Starting phenix.real_space_refine on Wed Mar 4 06:33:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318.map" model { file = "/net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pdw_20318/03_2026/6pdw_20318_neut_trim.cif" } resolution = 3.1 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= 0.005 sd= 0.076 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: 8 Type Number sf(0) Gaussians P 8 5.49 5 Mg 4 5.21 5 S 50 5.16 5 Be 3 3.05 5 C 7195 2.51 5 N 2050 2.21 5 O 2164 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11483 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2292 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 17, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2330 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 17, 'TRANS': 280} Chain breaks: 1 Chain: "D" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2339 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 17, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2327 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 17, 'TRANS': 280} Chain breaks: 1 Chain: "F" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2021 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 244} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.02, per 1000 atoms: 0.26 Number of scatterers: 11483 At special positions: 0 Unit cell: (80.484, 137.67, 133.434, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 50 16.00 P 8 15.00 Mg 4 11.99 F 9 9.00 O 2164 8.00 N 2050 7.00 C 7195 6.00 Be 3 4.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 620.8 milliseconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 6 sheets defined 54.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 44 through 65 removed outlier: 3.682A pdb=" N ILE B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.520A pdb=" N ASP B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 102 through 106' Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.819A pdb=" N LEU B 136 " --> pdb=" O MET B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 171 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.731A pdb=" N LEU B 183 " --> pdb=" O HIS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.656A pdb=" N ILE B 194 " --> pdb=" O ASP B 190 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.648A pdb=" N ASP B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 320 through 341 Proline residue: B 335 - end of helix Processing helix chain 'C' and resid 45 through 64 removed outlier: 3.944A pdb=" N ARG C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN C 64 " --> pdb=" O ILE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.871A pdb=" N GLN C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.658A pdb=" N ILE C 113 " --> pdb=" O PHE C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.568A pdb=" N LYS C 138 " --> pdb=" O HIS C 135 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 139 " --> pdb=" O LEU C 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 135 through 139' Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.922A pdb=" N LEU C 143 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 170 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 190 through 205 Processing helix chain 'C' and resid 214 through 219 removed outlier: 4.322A pdb=" N VAL C 218 " --> pdb=" O GLU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 243 removed outlier: 3.504A pdb=" N MET C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 247 removed outlier: 4.083A pdb=" N THR C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 264 through 268 removed outlier: 3.848A pdb=" N ASP C 267 " --> pdb=" O ARG C 264 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 268 " --> pdb=" O ILE C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 264 through 268' Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 286 through 298 removed outlier: 3.931A pdb=" N ARG C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.574A pdb=" N ILE C 312 " --> pdb=" O ASP C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 344 removed outlier: 4.034A pdb=" N ALA C 334 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Proline residue: C 335 - end of helix Processing helix chain 'D' and resid 43 through 64 removed outlier: 3.872A pdb=" N GLN D 64 " --> pdb=" O ILE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 3.853A pdb=" N VAL D 96 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU D 98 " --> pdb=" O ASN D 94 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 138 removed outlier: 4.289A pdb=" N LEU D 136 " --> pdb=" O MET D 133 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS D 138 " --> pdb=" O HIS D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 145 removed outlier: 3.576A pdb=" N ALA D 145 " --> pdb=" O ALA D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 4.538A pdb=" N GLY D 172 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 184 removed outlier: 3.671A pdb=" N LEU D 183 " --> pdb=" O HIS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 205 removed outlier: 3.828A pdb=" N PHE D 199 " --> pdb=" O VAL D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 218 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.619A