G 190 ARG cc_start: 0.7847 (mtm110) cc_final: 0.7551 (mtm110) REVERT: G 290 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: F 37 GLN cc_start: 0.7579 (tm-30) cc_final: 0.7000 (tm-30) REVERT: F 238 MET cc_start: 0.6997 (tpp) cc_final: 0.6063 (tpp) outliers start: 36 outliers final: 22 residues processed: 215 average time/residue: 0.0798 time to fit residues: 24.7104 Evaluate side-chains 194 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.099819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.073009 restraints weight = 29360.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.075240 restraints weight = 14044.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.076691 restraints weight = 8709.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.077522 restraints weight = 6412.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.078112 restraints weight = 5334.734| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 10488 Z= 0.335 Angle : 0.783 7.580 14218 Z= 0.403 Chirality : 0.048 0.170 1648 Planarity : 0.006 0.075 1817 Dihedral : 5.030 34.242 1445 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.96 % Allowed : 22.94 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.23), residues: 1314 helix: 1.48 (0.20), residues: 646 sheet: 0.03 (0.40), residues: 172 loop : -1.62 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 16 TYR 0.028 0.002 TYR B 234 PHE 0.025 0.002 PHE F 128 TRP 0.018 0.001 TRP G 225 HIS 0.015 0.002 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00749 (10488) covalent geometry : angle 0.78315 (14218) hydrogen bonds : bond 0.05634 ( 575) hydrogen bonds : angle 5.49536 ( 1794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 158 PHE cc_start: 0.8747 (m-80) cc_final: 0.8538 (m-80) REVERT: A 13 TYR cc_start: 0.8270 (OUTLIER) cc_final: 0.7503 (t80) REVERT: G 239 MET cc_start: 0.8319 (tpp) cc_final: 0.8063 (mmm) REVERT: F 15 MET cc_start: 0.8069 (tmm) cc_final: 0.7851 (tmm) REVERT: F 37 GLN cc_start: 0.7752 (tm-30) cc_final: 0.7195 (tm-30) REVERT: F 134 LYS cc_start: 0.8842 (tppt) cc_final: 0.8461 (tppt) REVERT: F 238 MET cc_start: 0.6615 (tpp) cc_final: 0.5975 (tpp) REVERT: C 85 PHE cc_start: 0.7163 (m-80) cc_final: 0.6919 (t80) outliers start: 65 outliers final: 42 residues processed: 220 average time/residue: 0.0778 time to fit residues: 25.3448 Evaluate side-chains 202 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 209 HIS Chi-restraints excluded: chain G residue 278 LEU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain C residue 68 TYR Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 10.0000 chunk 64 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076629 restraints weight = 28776.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078981 restraints weight = 13713.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.080498 restraints weight = 8435.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081385 restraints weight = 6198.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081863 restraints weight = 5142.648| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10488 Z= 0.129 Angle : 0.606 8.026 14218 Z= 0.308 Chirality : 0.042 0.170 1648 Planarity : 0.004 0.072 1817 Dihedral : 4.668 28.651 1445 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.40 % Allowed : 24.13 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.24), residues: 1314 helix: 1.93 (0.21), residues: 643 sheet: -0.30 (0.37), residues: 197 loop : -1.58 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 190 TYR 0.014 0.001 TYR A 234 PHE 0.020 0.001 PHE B 239 TRP 0.015 0.001 TRP G 225 HIS 0.005 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00280 (10488) covalent geometry : angle 0.60576 (14218) hydrogen bonds : bond 0.04348 ( 575) hydrogen bonds : angle 4.87937 ( 1794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 234 TYR cc_start: 0.9265 (t80) cc_final: 0.8914 (t80) REVERT: G 173 ARG cc_start: 0.6843 (mtm-85) cc_final: 0.6201 (ptp90) REVERT: G 199 GLN cc_start: 0.7634 (tp40) cc_final: 0.7242 (mm-40) REVERT: G 223 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: G 239 MET cc_start: 0.8311 (tpp) cc_final: 0.8105 (mmm) REVERT: G 330 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6922 (t80) REVERT: F 37 GLN cc_start: 0.7719 (tm-30) cc_final: 0.7189 (tm-30) REVERT: F 84 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: F 134 LYS cc_start: 0.8911 (tppt) cc_final: 0.8578 (tppt) REVERT: F 238 MET cc_start: 0.7211 (tpp) cc_final: 0.6570 (tpp) REVERT: C 85 PHE cc_start: 0.7272 (m-80) cc_final: 0.6991 (t80) outliers start: 48 outliers final: 30 residues processed: 211 average time/residue: 0.0827 time to fit residues: 25.3198 Evaluate side-chains 194 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 16 ILE Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.101269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.074980 restraints weight = 28443.