Starting phenix.real_space_refine on Tue Jul 29 17:43:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pdw_20318/07_2025/6pdw_20318_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pdw_20318/07_2025/6pdw_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_20318/07_2025/6pdw_20318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pdw_20318/07_2025/6pdw_20318.map" model { file = "/net/cci-nas-00/data/ceres_data/6pdw_20318/07_2025/6pdw_20318_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pdw_20318/07_2025/6pdw_20318_neut_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.45, per 1000 atoms: 0.74 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: 3.35 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.16 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: 3.31 Time building geometry restraints manager: 3.93 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.060 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- 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 : 39.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.004 TRP C 241 HIS 0.010 0.001 HIS F 343 PHE 0.019 0.002 PHE B 110 TYR 0.017 0.001 TYR B 339 ARG 0.007 0.001 ARG E 275 Details of bonding type rmsd hydrogen bonds : bond 0.18562 ( 472) hydrogen bonds : angle 7.43191 ( 1365) covalent geometry : bond 0.00479 (11675) covalent geometry : angle 0.80932 (15801) 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 : 1.378 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: 0.8526 (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: 0.8295 (mt) REVERT: C 339 TYR cc_start: 0.7959 (t80) cc_final: 0.7729 (t80) REVERT: D 60 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8008 (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: 0.7724 (t0) REVERT: F 274 ARG cc_start: 0.7141 (tmt170) cc_final: 0.6617 (ttp-170) REVERT: F 294 LEU cc_start: 0.9055 (mp) cc_final: 0.8854 (mm) outliers start: 9 outliers final: 2 residues processed: 375 average time/residue: 0.3075 time to fit residues: 151.4680 Evaluate side-chains 197 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 chunk 37 optimal weight: 0.0170 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.112289 restraints weight = 17095.325| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.23 r_work: 0.3189 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11678 Z= 0.158 Angle : 0.766 8.036 15801 Z= 0.367 Chirality : 0.047 0.247 1787 Planarity : 0.006 0.097 2048 Dihedral : 8.281 152.494 1649 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.05 % Favored : 90.88 % Rotamer: Outliers : 2.63 % Allowed : 11.74 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.22), residues: 1426 helix: -0.65 (0.19), residues: 696 sheet: -1.90 (0.39), residues: 152 loop : -2.18 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 241 HIS 0.005 0.001 HIS F 169 PHE 0.020 0.002 PHE B 110 TYR 0.010 0.001 TYR D 129 ARG 0.008 0.001 ARG B 59 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 472) hydrogen bonds : angle 5.41325 ( 1365) covalent geometry : bond 0.00369 (11675) covalent geometry : angle 0.76569 (15801) Misc. bond : bond 0.00198 ( 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 256 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 224 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 190 ASP cc_start: 0.7607 (t0) cc_final: 0.7323 (t0) REVERT: B 336 MET cc_start: 0.8960 (tpt) cc_final: 0.8678 (tpt) REVERT: C 153 TYR cc_start: 0.8917 (p90) cc_final: 0.8708 (p90) REVERT: C 216 ASP cc_start: 0.8751 (p0) cc_final: 0.8495 (p0) REVERT: C 267 ASP cc_start: 0.7312 (t70) cc_final: 0.6998 (t0) REVERT: C 293 ILE cc_start: 0.8704 (mm) cc_final: 0.8433 (mt) REVERT: D 111 ASN cc_start: 0.8386 (t0) cc_final: 0.8126 (t0) REVERT: D 269 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.7983 (p0) REVERT: E 51 ILE cc_start: 0.8563 (tt) cc_final: 0.8287 (tt) REVERT: E 180 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8206 (mm) REVERT: E 242 ASP cc_start: 0.8259 (t0) cc_final: 0.7936 (t0) REVERT: E 336 MET cc_start: 0.8551 (tpp) cc_final: 0.8325 (mmt) REVERT: F 294 LEU cc_start: 0.8969 (mp) cc_final: 0.8490 (tt) REVERT: F 319 MET cc_start: 0.7629 (mtp) cc_final: 0.7077 (mtp) outliers start: 32 outliers final: 12 residues processed: 247 average time/residue: 0.2528 time to fit residues: 85.4790 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 : 1.241 ------------------------------------------------------------------------------- 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 223 ARG Chi-restraints excluded: chain E residue 245 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 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.0070 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 117 optimal weight: 8.9990 chunk 133 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- 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 179 HIS ** C 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS F 254 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.109700 restraints weight = 17382.267| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.34 r_work: 0.3164 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3730 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= 0.161 Angle : 0.749 10.284 15801 Z= 0.357 Chirality : 0.046 0.229 1787 Planarity : 0.006 0.089 2048 Dihedral : 8.190 174.656 1641 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.91 % Favored : 91.02 % Rotamer: Outliers : 3.78 % Allowed : 13.22 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.23), residues: 1426 helix: -0.21 (0.20), residues: 700 sheet: -1.65 (0.40), residues: 152 loop : -2.00 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 241 HIS 0.023 0.001 HIS C 343 PHE 0.013 0.002 PHE B 110 TYR 0.014 0.001 TYR F 339 ARG 0.007 0.001 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 472) hydrogen bonds : angle 5.11611 ( 1365) covalent geometry : bond 0.00376 (11675) covalent geometry : angle 0.74853 (15801) Misc. bond : bond 0.00277 ( 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 234 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7518 (mmm160) cc_final: 0.7148 (tmt170) REVERT: B 95 GLN cc_start: 0.8223 (mt0) cc_final: 0.7995 (mt0) REVERT: B 336 MET cc_start: 0.8977 (tpt) cc_final: 0.8698 (tpt) REVERT: C 151 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8852 (tp) REVERT: C 153 TYR cc_start: 0.8913 (p90) cc_final: 0.8712 (p90) REVERT: C 176 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8039 (mt) REVERT: C 216 ASP cc_start: 0.8744 (p0) cc_final: 0.8445 (p0) REVERT: C 267 ASP cc_start: 0.7275 (t70) cc_final: 0.6928 (t0) REVERT: C 293 ILE cc_start: 0.8778 (mm) cc_final: 0.8505 (mt) REVERT: C 342 GLN cc_start: 0.8661 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 343 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7751 (t-90) REVERT: D 111 ASN cc_start: 0.8505 (t0) cc_final: 0.8258 (t0) REVERT: D 311 TYR cc_start: 0.8669 (t80) cc_final: 0.8259 (t80) REVERT: E 51 ILE cc_start: 0.8641 (tt) cc_final: 0.8338 (tt) REVERT: E 180 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8245 (mm) REVERT: E 336 MET cc_start: 0.8457 (tpp) cc_final: 0.8230 (mmt) REVERT: F 90 ASN cc_start: 0.7115 (p0) cc_final: 0.6892 (p0) REVERT: F 289 GLN cc_start: 0.9097 (pm20) cc_final: 0.8668 (pm20) REVERT: F 294 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8473 (tt) outliers start: 46 outliers final: 23 residues processed: 223 average time/residue: 0.2416 time to fit residues: 76.3028 Evaluate side-chains 198 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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 C residue 343 HIS Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 132 THR 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 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 294 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 56 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 38 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 50 optimal weight: 0.0370 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.3458 ------------------------------------------------------------------------------- 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 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS ** D 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN D 343 HIS D 354 ASN F 94 ASN F 95 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.146534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111834 restraints weight = 17276.590| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.15 r_work: 0.3217 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11678 Z= 0.131 Angle : 0.706 8.759 15801 Z= 0.334 Chirality : 0.045 0.221 1787 Planarity : 0.005 0.084 2048 Dihedral : 7.907 172.635 1641 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.12 % Allowed : 14.29 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.19 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.23), residues: 1426 helix: 0.18 (0.20), residues: 698 sheet: -1.49 (0.41), residues: 153 loop : -1.90 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 241 HIS 0.008 0.001 HIS C 343 PHE 0.016 0.001 PHE F 307 TYR 0.014 0.001 TYR B 311 ARG 0.006 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03205 ( 472) hydrogen bonds : angle 4.90367 ( 1365) covalent geometry : bond 0.00293 (11675) covalent geometry : angle 0.70577 (15801) Misc. bond : bond 0.00199 ( 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 229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 191 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7115 (tmt170) REVERT: B 227 HIS cc_start: 0.7567 (t-90) cc_final: 0.7325 (t-90) REVERT: B 289 GLN cc_start: 0.8453 (mp10) cc_final: 0.8245 (mp10) REVERT: B 307 PHE cc_start: 0.8198 (t80) cc_final: 0.7997 (t80) REVERT: B 308 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7822 (t70) REVERT: C 59 ARG cc_start: 0.6304 (tmt170) cc_final: 0.5872 (tmm160) REVERT: C 151 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8872 (tp) REVERT: C 216 ASP cc_start: 0.8780 (p0) cc_final: 0.8535 (p0) REVERT: C 267 ASP cc_start: 0.7319 (t70) cc_final: 0.7094 (t0) REVERT: C 293 ILE cc_start: 0.8836 (mm) cc_final: 0.8574 (mt) REVERT: C 342 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8477 (tm-30) REVERT: D 61 ARG cc_start: 0.6571 (mpt-90) cc_final: 0.6331 (mpt-90) REVERT: D 221 THR cc_start: 0.8970 (m) cc_final: 0.8692 (m) REVERT: D 311 TYR cc_start: 0.8723 (t80) cc_final: 0.8247 (t80) REVERT: E 51 ILE cc_start: 0.8678 (tt) cc_final: 0.8339 (tt) REVERT: E 180 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8273 (mm) REVERT: F 94 ASN cc_start: 0.8871 (m-40) cc_final: 0.8660 (m-40) REVERT: F 269 ASP cc_start: 0.7931 (t70) cc_final: 0.7620 (t0) REVERT: F 294 LEU cc_start: 0.8987 (mp) cc_final: 0.8522 (tt) REVERT: F 325 LYS cc_start: 0.3626 (mttt) cc_final: 0.3293 (mttm) REVERT: F 336 MET cc_start: 0.9316 (tmm) cc_final: 0.8966 (tmm) outliers start: 38 outliers final: 17 residues processed: 221 average time/residue: 0.2368 time to fit residues: 73.9362 Evaluate side-chains 190 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 151 LEU Chi-restraints excluded: chain C residue 218 VAL 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 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 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 353 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 94 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 0.0570 chunk 122 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 95 GLN D 343 HIS D 354 ASN ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.144805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111482 restraints weight = 17206.989| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.37 r_work: 0.3162 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4396 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= 0.140 Angle : 0.700 8.459 15801 Z= 0.329 Chirality : 0.045 0.237 1787 Planarity : 0.005 0.055 2048 Dihedral : 7.706 163.976 1641 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.87 % Allowed : 15.27 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.23), residues: 1426 helix: 0.40 (0.21), residues: 698 sheet: -1.44 (0.41), residues: 153 loop : -1.89 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 241 HIS 0.004 0.001 HIS F 343 PHE 0.011 0.002 PHE C 199 TYR 0.015 0.001 TYR B 137 ARG 0.008 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 472) hydrogen bonds : angle 4.76394 ( 1365) covalent geometry : bond 0.00324 (11675) covalent geometry : angle 0.69996 (15801) Misc. bond : bond 0.00214 ( 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 213 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.8977 (mp) cc_final: 0.8773 (mp) REVERT: B 227 HIS cc_start: 0.7415 (t-90) cc_final: 0.7192 (t-90) REVERT: B 289 GLN cc_start: 0.8298 (mp10) cc_final: 0.7969 (mp10) REVERT: B 308 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7777 (t70) REVERT: C 176 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.7955 (mt) REVERT: C 216 ASP cc_start: 0.8715 (p0) cc_final: 0.8456 (p0) REVERT: C 267 ASP cc_start: 0.7052 (t70) cc_final: 0.6714 (t0) REVERT: C 342 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8418 (tm-30) REVERT: D 61 ARG cc_start: 0.6618 (mpt-90) cc_final: 0.6414 (mpt-90) REVERT: D 311 TYR cc_start: 0.8640 (t80) cc_final: 0.8162 (t80) REVERT: E 51 ILE cc_start: 0.8608 (tt) cc_final: 0.8237 (tt) REVERT: E 104 GLU cc_start: 0.7674 (mp0) cc_final: 0.7343 (tp30) REVERT: E 138 LYS cc_start: 0.8620 (tppt) cc_final: 0.8295 (tptt) REVERT: E 180 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8365 (mm) REVERT: F 137 TYR cc_start: 0.8117 (m-80) cc_final: 0.7886 (m-80) REVERT: F 289 GLN cc_start: 0.9081 (pm20) cc_final: 0.8794 (pm20) REVERT: F 294 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8492 (tt) outliers start: 35 outliers final: 26 residues processed: 204 average time/residue: 0.2929 time to fit residues: 83.9481 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 : 1.617 ------------------------------------------------------------------------------- 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 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN 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 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 287 LEU 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 294 LEU Chi-restraints excluded: chain F residue 304 ASP 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 91 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 123 optimal weight: 8.9990 chunk 18 optimal weight: 0.0000 overall best weight: 1.7390 ------------------------------------------------------------------------------- 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 95 GLN D 95 GLN D 279 GLN E 95 GLN E 192 ASN F 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.140707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.103369 restraints weight = 17522.173| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.51 r_work: 0.3120 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11678 Z= 0.240 Angle : 0.780 8.648 15801 Z= 0.370 Chirality : 0.049 0.242 1787 Planarity : 0.005 0.065 2048 Dihedral : 8.018 164.740 1641 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 3.69 % Allowed : 15.27 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.23), residues: 1426 helix: 0.32 (0.20), residues: 688 sheet: -1.45 (0.41), residues: 153 loop : -1.78 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP E 241 HIS 0.005 0.001 HIS B 227 PHE 0.026 0.003 PHE D 307 TYR 0.013 0.001 TYR B 153 ARG 0.010 0.001 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 472) hydrogen bonds : angle 4.95773 ( 1365) covalent geometry : bond 0.00585 (11675) covalent geometry : angle 0.78039 (15801) Misc. bond : bond 0.00420 ( 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 215 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9066 (mp) cc_final: 0.8828 (mp) REVERT: B 227 HIS cc_start: 0.7642 (t-90) cc_final: 0.7306 (t-90) REVERT: B 236 GLU cc_start: 0.8810 (tp30) cc_final: 0.8561 (tp30) REVERT: B 289 GLN cc_start: 0.8490 (mp10) cc_final: 0.7957 (mp10) REVERT: B 308 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7638 (t70) REVERT: B 336 MET cc_start: 0.9166 (tpt) cc_final: 0.8644 (tpp) REVERT: C 176 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8209 (mt) REVERT: C 267 ASP cc_start: 0.7937 (t70) cc_final: 0.7591 (t0) REVERT: C 319 MET cc_start: 0.8836 (mtp) cc_final: 0.8490 (mtp) REVERT: D 268 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8741 (mm) REVERT: D 311 TYR cc_start: 0.8696 (t80) cc_final: 0.8148 (t80) REVERT: E 51 ILE cc_start: 0.8237 (tt) cc_final: 0.7907 (tt) REVERT: E 104 GLU cc_start: 0.8235 (mp0) cc_final: 0.7492 (tp30) REVERT: E 138 LYS cc_start: 0.9014 (tppt) cc_final: 0.8717 (tptt) REVERT: E 180 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8418 (mm) REVERT: F 95 GLN cc_start: 0.8870 (tp40) cc_final: 0.8526 (tp-100) REVERT: F 289 GLN cc_start: 0.9195 (pm20) cc_final: 0.8808 (pm20) REVERT: F 294 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8600 (tt) outliers start: 45 outliers final: 31 residues processed: 198 average time/residue: 0.4662 time to fit residues: 131.2546 Evaluate side-chains 197 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 308 ASP 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 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 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 221 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 265 ILE 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 