pdb=" N ASP D 242 " --> pdb=" O MET D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.512A pdb=" N ILE D 268 " --> pdb=" O ILE D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 Processing helix chain 'D' and resid 286 through 298 removed outlier: 3.639A pdb=" N ARG D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 4.039A pdb=" N ILE D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 344 Proline residue: D 335 - end of helix Processing helix chain 'E' and resid 45 through 64 removed outlier: 4.106A pdb=" N GLN E 64 " --> pdb=" O ILE E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 117 through 127 removed outlier: 3.565A pdb=" N LYS E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 137 removed outlier: 3.921A pdb=" N LEU E 136 " --> pdb=" O MET E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 removed outlier: 4.252A pdb=" N LEU E 143 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA E 145 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 170 removed outlier: 3.562A pdb=" N ALA E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 removed outlier: 3.648A pdb=" N LEU E 183 " --> pdb=" O HIS E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.708A pdb=" N LYS E 203 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 removed outlier: 3.799A pdb=" N VAL E 218 " --> pdb=" O GLU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 242 removed outlier: 3.589A pdb=" N GLU E 236 " --> pdb=" O MET E 232 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'E' and resid 309 through 316 removed outlier: 3.560A pdb=" N THR E 316 " --> pdb=" O ILE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 342 Proline residue: E 335 - end of helix Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.629A pdb=" N LEU F 98 " --> pdb=" O ASN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 132 removed outlier: 4.838A pdb=" N TYR F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Proline residue: F 130 - end of helix Processing helix chain 'F' and resid 133 through 138 removed outlier: 3.533A pdb=" N LEU F 136 " --> pdb=" O MET F 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 171 removed outlier: 4.015A pdb=" N ALA F 166 " --> pdb=" O MET F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 205 Processing helix chain 'F' and resid 229 through 243 removed outlier: 3.526A pdb=" N ASP F 242 " --> pdb=" O MET F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 274 removed outlier: 3.572A pdb=" N ARG F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 298 Processing helix chain 'F' and resid 308 through 314 Processing helix chain 'F' and resid 315 through 317 No H-bonds generated for 'chain 'F' and resid 315 through 317' Processing helix chain 'F' and resid 320 through 332 Processing helix chain 'F' and resid 333 through 346 removed outlier: 3.605A pdb=" N GLU F 338 " --> pdb=" O ALA F 334 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 150 through 153 removed outlier: 6.681A pdb=" N LEU B 151 " --> pdb=" O PHE B 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 175 through 177 removed outlier: 6.580A pdb=" N ILE B 176 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE B 210 " --> pdb=" O LEU B 259 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 175 through 178 removed outlier: 6.662A pdb=" N ILE C 176 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N ASP C 213 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU C 178 " --> pdb=" O ASP C 213 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER C 208 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU C 259 " --> pdb=" O SER C 208 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ILE C 210 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA C 261 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ILE C 212 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS C 278 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 175 through 178 removed outlier: 6.760A pdb=" N ILE D 176 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ASP D 213 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU D 178 " --> pdb=" O ASP D 213 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 150 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 175 through 178 removed outlier: 4.438A pdb=" N ASP E 213 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 278 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 175 through 178 removed outlier: 3.534A pdb=" N PHE F 211 " --> pdb=" O ILE F 176 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N SER F 208 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU F 259 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE F 210 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ALA F 261 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 212 " --> pdb=" O ALA F 261 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1365 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: 1.40 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1952 1.31 - 1.44: 2775 1.44 - 1.56: 6845 1.56 - 1.69: 12 1.69 - 1.81: 91 Bond restraints: 11675 Sorted by residual: bond pdb=" N PRO B 349 " pdb=" CD PRO B 349 " ideal model