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077276 restraints weight = 13460.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078726 restraints weight = 8249.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.079641 restraints weight = 6022.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.080103 restraints weight = 4961.314| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10488 Z= 0.202 Angle : 0.644 8.143 14218 Z= 0.330 Chirality : 0.044 0.159 1648 Planarity : 0.004 0.068 1817 Dihedral : 4.682 30.752 1445 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.95 % Allowed : 24.50 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1314 helix: 1.94 (0.21), residues: 645 sheet: -0.34 (0.37), residues: 187 loop : -1.59 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 190 TYR 0.017 0.002 TYR B 82 PHE 0.022 0.001 PHE G 13 TRP 0.013 0.001 TRP G 225 HIS 0.008 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00457 (10488) covalent geometry : angle 0.64429 (14218) hydrogen bonds : bond 0.04574 ( 575) hydrogen bonds : angle 4.89830 ( 1794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8032 (OUTLIER) cc_final: 0.7317 (t80) REVERT: A 91 ARG cc_start: 0.7834 (mpt90) cc_final: 0.7621 (mpt90) REVERT: A 133 ASN cc_start: 0.8452 (m-40) cc_final: 0.8165 (t0) REVERT: A 234 TYR cc_start: 0.9293 (t80) cc_final: 0.9052 (t80) REVERT: G 17 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8955 (mt) REVERT: G 223 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: G 330 PHE cc_start: 0.7440 (OUTLIER) cc_final: 0.7059 (t80) REVERT: F 37 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7529 (tm-30) REVERT: F 42 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5202 (mp) REVERT: F 84 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: F 134 LYS cc_start: 0.8892 (tppt) cc_final: 0.8599 (tppt) REVERT: F 238 MET cc_start: 0.7088 (tpp) cc_final: 0.6454 (tpp) REVERT: C 63 ASP cc_start: 0.6750 (OUTLIER) cc_final: 0.6473 (p0) REVERT: C 85 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7314 (t80) outliers start: 54 outliers final: 36 residues processed: 207 average time/residue: 0.0746 time to fit residues: 22.7154 Evaluate side-chains 201 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 17 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 27 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 85 PHE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 51 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 103 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 55 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.103105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.076965 restraints weight = 28182.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.079293 restraints weight = 13054.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080770 restraints weight = 7894.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.081711 restraints weight = 5720.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.082230 restraints weight = 4685.122| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10488 Z= 0.115 Angle : 0.600 8.276 14218 Z= 0.302 Chirality : 0.043 0.185 1648 Planarity : 0.004 0.077 1817 Dihedral : 4.478 26.819 1445 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.31 % Allowed : 24.86 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1314 helix: 2.15 (0.21), residues: 635 sheet: -0.14 (0.35), residues: 218 loop : -1.40 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 190 TYR 0.018 0.001 TYR F 235 PHE 0.020 0.001 PHE G 13 TRP 0.015 0.001 TRP G 225 HIS 0.006 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00251 (10488) covalent geometry : angle 0.59968 (14218) hydrogen bonds : bond 0.03946 ( 575) hydrogen bonds : angle 4.59739 ( 1794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 177 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7850 (OUTLIER) cc_final: 0.7158 (t80) REVERT: A 133 ASN cc_start: 0.8450 (m-40) cc_final: 0.8176 (t0) REVERT: G 103 MET cc_start: 0.8417 (tpp) cc_final: 0.8045 (tpp) REVERT: G 155 GLU cc_start: 0.7783 (tt0) cc_final: 0.7439 (tt0) REVERT: G 199 GLN cc_start: 0.7446 (tp40) cc_final: 0.7168 (mm-40) REVERT: G 223 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6274 (mt-10) REVERT: G 229 LEU cc_start: 0.8718 (pt) cc_final: 0.8331 (pp) REVERT: G 330 