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 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 239 THR Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 304 ASP 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 38 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 110 optimal weight: 0.0170 chunk 73 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 83 optimal weight: 0.1980 chunk 77 optimal weight: 0.4980 chunk 132 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 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 = 0.3874 r_free = 0.3874 target = 0.144943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109716 restraints weight = 17529.150| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.40 r_work: 0.3194 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11678 Z= 0.130 Angle : 0.707 9.347 15801 Z= 0.335 Chirality : 0.045 0.225 1787 Planarity : 0.005 0.056 2048 Dihedral : 7.661 161.735 1641 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.28 % Allowed : 16.09 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1426 helix: 0.60 (0.21), residues: 684 sheet: -1.42 (0.41), residues: 153 loop : -1.82 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 187 HIS 0.004 0.001 HIS F 343 PHE 0.031 0.002 PHE D 307 TYR 0.017 0.001 TYR B 137 ARG 0.006 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 472) hydrogen bonds : angle 4.77205 ( 1365) covalent geometry : bond 0.00296 (11675) covalent geometry : angle 0.70729 (15801) Misc. bond : bond 0.00198 ( 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 215 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9050 (mp) cc_final: 0.8813 (mp) REVERT: B 236 GLU cc_start: 0.8707 (tp30) cc_final: 0.8366 (tp30) REVERT: B 289 GLN cc_start: 0.8339 (mp10) cc_final: 0.7778 (mp10) REVERT: B 308 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7444 (t70) REVERT: B 311 TYR cc_start: 0.7657 (t80) cc_final: 0.7395 (t80) REVERT: C 176 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7736 (mt) REVERT: C 216 ASP cc_start: 0.8694 (p0) cc_final: 0.8476 (p0) REVERT: C 267 ASP cc_start: 0.7344 (t70) cc_final: 0.6961 (t0) REVERT: D 268 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8637 (mm) REVERT: E 51 ILE cc_start: 0.8116 (tt) cc_final: 0.7753 (tt) REVERT: E 104 GLU cc_start: 0.7969 (mp0) cc_final: 0.7206 (tp30) REVERT: E 138 LYS cc_start: 0.8900 (tppt) cc_final: 0.8621 (tptt) REVERT: F 95 GLN cc_start: 0.8861 (tp40) cc_final: 0.8485 (tp-100) REVERT: F 289 GLN cc_start: 0.9154 (pm20) cc_final: 0.8757 (pm20) REVERT: F 294 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8587 (tt) REVERT: F 325 LYS cc_start: 0.3839 (mttt) cc_final: 0.3586 (mttm) outliers start: 40 outliers final: 24 residues processed: 205 average time/residue: 0.3450 time to fit residues: 98.5417 Evaluate side-chains 192 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 111 ASN Chi-restraints excluded: chain C residue 176 ILE 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 C residue 354 ASN 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 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 245 THR 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 294 LEU Chi-restraints excluded: chain F residue 304 ASP 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 130 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103463 restraints weight = 17387.134| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.63 r_work: 0.3118 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11678 Z= 0.216 Angle : 0.769 10.818 15801 Z= 0.366 Chirality : 0.048 0.239 1787 Planarity : 0.005 0.061 2048 Dihedral : 7.902 162.920 1641 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 3.37 % Allowed : 16.58 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1426 helix: 0.54 (0.21), residues: 683 sheet: -1.36 (0.42), residues: 153 loop : -1.77 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 241 HIS 0.005 0.001 HIS B 227 PHE 0.019 0.002 PHE D 175 TYR 0.012 0.001 TYR D 92 ARG 0.010 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 472) hydrogen bonds : angle 4.88012 ( 1365) covalent geometry : bond 0.00521 (11675) covalent geometry : angle 0.76909 (15801) Misc. bond : bond 0.00372 ( 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 208 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 167 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 LEU cc_start: 0.9074 (mp) cc_final: 0.8822 (mp) REVERT: B 236 GLU cc_start: 0.8798 (tp30) cc_final: 0.8435 (tp30) REVERT: B 289 GLN cc_start: 0.8461 (mp10) cc_final: 0.7883 (mp10) REVERT: B 308 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7546 (t70) REVERT: B 311 TYR cc_start: 0.7793 (t80) cc_final: 0.7465 (t80) REVERT: B 336 MET cc_start: 0.9130 (tpt) cc_final: 0.8559 (tpp) REVERT: C 176 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8084 (mt) REVERT: C 319 MET cc_start: 0.8754 (mtp) cc_final: 0.8372 (mtp) REVERT: D 268 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8702 (mm) REVERT: D 311 TYR cc_start: 0.8656 (t80) cc_final: 0.8108 (t80) REVERT: E 51 ILE cc_start: 0.8202 (tt) cc_final: 0.7859 (tt) REVERT: E 104 GLU cc_start: 0.8296 (mp0) cc_final: 0.7491 (tp30) REVERT: E 138 LYS cc_start: 0.8980 (tppt) cc_final: 0.8714 (tptt) REVERT: E 354 ASN cc_start: 0.8030 (p0) cc_final: 0.7688 (m110) REVERT: E 361 ILE cc_start: 0.6925 (OUTLIER) cc_final: 0.6622 (pp) REVERT: F 95 GLN cc_start: 0.8850 (tp40) cc_final: 0.8481 (tp-100) REVERT: F 289 GLN cc_start: 0.9181 (pm20) cc_final: 0.8751 (pm20) REVERT: F 294 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8593 (tt) REVERT: F 325 LYS cc_start: 0.4040 (mttt) cc_final: 0.3707 (mttm) outliers start: 41 outliers final: 29 residues processed: 197 average time/residue: 0.2436 time to fit residues: 67.7394 Evaluate side-chains 198 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 308 ASP 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 306 ASP Chi-restraints excluded: chain C residue 354 ASN 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 101 VAL 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 E residue 361 ILE Chi-restraints excluded: chain F residue 143 LEU Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 294 LEU 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 39 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.3980 chunk 74 optimal weight: 0.0370 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.144774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.107823 restraints weight = 17419.366| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.56 r_work: 0.3190 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11678 Z= 0.133 Angle : 0.717 10.437 15801 Z= 0.340 Chirality : 0.045 0.238 1787 Planarity : 0.005 0.052 2048 Dihedral : 7.582 157.983 1641 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.87 % Allowed : 17.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.23), residues: 1426 helix: 0.70 (0.21), residues: 697 sheet: -1.32 (0.42), residues: 152 loop : -1.82 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.004 0.001 HIS B 227 PHE 0.021 0.001 PHE F 307 TYR 0.015 0.001 TYR B 137 ARG 0.008 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03055 ( 472) hydrogen bonds : angle 4.72088 ( 1365) covalent geometry : bond 0.00303 (11675) covalent geometry : angle 0.71679 (15801) Misc. bond : bond 0.00200 ( 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 203 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 GLU cc_start: 0.8587 (tp30) cc_final: 0.8350 (tp30) REVERT: B 289 GLN cc_start: 0.8361 (mp10) cc_final: 0.7769 (mp10) REVERT: B 308 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7405 (t70) REVERT: B 311 TYR cc_start: 0.7636 (t80) cc_final: 0.7394 (t80) REVERT: C 176 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.7673 (mt) REVERT: C 216 ASP cc_start: 0.8706 (p0) cc_final: 0.8492 (p0) REVERT: D 268 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8632 (mm) REVERT: E 51 ILE cc_start: 0.8159 (tt) cc_final: 0.7795 (tt) REVERT: E 104 GLU cc_start: 0.8008 (mp0) cc_final: 0.7225 (tp30) REVERT: E 138 LYS cc_start: 0.8908 (tppt) cc_final: 0.8634 (tptt) REVERT: E 361 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6484 (pp) REVERT: F 95 GLN cc_start: 0.8837 (tp40) cc_final: 0.8505 (tp-100) REVERT: F 289 GLN cc_start: 0.9152 (pm20) cc_final: 0.8674 (pm20) REVERT: F 294 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8536 (tt) REVERT: F 325 LYS cc_start: 0.3494 (mttt) cc_final: 0.3201 (mttm) outliers start: 35 outliers final: 27 residues processed: 194 average time/residue: 0.2596 time to fit residues: 70.6749 Evaluate side-chains 192 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN 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 192 ASN 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 316 THR Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 