delta sigma weight residual 1.473 1.690 -0.217 1.40e-02 5.10e+03 2.40e+02 bond pdb=" F2 BEF B 502 " pdb="BE BEF B 502 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" F2 BEF C 503 " pdb="BE BEF C 503 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" F2 BEF D 502 " pdb="BE BEF D 502 " ideal model delta sigma weight residual 1.476 1.559 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C ALA D 271 " pdb=" O ALA D 271 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.28e-02 6.10e+03 1.32e+01 ... (remaining 11670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 15574 2.77 - 5.54: 195 5.54 - 8.31: 19 8.31 - 11.09: 8 11.09 - 13.86: 5 Bond angle restraints: 15801 Sorted by residual: angle pdb=" N PRO B 349 " pdb=" CA PRO B 349 " pdb=" CB PRO B 349 " ideal model delta sigma weight residual 103.36 112.01 -8.65 8.80e-01 1.29e+00 9.67e+01 angle pdb=" CA PRO B 349 " pdb=" N PRO B 349 " pdb=" CD PRO B 349 " ideal model delta sigma weight residual 112.00 100.96 11.04 1.40e+00 5.10e-01 6.22e+01 angle pdb=" C ILE D 268 " pdb=" N ASP D 269 " pdb=" CA ASP D 269 " ideal model delta sigma weight residual 121.54 133.45 -11.91 1.91e+00 2.74e-01 3.89e+01 angle pdb=" N LYS F 204 " pdb=" CA LYS F 204 " pdb=" C LYS F 204 " ideal model delta sigma weight residual 111.07 105.02 6.05 1.07e+00 8.73e-01 3.19e+01 angle pdb=" O ILE D 268 " pdb=" C ILE D 268 " pdb=" N ASP D 269 " ideal model delta sigma weight residual 121.83 127.54 -5.71 1.03e+00 9.43e-01 3.08e+01 ... (remaining 15796 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.55: 7084 31.55 - 63.11: 81 63.11 - 94.66: 5 94.66 - 126.22: 2 126.22 - 157.77: 1 Dihedral angle restraints: 7173 sinusoidal: 2996 harmonic: 4177 Sorted by residual: dihedral pdb=" CA ARG D 303 " pdb=" C ARG D 303 " pdb=" N ASP D 304 " pdb=" CA ASP D 304 " ideal model delta harmonic sigma weight residual 180.00 143.35 36.65 0 5.00e+00 4.00e-02 5.37e+01 dihedral pdb=" CA ASP F 304 " pdb=" C ASP F 304 " pdb=" N PRO F 305 " pdb=" CA PRO F 305 " ideal model delta harmonic sigma weight residual 180.00 144.82 35.18 0 5.00e+00 4.00e-02 4.95e+01 dihedral pdb=" C5' ADP E 501 " pdb=" O5' ADP E 501 " pdb=" PA ADP E 501 " pdb=" O2A ADP E 501 " ideal model delta sinusoidal sigma weight residual -60.00 97.77 -157.77 1 2.00e+01 2.50e-03 4.62e+01 ... (remaining 7170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1632 0.081 - 0.162: 148 0.162 - 0.243: 4 0.243 - 0.324: 2 0.324 - 0.405: 1 Chirality restraints: 1787 Sorted by residual: chirality pdb=" CA ASP D 269 " pdb=" N ASP D 269 " pdb=" C ASP D 269 " pdb=" CB ASP D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA GLU D 270 " pdb=" N GLU D 270 " pdb=" C GLU D 270 " pdb=" CB GLU D 270 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE D 268 " pdb=" N ILE D 268 " pdb=" C ILE D 268 " pdb=" CB ILE D 268 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1784 not shown) Planarity restraints: 2048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 267 " 0.027 2.00e-02 2.50e+03 5.53e-02 3.06e+01 pdb=" C ASP D 267 " -0.096 2.00e-02 2.50e+03 pdb=" O ASP D 267 " 0.036 2.00e-02 2.50e+03 pdb=" N ILE D 268 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 304 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO F 305 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO F 305 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO F 305 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 241 " 0.023 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP C 241 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP C 241 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 241 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 241 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 241 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 241 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 241 " 0.006 2.00e-02 2.50e+03 ... (remaining 2045 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 72 2.41 - 3.04: 7493 3.04 - 3.66: 17752 3.66 - 4.28: 26071 4.28 - 4.90: 42723 Nonbonded interactions: 94111 Sorted by model distance: nonbonded pdb=" O LEU D 219 " pdb=" O ILE D 268 " model vdw 1.792 3.040 nonbonded pdb=" O ALA F 202 " pdb=" O LEU F 205 " model vdw 1.961 3.040 nonbonded pdb=" OG1 THR B 161 " pdb="MG MG B 503 " model vdw 1.982 2.170 nonbonded pdb=" OG1 THR C 161 " pdb="MG MG C 502 " model vdw 1.984 2.170 nonbonded pdb=" O3B ADP E 501 " pdb="MG MG E 502 " model vdw 1.989 2.170 ... (remaining 94106 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 'B' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'C' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'D' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'E' and (resid 87 through 159 or (resid 160 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 220 or resid 228 through 244 or \ resid 254 through 361)) selection = (chain 'F' and resid 87 through 361) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.110 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.014 0.856 11678 Z= 1.353 Angle : 0.809 13.857 15801 Z= 0.445 Chirality : 0.047 0.405 1787 Planarity : 0.006 0.101 2048 Dihedral : 10.944 157.770 4479 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 39.