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7067 (t80) REVERT: F 37 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7535 (tm-30) REVERT: F 42 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5290 (mp) REVERT: F 84 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6986 (mp0) REVERT: F 238 MET cc_start: 0.7061 (tpp) cc_final: 0.6539 (tpp) REVERT: C 63 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6673 (p0) outliers start: 47 outliers final: 34 residues processed: 209 average time/residue: 0.0769 time to fit residues: 23.7831 Evaluate side-chains 202 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 116 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 115 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 chunk 119 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.100158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073502 restraints weight = 28583.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.075764 restraints weight = 13611.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.077216 restraints weight = 8420.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.078034 restraints weight = 6203.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.078651 restraints weight = 5174.855| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10488 Z= 0.214 Angle : 0.661 8.096 14218 Z= 0.338 Chirality : 0.045 0.191 1648 Planarity : 0.005 0.068 1817 Dihedral : 4.641 30.710 1445 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.57 % Favored : 95.36 % Rotamer: Outliers : 5.50 % Allowed : 24.31 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.24), residues: 1314 helix: 1.95 (0.21), residues: 643 sheet: -0.04 (0.36), residues: 203 loop : -1.58 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 190 TYR 0.035 0.002 TYR F 235 PHE 0.023 0.001 PHE G 13 TRP 0.011 0.001 TRP G 225 HIS 0.010 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00485 (10488) covalent geometry : angle 0.66132 (14218) hydrogen bonds : bond 0.04543 ( 575) hydrogen bonds : angle 4.78350 ( 1794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 160 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.7229 (t80) REVERT: A 133 ASN cc_start: 0.8509 (m-40) cc_final: 0.8255 (t0) REVERT: G 114 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9057 (tp) REVERT: G 199 GLN cc_start: 0.7532 (tp40) cc_final: 0.7162 (mm-40) REVERT: G 223 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6604 (mt-10) REVERT: G 239 MET cc_start: 0.8203 (tpp) cc_final: 0.7956 (mmm) REVERT: G 330 PHE cc_start: 0.7628 (OUTLIER) cc_final: 0.7313 (t80) REVERT: F 37 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7604 (tm-30) REVERT: F 42 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5205 (mp) REVERT: F 84 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: F 140 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6136 (pm20) REVERT: F 238 MET cc_start: 0.6905 (tpp) cc_final: 0.6339 (tpp) REVERT: C 53 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7814 (mm-30) REVERT: C 63 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6611 (p0) outliers start: 60 outliers final: 45 residues processed: 203 average time/residue: 0.0891 time to fit residues: 26.9262 Evaluate side-chains 209 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 156 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 92 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 36 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 58 optimal weight: 0.2980 chunk 129 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 ASN ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.103292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.076415 restraints weight = 28747.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.078762 restraints weight = 13662.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.080292 restraints weight = 8402.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.081153 restraints weight = 6130.