294 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 97 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 4 optimal weight: 0.0570 chunk 93 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** ** F 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.143962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.108150 restraints weight = 17277.776| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.33 r_work: 0.3184 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4903 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= 0.147 Angle : 0.722 10.925 15801 Z= 0.342 Chirality : 0.046 0.249 1787 Planarity : 0.005 0.051 2048 Dihedral : 7.508 151.952 1641 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.87 % Allowed : 17.41 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.23), residues: 1426 helix: 0.75 (0.21), residues: 689 sheet: -1.28 (0.42), residues: 152 loop : -1.75 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 187 HIS 0.004 0.001 HIS F 343 PHE 0.022 0.002 PHE F 307 TYR 0.017 0.001 TYR D 92 ARG 0.008 0.000 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 472) hydrogen bonds : angle 4.68011 ( 1365) covalent geometry : bond 0.00346 (11675) covalent geometry : angle 0.72233 (15801) Misc. bond : bond 0.00236 ( 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 192 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 ARG cc_start: 0.7377 (mmm160) cc_final: 0.7069 (mmm160) REVERT: B 236 GLU cc_start: 0.8681 (tp30) cc_final: 0.8461 (tp30) REVERT: B 289 GLN cc_start: 0.8488 (mp10) cc_final: 0.7910 (mp10) REVERT: B 308 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7466 (t70) REVERT: B 311 TYR cc_start: 0.7686 (t80) cc_final: 0.7428 (t80) REVERT: C 176 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.7897 (mt) REVERT: C 216 ASP cc_start: 0.8853 (p0) cc_final: 0.8627 (p0) REVERT: D 268 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8704 (mm) REVERT: E 51 ILE cc_start: 0.8196 (tt) cc_final: 0.7854 (tt) REVERT: E 104 GLU cc_start: 0.8195 (mp0) cc_final: 0.7335 (tp30) REVERT: E 138 LYS cc_start: 0.8994 (tppt) cc_final: 0.8722 (tptt) REVERT: E 361 ILE cc_start: 0.6799 (OUTLIER) cc_final: 0.6524 (pp) REVERT: F 95 GLN cc_start: 0.8841 (tp40) cc_final: 0.8496 (tp-100) REVERT: F 289 GLN cc_start: 0.9168 (pm20) cc_final: 0.8681 (pm20) REVERT: F 294 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8523 (tt) REVERT: F 325 LYS cc_start: 0.3870 (mttt) cc_final: 0.3526 (mttm) outliers start: 35 outliers final: 28 residues processed: 183 average time/residue: 0.2391 time to fit residues: 62.1058 Evaluate side-chains 192 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 308 ASP 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 306 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 354 ASN 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 192 ASN 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 E residue 361 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 294 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 79 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 0.0470 chunk 96 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 85 optimal weight: 0.8980 chunk 120 optimal weight: 0.0070 chunk 125 optimal weight: 1.9990 overall best weight: 0.2496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 HIS E 192 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112118 restraints weight = 17360.521| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.54 r_work: 0.3242 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11678 Z= 0.123 Angle : 0.701 10.657 15801 Z= 0.331 Chirality : 0.044 0.250 1787 Planarity : 0.005 0.052 2048 Dihedral : 7.137 139.845 1641 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.71 % Allowed : 17.98 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1426 helix: 0.88 (0.21), residues: 700 sheet: -1.23 (0.41), residues: 153 loop : -1.74 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 187 HIS 0.004 0.001 HIS F 343 PHE 0.019 0.001 PHE F 307 TYR 0.009 0.001 TYR F 339 ARG 0.006 0.000 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 472) hydrogen bonds : angle 4.55774 ( 1365) covalent geometry : bond 0.00274 (11675) covalent geometry : angle 0.70083 (15801) Misc. bond : bond 0.00181 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7006.45 seconds wall clock time: 126 minutes 50.25 seconds (7610.25 seconds total)