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.66 % Favored : 89.27 % Rotamer: Outliers : 0.74 % Allowed : 5.67 % Favored : 93.60 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.15 % 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: -3.33 (0.20), residues: 1426 helix: -1.63 (0.17), residues: 665 sheet: -2.75 (0.34), residues: 147 loop : -2.63 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 275 TYR 0.017 0.001 TYR B 339 PHE 0.019 0.002 PHE B 110 TRP 0.052 0.004 TRP C 241 HIS 0.010 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00479 (11675) covalent geometry : angle 0.80932 (15801) hydrogen bonds : bond 0.18562 ( 472) hydrogen bonds : angle 7.43191 ( 1365) Misc. bond : bond 0.82726 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 368 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 TYR cc_start: 0.8199 (m-80) cc_final: 0.7945 (m-80) REVERT: C 153 TYR cc_start: 0.8785 (p90) cc_final: 0.8527 (p90) REVERT: C 267 ASP cc_start: 0.7007 (t70) cc_final: 0.6759 (t0) REVERT: C 293 ILE cc_start: 0.8514 (mm) cc_final: 0.8294 (mt) REVERT: C 339 TYR cc_start: 0.7959 (t80) cc_final: 0.7535 (t80) REVERT: D 60 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8007 (mp) REVERT: D 111 ASN cc_start: 0.8308 (t0) cc_final: 0.8051 (t0) REVERT: D 176 ILE cc_start: 0.8423 (pt) cc_final: 0.8165 (mt) REVERT: D 269 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8401 (p0) REVERT: D 311 TYR cc_start: 0.8612 (t80) cc_final: 0.8382 (t80) REVERT: F 98 LEU cc_start: 0.9140 (mt) cc_final: 0.8865 (tt) REVERT: F 200 SER cc_start: 0.8987 (t) cc_final: 0.8592 (p) REVERT: F 269 ASP cc_start: 0.7999 (t70) cc_final: 0.7725 (t0) REVERT: F 274 ARG cc_start: 0.7141 (tmt170) cc_final: 0.6621 (ttp-170) REVERT: F 294 LEU cc_start: 0.9055 (mp) cc_final: 0.8853 (mm) outliers start: 9 outliers final: 2 residues processed: 375 average time/residue: 0.1388 time to fit residues: 68.2228 Evaluate side-chains 193 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 189 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 203 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0570 chunk 55 optimal weight: 0.0570 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS B 192 ASN B 248 ASN B 279 GLN C 179 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS E 54 GLN E 192 ASN E 263 ASN F 192 ASN F 254 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.112678 restraints weight = 17330.060| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.32 r_work: 0.3179 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11678 Z= 0.153 Angle : 0.773 8.980 15801 Z= 0.371 Chirality : 0.048 0.246 1787 Planarity : 0.006 0.097 2048 Dihedral : 8.260 150.384 1649 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.77 % Favored : 91.16 % Rotamer: Outliers : 2.79 % Allowed : 11.74 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % 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: -2.11 (0.22), residues: 1426 helix: -0.67 (0.19), residues: 705 sheet: -1.87 (0.39), residues: 151 loop : -2.10 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 59 TYR 0.010 0.001 TYR E 153 PHE 0.020 0.002 PHE B 110 TRP 0.030 0.002 TRP C 241 HIS 0.005 0.001 HIS F 169 Details of bonding type rmsd covalent geometry : bond 0.00348 (11675) covalent geometry : angle 0.77342 (15801) hydrogen bonds : bond 0.04037 ( 472) hydrogen bonds : angle 5.39647 ( 1365) Misc. bond : bond 0.00106 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7223 (mmm160) cc_final: 0.6676 (tmm160) REVERT: B 190 ASP cc_start: 0.7631 (t0) cc_final: 0.7339 (t0) REVERT: B 336 MET cc_start: 0.8977 (tpt) cc_final: 0.8705 (tpt) REVERT: C 153 TYR cc_start: 0.8903 (p90) cc_final: 0.8700 (p90) REVERT: C 216 ASP cc_start: 0.8758 (p0) cc_final: 0.8493 (p0) REVERT: C 267 ASP cc_start: 0.7343 (t70) cc_final: 0.7032 (t0) REVERT: C 293 ILE cc_start: 0.8702 (mm) cc_final: 0.8424 (mt) REVERT: C 343 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7781 (t70) REVERT: D 111 ASN cc_start: 0.8380 (t0) cc_final: 0.8125 (t0) REVERT: D 269 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7960 (p0) REVERT: E 51 ILE cc_start: 0.8557 (tt) cc_final: 0.8286 (tt) REVERT: E 180 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8209 (mm) REVERT: E 242 ASP cc_start: 0.8258 (t0) cc_final: 0.7846 (t0) REVERT: F 128 ILE cc_start: 0.9142 (mp) cc_final: 0.8926 (mp) REVERT: F 319 MET cc_start: 0.7762 (mtp) cc_final: 0.7236 (mtp) outliers start: 34 outliers final: 11 residues processed: 249 average time/residue: 0.1141 time to fit residues: 39.6327 Evaluate side-chains 191 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 254 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 126 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 343 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.143233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108756 restraints weight = 17386.298| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.12 r_work: 0.3171 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11678 Z= 0.163 Angle : 0.754 10.352 15801 Z= 0.359 Chirality : 0.046 0.220 1787 Planarity : 0.006 0.089 2048 Dihedral : 8.192 172.977 1641 