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.081774 restraints weight = 5072.207| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10488 Z= 0.126 Angle : 0.622 8.188 14218 Z= 0.314 Chirality : 0.043 0.220 1648 Planarity : 0.004 0.060 1817 Dihedral : 4.521 27.776 1445 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.65 % Favored : 96.27 % Rotamer: Outliers : 4.77 % Allowed : 25.50 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.24), residues: 1314 helix: 2.14 (0.21), residues: 635 sheet: -0.19 (0.34), residues: 219 loop : -1.40 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 190 TYR 0.028 0.001 TYR A 234 PHE 0.022 0.001 PHE G 13 TRP 0.011 0.001 TRP G 225 HIS 0.006 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00283 (10488) covalent geometry : angle 0.62159 (14218) hydrogen bonds : bond 0.03987 ( 575) hydrogen bonds : angle 4.56272 ( 1794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 13 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.7122 (t80) REVERT: G 103 MET cc_start: 0.8481 (tpp) cc_final: 0.8133 (tpp) REVERT: G 190 ARG cc_start: 0.7655 (mtp-110) cc_final: 0.7248 (mtm110) REVERT: G 199 GLN cc_start: 0.7497 (tp40) cc_final: 0.7231 (mm-40) REVERT: G 223 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: G 239 MET cc_start: 0.8231 (tpp) cc_final: 0.7982 (mmm) REVERT: G 330 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7210 (t80) REVERT: F 15 MET cc_start: 0.8260 (tmm) cc_final: 0.7964 (tmm) REVERT: F 37 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7561 (tm-30) REVERT: F 42 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5213 (mp) REVERT: F 84 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: F 140 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6206 (pm20) REVERT: F 235 TYR cc_start: 0.7285 (t80) cc_final: 0.7068 (t80) REVERT: F 238 MET cc_start: 0.6926 (tpp) cc_final: 0.6473 (tpp) REVERT: C 53 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7826 (mm-30) REVERT: C 63 ASP cc_start: 0.6939 (OUTLIER) cc_final: 0.6600 (p0) outliers start: 52 outliers final: 39 residues processed: 197 average time/residue: 0.0828 time to fit residues: 25.1560 Evaluate side-chains 205 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 290 PHE Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 129 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN G 165 ASN ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.101913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.075354 restraints weight = 28566.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.077647 restraints weight = 13552.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.079084 restraints weight = 8340.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080031 restraints weight = 6116.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.080518 restraints weight = 5049.010| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10488 Z= 0.137 Angle : 0.619 8.308 14218 Z= 0.312 Chirality : 0.043 0.192 1648 Planarity : 0.004 0.065 1817 Dihedral : 4.443 27.281 1445 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 3.94 % Allowed : 26.15 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.24), residues: 1314 helix: 2.17 (0.21), residues: 636 sheet: -0.15 (0.35), residues: 219 loop : -1.42 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 127 TYR 0.025 0.001 TYR A 234 PHE 0.022 0.001 PHE G 13 TRP 0.011 0.001 TRP G 225 HIS 0.006 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00315 (10488) covalent geometry : angle 0.61942 (14218) hydrogen bonds : bond 0.03958 ( 575) hydrogen bonds : angle 4.51528 ( 1794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: B 123 GLN cc_start: 0.8861 (tp40) cc_final: 0.8516 (mm-40) REVERT: A 13 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7115 (t80) REVERT: G 103 MET cc_start: 0.8499 (tpp) cc_final: 0.8187 (tpp) REVERT: G 190 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7285 (mtm110) REVERT: G 199 GLN cc_start: 0.7504 (tp40) cc_final: 0.7252 (mm-40) REVERT: G 223 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6650 (mt-10) REVERT: G 330 PHE cc_start: 0.7655 (OUTLIER) cc_final: 0.7263 (t80) REVERT: F 37 GLN cc_start: 0.7817 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 42 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5139 (mp) REVERT: F 84 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: F 140 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6291 (pm20) REVERT: F 238 MET cc_start: 0.6920 (tpp) cc_final: 0.6480 (tpp) REVERT: C 53 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7812 (mm-30) REVERT: C 63 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6675 (p0) REVERT: C 74 LYS cc_start: 0.8723 (pttm) cc_final: 0.8407 (ptpp) REVERT: C 89 PRO cc_start: 0.6842 (Cg_endo) cc_final: 0.6378 (Cg_exo) outliers start: 43 outliers final: 35 residues processed: 201 average time/residue: 0.0899 time to fit residues: 26.9256 Evaluate side-chains 203 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 34 TYR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN G 165 ASN ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075270 restraints weight = 28258.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.077562 restraints weight = 13460.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.079057 restraints weight = 8304.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.079883 restraints weight = 6083.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.080519 restraints weight = 5071.809| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10488 Z= 0.147 Angle : 0.643 11.503 14218 Z= 0.320 Chirality : 0.044 0.196 1648 Planarity : 0.004 0.055 1817 Dihedral : 4.421 27.736 1445 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.11 % Favored : 95.81 % Rotamer: Outliers : 4.22 % Allowed : 26.06 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.24), residues: 1314 helix: 2.17 (0.21), residues: 638 sheet: -0.07 (0.35), residues: 208 loop : -1.50 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 192 TYR 0.025 0.002 TYR A 234 PHE 0.023 0.001 PHE G 13 TRP 0.012 0.001 TRP G 198 HIS 0.006 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00340 (10488) covalent geometry : angle 0.64270 (14218) hydrogen bonds : bond 0.03968 ( 575) hydrogen bonds : angle 4.51688 ( 1794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2628 Ramachandran restraints generated. 1314 Oldfield, 0 Emsley, 1314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 123 GLN cc_start: 0.8883 (tp40) cc_final: 0.8518 (mm-40) REVERT: A 13 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7188 (t80) REVERT: G 103 MET cc_start: 0.8516 (tpp) cc_final: 0.8218 (tpp) REVERT: G 190 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.7338 (mtm110) REVERT: G 223 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: G 239 MET cc_start: 0.8145 (mmm) cc_final: 0.7693 (mtt) REVERT: G 330 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7306 (t80) REVERT: F 37 GLN cc_start: 0.7820 (tm-30) cc_final: 0.7578 (tm-30) REVERT: F 42 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5056 (mp) REVERT: F 84 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: F 140 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6241 (pm20) REVERT: F 238 MET cc_start: 0.6959 (tpp) cc_final: 0.6522 (tpp) REVERT: C 53 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7774 (mm-30) REVERT: C 63 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6667 (p0) REVERT: C 74 LYS cc_start: 0.8705 (pttm) cc_final: 0.8490 (ptpp) outliers start: 46 outliers final: 37 residues processed: 198 average time/residue: 0.0863 time to fit residues: 25.8767 Evaluate side-chains 209 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 165 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain A residue 13 TYR Chi-restraints excluded: chain A residue 38 ASN Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain G residue 330 PHE Chi-restraints excluded: chain G residue 343 CYS Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 56 ILE Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain F residue 84 GLU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 312 MET Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain F residue 356 LEU Chi-restraints excluded: chain C residue 63 ASP Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 99 GLN Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 159 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN G 165 ASN ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.102684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.076175 restraints weight = 28542.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.078499 restraints weight = 13427.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080008 restraints weight = 8235.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.080939 restraints weight = 6016.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.081455 restraints weight = 4960.663| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10488 Z= 0.125 Angle : 0.632 10.821 14218 Z= 0.312 Chirality : 0.043 0.195 1648 Planarity : 0.004 0.056 1817 Dihedral : 4.315 25.913 1445 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.03 % Favored : 95.89 % Rotamer: Outliers : 4.13 % Allowed : 26.42 % Favored : 69.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.24), residues: 1314 helix: 2.21 (0.21), residues: 640 sheet: -0.24 (0.35), residues: 226 loop : -1.49 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 192 TYR 0.024 0.001 TYR A 234 PHE 0.022 0.001 PHE G 13 TRP 0.013 0.001 TRP G 225 HIS 0.005 0.001 HIS G 158 Details of bonding type rmsd covalent geometry : bond 0.00287 (10488) covalent geometry : angle 0.63160 (14218) hydrogen bonds : bond 0.03786 ( 575) hydrogen bonds : angle 4.41413 ( 1794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.96 seconds wall clock time: 32 minutes 41.66 seconds (1961.66 seconds total)