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.12 % Favored : 90.81 % Rotamer: Outliers : 3.45 % Allowed : 14.12 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.23), residues: 1426 helix: -0.18 (0.20), residues: 700 sheet: -1.59 (0.41), residues: 152 loop : -2.01 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 59 TYR 0.016 0.001 TYR F 339 PHE 0.013 0.002 PHE B 110 TRP 0.024 0.002 TRP E 241 HIS 0.013 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00383 (11675) covalent geometry : angle 0.75409 (15801) hydrogen bonds : bond 0.03607 ( 472) hydrogen bonds : angle 5.11306 ( 1365) Misc. bond : bond 0.00280 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7348 (ttm170) cc_final: 0.7092 (ttm170) REVERT: B 59 ARG cc_start: 0.7382 (mmm160) cc_final: 0.6994 (tmt170) REVERT: B 95 GLN cc_start: 0.8264 (mt0) cc_final: 0.8039 (mt0) REVERT: B 336 MET cc_start: 0.9110 (tpt) cc_final: 0.8842 (tpt) REVERT: C 151 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8885 (tp) REVERT: C 176 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8072 (mt) REVERT: C 216 ASP cc_start: 0.8891 (p0) cc_final: 0.8579 (p0) REVERT: C 267 ASP cc_start: 0.7640 (t70) cc_final: 0.7310 (t0) REVERT: C 293 ILE cc_start: 0.8899 (mm) cc_final: 0.8606 (mt) REVERT: D 111 ASN cc_start: 0.8710 (t0) cc_final: 0.8438 (t0) REVERT: D 223 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7763 (mtp-110) REVERT: D 311 TYR cc_start: 0.8795 (t80) cc_final: 0.8384 (t80) REVERT: E 51 ILE cc_start: 0.8704 (tt) cc_final: 0.8403 (tt) REVERT: E 180 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8292 (mm) REVERT: F 90 ASN cc_start: 0.7218 (p0) cc_final: 0.6980 (p0) REVERT: F 99 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7680 (pm20) REVERT: F 289 GLN cc_start: 0.9066 (pm20) cc_final: 0.8637 (pm20) REVERT: F 294 LEU cc_start: 0.8685 (pp) cc_final: 0.8477 (tt) outliers start: 42 outliers final: 20 residues processed: 223 average time/residue: 0.1046 time to fit residues: 33.4067 Evaluate side-chains 197 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 163 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 223 ARG Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 34 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 56 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS D 95 GLN D 343 HIS D 354 ASN F 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.143711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.110443 restraints weight = 17404.398| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.40 r_work: 0.3185 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11678 Z= 0.145 Angle : 0.726 8.499 15801 Z= 0.342 Chirality : 0.045 0.226 1787 Planarity : 0.005 0.084 2048 Dihedral : 7.994 172.753 1641 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.37 % Allowed : 14.20 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.23), residues: 1426 helix: 0.13 (0.20), residues: 700 sheet: -1.43 (0.42), residues: 153 loop : -1.86 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.014 0.001 TYR F 339 PHE 0.012 0.002 PHE D 175 TRP 0.018 0.002 TRP E 241 HIS 0.004 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00336 (11675) covalent geometry : angle 0.72611 (15801) hydrogen bonds : bond 0.03335 ( 472) hydrogen bonds : angle 4.93328 ( 1365) Misc. bond : bond 0.00233 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7088 (ttm170) REVERT: B 227 HIS cc_start: 0.7682 (t-90) cc_final: 0.7449 (t-90) REVERT: B 289 GLN cc_start: 0.8450 (mp10) cc_final: 0.8216 (mp10) REVERT: B 308 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.7840 (t70) REVERT: C 151 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8900 (tp) REVERT: C 176 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8007 (mt) REVERT: C 216 ASP cc_start: 0.8834 (p0) cc_final: 0.8555 (p0) REVERT: C 267 ASP cc_start: 0.7523 (t70) cc_final: 0.7212 (t0) REVERT: C 293 ILE cc_start: 0.8855 (mm) cc_final: 0.8612 (mt) REVERT: C 342 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8336 (tm-30) REVERT: D 61 ARG cc_start: 0.6546 (mpt-90) cc_final: 0.6315 (mpt-90) REVERT: D 223 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7911 (mtp-110) REVERT: D 311 TYR cc_start: 0.8758 (t80) cc_final: 0.8290 (t80) REVERT: E 51 ILE cc_start: 0.8680 (tt) cc_final: 0.8341 (tt) REVERT: E 104 GLU cc_start: 0.8361 (tp30) cc_final: 0.8086 (tp30) REVERT: E 138 LYS cc_start: 0.8791 (tppt) cc_final: 0.8454 (tptt) REVERT: E 180 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8278 (mm) REVERT: F 137 TYR cc_start: 0.8174 (m-80) cc_final: 0.7962 (m-80) REVERT: F 269 ASP cc_start: 0.7942 (t70) cc_final: 0.7631 (t0) REVERT: F 289 GLN cc_start: 0.9093 (pm20) cc_final: 0.8690 (pm20) outliers start: 41 outliers final: 21 residues processed: 212 average time/residue: 0.0979 time to fit residues: 29.9277 Evaluate side-chains 195 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 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 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS D 95 GLN D 343 HIS D 354 ASN E 95 GLN F 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108685 restraints weight = 17375.185| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.09 r_work: 0.3166 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11678 Z= 0.149 Angle : 0.710 8.337 15801 Z= 0.335 Chirality : 0.045 0.233 1787 Planarity : 0.005 0.057 2048 Dihedral : 7.845 166.775 1641 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 2.79 % Allowed : 15.27 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1426 helix: 0.38 (0.21), residues: 688 sheet: -1.41 (0.42), residues: 153 loop : -1.80 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.017 0.001 TYR B 137 PHE 0.015 0.002 PHE F 307 TRP 0.017 0.002 TRP E 241 HIS 0.021 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00350 (11675) covalent geometry : angle 0.70953 (15801) hydrogen bonds : bond 0.03268 ( 472) hydrogen bonds : angle 4.82798 ( 1365) Misc. bond : bond 0.00258 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9000 (mp) cc_final: 0.8788 (mp) REVERT: B 58 ARG cc_start: 0.7406 (ttm170) cc_final: 0.7175 (ttm170) REVERT: B 227 HIS cc_start: 0.7539 (t-90) cc_final: 0.7304 (t-90) REVERT: B 289 GLN cc_start: 0.8457 (mp10) cc_final: 0.8150 (mp10) REVERT: B 308 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7914 (t70) REVERT: C 176 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8024 (mt) REVERT: C 216 ASP cc_start: 0.8820 (p0) cc_final: 0.8517 (p0) REVERT: C 267 ASP cc_start: 0.7454 (t70) cc_final: 0.7154 (t0) REVERT: C 293 ILE cc_start: 0.8864 (mm) cc_final: 0.8639 (mt) REVERT: C 342 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8401 (tm-30) REVERT: D 223 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8086 (mtp-110) REVERT: D 311 TYR cc_start: 0.8749 (t80) cc_final: 0.8320 (t80) REVERT: E 51 ILE cc_start: 0.8765 (tt) cc_final: 0.8404 (tt) REVERT: E 104 GLU cc_start: 0.8327 (tp30) cc_final: 0.8081 (tp30) REVERT: E 138 LYS cc_start: 0.8688 (tppt) cc_final: 0.8357 (tptt) REVERT: E 180 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8422 (mm) REVERT: F 289 GLN cc_start: 0.8995 (pm20) cc_final: 0.8603 (pm20) outliers start: 34 outliers final: 25 residues processed: 207 average time/residue: 0.1065 time to fit residues: 30.8171 Evaluate side-chains 195 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 7 optimal weight: 0.2980 chunk 5 optimal weight: 0.0170 chunk 129 optimal weight: 4.9990 chunk 65 optimal weight: 0.0040 chunk 117 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 overall best weight: 0.0826 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS D 95 GLN E 95 GLN F 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.148379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.109922 restraints weight = 17571.946| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.60 r_work: 0.3252 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11678 Z= 0.120 Angle : 0.697 9.147 15801 Z= 0.327 Chirality : 0.044 0.234 1787 Planarity : 0.005 0.048 2048 Dihedral : 7.476 159.662 1641 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 3.04 % Allowed : 15.76 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.87 (0.23), residues: 1426 helix: 0.67 (0.21), residues: 692 sheet: -1.40 (0.41), residues: 153 loop : -1.87 (0.27), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 62 TYR 0.010 0.001 TYR B 311 PHE 0.020 0.001 PHE F 307 TRP 0.012 0.001 TRP F 187 HIS 0.028 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00261 (11675) covalent geometry : angle 0.69712 (15801) hydrogen bonds : bond 0.02988 ( 472) hydrogen bonds : angle 4.66895 ( 1365) Misc. bond : bond 0.00166 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9017 (mp) cc_final: 0.8777 (mp) REVERT: B 58 ARG cc_start: 0.7077 (ttm170) cc_final: 0.6866 (ttm170) REVERT: B 289 GLN cc_start: 0.8366 (mp10) cc_final: 0.7869 (mp10) REVERT: B 308 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7413 (t70) REVERT: C 95 GLN cc_start: 0.8147 (tt0) cc_final: 0.7916 (mt0) REVERT: C 216 ASP cc_start: 0.8592 (p0) cc_final: 0.8375 (p0) REVERT: C 342 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 223 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7954 (mtp-110) REVERT: D 268 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8750 (mm) REVERT: E 51 ILE cc_start: 0.8282 (tt) cc_final: 0.7914 (tt) REVERT: E 104 GLU cc_start: 0.8301 (tp30) cc_final: 0.7990 (tp30) REVERT: E 138 LYS cc_start: 0.8821 (tppt) cc_final: 0.8481 (tptt) REVERT: F 94 ASN cc_start: 0.8773 (m110) cc_final: 0.8565 (m-40) REVERT: F 95 GLN cc_start: 0.8770 (tp40) cc_final: 0.8453 (tp-100) outliers start: 37 outliers final: 26 residues processed: 223 average time/residue: 0.1025 time to fit residues: 32.3136 Evaluate side-chains 194 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 124 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 206 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.144867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108077 restraints weight = 17412.805| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.56 r_work: 0.3197 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11678 Z= 0.150 Angle : 0.737 15.258 15801 Z= 0.344 Chirality : 0.046 0.251 1787 Planarity : 0.005 0.047 2048 Dihedral : 7.480 154.619 1641 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.04 % Allowed : 16.34 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1426 helix: 0.71 (0.21), residues: 690 sheet: -1.38 (0.41), residues: 153 loop : -1.80 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 59 TYR 0.019 0.001 TYR B 153 PHE 0.019 0.002 PHE F 307 TRP 0.016 0.002 TRP E 241 HIS 0.011 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00350 (11675) covalent geometry : angle 0.73740 (15801) hydrogen bonds : bond 0.03203 ( 472) hydrogen bonds : angle 4.68159 ( 1365) Misc. bond : bond 0.00243 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9055 (mp) cc_final: 0.8808 (mp) REVERT: B 58 ARG cc_start: 0.7110 (ttm170) cc_final: 0.6860 (ttm170) REVERT: B 237 PHE cc_start: 0.8864 (t80) cc_final: 0.8588 (t80) REVERT: B 289 GLN cc_start: 0.8316 (mp10) cc_final: 0.7796 (mp10) REVERT: B 308 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7323 (t70) REVERT: C 216 ASP cc_start: 0.8717 (p0) cc_final: 0.8512 (p0) REVERT: C 267 ASP cc_start: 0.7425 (t70) cc_final: 0.7203 (t0) REVERT: C 339 TYR cc_start: 0.8445 (t80) cc_final: 0.8215 (t80) REVERT: C 342 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8358 (tm-30) REVERT: D 223 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7857 (mtp-110) REVERT: D 268 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8659 (mm) REVERT: D 311 TYR cc_start: 0.8588 (t80) cc_final: 0.8014 (t80) REVERT: D 333 MET cc_start: 0.8247 (tpp) cc_final: 0.7777 (mmm) REVERT: E 51 ILE cc_start: 0.8108 (tt) cc_final: 0.7766 (tt) REVERT: E 104 GLU cc_start: 0.8323 (tp30) cc_final: 0.8002 (tp30) REVERT: E 138 LYS cc_start: 0.8906 (tppt) cc_final: 0.8595 (tptt) REVERT: F 94 ASN cc_start: 0.8777 (m110) cc_final: 0.8485 (m110) REVERT: F 289 GLN cc_start: 0.9140 (pm20) cc_final: 0.8752 (pm20) outliers start: 37 outliers final: 30 residues processed: 199 average time/residue: 0.1027 time to fit residues: 29.3384 Evaluate side-chains 195 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 127 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 137 optimal weight: 9.9990 chunk 5 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS C 95 GLN C 343 HIS D 95 GLN E 95 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.108581 restraints weight = 17358.540| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.51 r_work: 0.3200 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11678 Z= 0.144 Angle : 0.726 10.489 15801 Z= 0.339 Chirality : 0.045 0.247 1787 Planarity : 0.005 0.048 2048 Dihedral : 7.428 151.546 1641 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.12 % Allowed : 16.75 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.76 (0.24), residues: 1426 helix: 0.73 (0.21), residues: 686 sheet: -1.34 (0.41), residues: 153 loop : -1.75 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.019 0.001 TYR B 153 PHE 0.020 0.002 PHE F 307 TRP 0.014 0.001 TRP E 241 HIS 0.013 0.001 HIS C 343 Details of bonding type rmsd covalent geometry : bond 0.00334 (11675) covalent geometry : angle 0.72590 (15801) hydrogen bonds : bond 0.03125 ( 472) hydrogen bonds : angle 4.66210 ( 1365) Misc. bond : bond 0.00240 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9067 (mp) cc_final: 0.8827 (mp) REVERT: B 58 ARG cc_start: 0.7087 (ttm170) cc_final: 0.6838 (ttm170) REVERT: B 237 PHE cc_start: 0.8824 (t80) cc_final: 0.8555 (t80) REVERT: B 289 GLN cc_start: 0.8330 (mp10) cc_final: 0.7804 (mp10) REVERT: B 308 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7388 (t70) REVERT: C 176 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.7901 (mt) REVERT: C 216 ASP cc_start: 0.8700 (p0) cc_final: 0.8494 (p0) REVERT: C 342 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8480 (tm-30) REVERT: D 223 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7857 (mtp-110) REVERT: D 268 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8647 (mm) REVERT: E 51 ILE cc_start: 0.8097 (tt) cc_final: 0.7752 (tt) REVERT: E 104 GLU cc_start: 0.8314 (tp30) cc_final: 0.8002 (tp30) REVERT: E 138 LYS cc_start: 0.8913 (tppt) cc_final: 0.8599 (tptt) REVERT: F 94 ASN cc_start: 0.8825 (m110) cc_final: 0.8540 (m110) REVERT: F 289 GLN cc_start: 0.9130 (pm20) cc_final: 0.8724 (pm20) outliers start: 38 outliers final: 27 residues processed: 195 average time/residue: 0.1019 time to fit residues: 28.3442 Evaluate side-chains 191 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 322 SER Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 95 GLN D 95 GLN E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.143633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.108704 restraints weight = 17266.304| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.32 r_work: 0.3178 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11678 Z= 0.164 Angle : 0.734 10.653 15801 Z= 0.346 Chirality : 0.046 0.254 1787 Planarity : 0.005 0.049 2048 Dihedral : 7.480 148.730 1641 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.71 % Allowed : 17.24 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.66 (0.24), residues: 1426 helix: 0.78 (0.21), residues: 678 sheet: -1.29 (0.42), residues: 153 loop : -1.62 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 59 TYR 0.019 0.001 TYR B 153 PHE 0.021 0.002 PHE F 307 TRP 0.017 0.002 TRP E 241 HIS 0.004 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00391 (11675) covalent geometry : angle 0.73423 (15801) hydrogen bonds : bond 0.03210 ( 472) hydrogen bonds : angle 4.71545 ( 1365) Misc. bond : bond 0.00282 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9080 (mp) cc_final: 0.8827 (mp) REVERT: B 58 ARG cc_start: 0.7295 (ttm170) cc_final: 0.7030 (ttm170) REVERT: B 236 GLU cc_start: 0.8933 (tp30) cc_final: 0.8690 (tp30) REVERT: B 237 PHE cc_start: 0.8871 (t80) cc_final: 0.8623 (t80) REVERT: B 289 GLN cc_start: 0.8447 (mp10) cc_final: 0.7905 (mp10) REVERT: B 308 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7481 (t70) REVERT: B 336 MET cc_start: 0.9101 (tpt) cc_final: 0.8819 (tpt) REVERT: C 176 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8123 (mt) REVERT: C 272 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 342 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 223 ARG cc_start: 0.8112 (mtm-85) cc_final: 0.7794 (mtp-110) REVERT: D 268 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8696 (mm) REVERT: E 51 ILE cc_start: 0.8207 (tt) cc_final: 0.7861 (tt) REVERT: E 104 GLU cc_start: 0.8492 (tp30) cc_final: 0.8180 (tp30) REVERT: E 138 LYS cc_start: 0.8991 (tppt) cc_final: 0.8674 (tptt) REVERT: E 180 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8350 (mm) outliers start: 33 outliers final: 27 residues processed: 180 average time/residue: 0.1008 time to fit residues: 25.5496 Evaluate side-chains 189 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 124 optimal weight: 0.5980 chunk 117 optimal weight: 0.0370 chunk 76 optimal weight: 0.0870 chunk 110 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN F 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.110059 restraints weight = 17379.184| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.46 r_work: 0.3223 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11678 Z= 0.129 Angle : 0.720 14.594 15801 Z= 0.338 Chirality : 0.045 0.251 1787 Planarity : 0.005 0.048 2048 Dihedral : 7.227 141.320 1641 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 2.46 % Allowed : 17.90 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 1426 helix: 0.89 (0.21), residues: 687 sheet: -1.25 (0.41), residues: 153 loop : -1.68 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 59 TYR 0.016 0.001 TYR B 153 PHE 0.022 0.001 PHE F 307 TRP 0.014 0.001 TRP B 241 HIS 0.004 0.001 HIS F 343 Details of bonding type rmsd covalent geometry : bond 0.00291 (11675) covalent geometry : angle 0.72017 (15801) hydrogen bonds : bond 0.02979 ( 472) hydrogen bonds : angle 4.59819 ( 1365) Misc. bond : bond 0.00197 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9056 (mp) cc_final: 0.8808 (mp) REVERT: B 237 PHE cc_start: 0.8782 (t80) cc_final: 0.8488 (t80) REVERT: B 289 GLN cc_start: 0.8321 (mp10) cc_final: 0.7768 (mp10) REVERT: B 308 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7326 (t70) REVERT: B 311 TYR cc_start: 0.7588 (t80) cc_final: 0.7343 (t80) REVERT: C 176 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.7723 (mt) REVERT: C 216 ASP cc_start: 0.8689 (p0) cc_final: 0.8442 (p0) REVERT: C 272 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7826 (mt) REVERT: C 342 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8530 (tm-30) REVERT: D 268 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8656 (mm) REVERT: E 51 ILE cc_start: 0.8093 (tt) cc_final: 0.7735 (tt) REVERT: E 104 GLU cc_start: 0.8297 (tp30) cc_final: 0.8011 (tp30) REVERT: E 138 LYS cc_start: 0.8836 (tppt) cc_final: 0.8557 (tptt) REVERT: F 95 GLN cc_start: 0.8826 (tp40) cc_final: 0.8288 (tp-100) outliers start: 30 outliers final: 24 residues processed: 191 average time/residue: 0.1022 time to fit residues: 27.7105 Evaluate side-chains 189 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ASP Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 182 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain E residue 57 LEU Chi-restraints excluded: chain E residue 59 ARG Chi-restraints excluded: chain E residue 176 ILE Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 353 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107037 restraints weight = 17382.407| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.53 r_work: 0.3174 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11678 Z= 0.158 Angle : 0.743 11.096 15801 Z= 0.351 Chirality : 0.046 0.261 1787 Planarity : 0.005 0.052 2048 Dihedral : 7.301 138.881 1641 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.71 % Allowed : 17.82 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.60 (0.24), residues: 1426 helix: 0.83 (0.21), residues: 692 sheet: -1.19 (0.42), residues: 153 loop : -1.67 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.017 0.001 TYR B 153 PHE 0.020 0.002 PHE F 307 TRP 0.016 0.002 TRP E 241 HIS 0.005 0.001 HIS B 227 Details of bonding type rmsd covalent geometry : bond 0.00373 (11675) covalent geometry : angle 0.74334 (15801) hydrogen bonds : bond 0.03146 ( 472) hydrogen bonds : angle 4.65573 ( 1365) Misc. bond : bond 0.00247 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2861.55 seconds wall clock time: 49 minutes 39.96 seconds (2979.96 seconds total)