Starting phenix.real_space_refine on Sat Jul 4 02:23:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.map" model { file = "/net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2i_62776/07_2026/9l2i_62776.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.051 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: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 38 5.16 5 C 10926 2.51 5 N 2966 2.21 5 O 3158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17092 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4129 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 22, 'TRANS': 487} Chain: "B" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3129 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 13, 'TRANS': 371} Chain: "C" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1283 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' FE': 2} Chain breaks: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: D, E, F Time building chain proxies: 4.64, per 1000 atoms: 0.27 Number of scatterers: 17092 At special positions: 0 Unit cell: (78.351, 140.343, 108.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 38 16.00 O 3158 8.00 N 2966 7.00 C 10926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 470.1 milliseconds 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3932 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 2 sheets defined 70.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 24 through 35 removed outlier: 4.250A pdb=" N VAL A 28 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 33 " --> pdb=" O HIS A 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 removed outlier: 3.637A pdb=" N LYS A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 127 removed outlier: 3.860A pdb=" N VAL A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.219A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 188 removed outlier: 3.936A pdb=" N GLY A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.889A pdb=" N PHE A 192 " --> pdb=" O PHE A 188 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 205 Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.790A pdb=" N VAL A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 258 removed outlier: 4.274A pdb=" N THR A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 235 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 292 removed outlier: 5.724A pdb=" N ASN A 268 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.732A pdb=" N THR A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N TRP A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N HIS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N HIS A 344 " --> pdb=" O TYR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.832A pdb=" N HIS A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 450 through 460 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 477 through 485 Processing helix chain 'A' and resid 508 through 516 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 108 through 134 Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 140 through 166 removed outlier: 4.551A pdb=" N LEU B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASN B 149 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY B 153 " --> pdb=" O ASN B 149 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA B 154 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 155 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 156 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B 157 " --> pdb=" O GLY B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.863A pdb=" N ARG B 171 " --> pdb=" O SER B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 207 Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.556A pdb=" N ASP B 224 " --> pdb=" O ILE B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 240 removed outlier: 3.664A pdb=" N GLN B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 253 Processing helix chain 'B' and resid 253 through 266 removed outlier: 4.459A pdb=" N GLN B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 4.374A pdb=" N ALA B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 306 removed outlier: 3.967A pdb=" N PHE B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 339 Processing helix chain 'B' and resid 339 through 345 removed outlier: 4.143A pdb=" N ALA B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 372 Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 381 through 391 removed outlier: 3.810A pdb=" N LYS B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 21 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 53 through 69 removed outlier: 3.554A pdb=" N ILE C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 81 Processing helix chain 'C' and resid 87 through 101 Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'D' and resid 24 through 35 removed outlier: 4.250A pdb=" N VAL D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 90 removed outlier: 3.636A pdb=" N LYS D 74 " --> pdb=" O MET D 70 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 127 removed outlier: 3.860A pdb=" N VAL D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 162 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 173 through 178 removed outlier: 4.219A pdb=" N ALA D 176 " --> pdb=" O ARG D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 188 removed outlier: 3.936A pdb=" N GLY D 183 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.890A pdb=" N PHE D 192 " --> pdb=" O PHE D 188 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 205 Processing helix chain 'D' and resid 205 through 212 Processing helix chain 'D' and resid 212 through 228 removed outlier: 3.790A pdb=" N VAL D 218 " --> pdb=" O ASN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 258 removed outlier: 4.274A pdb=" N THR D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL D 235 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 292 removed outlier: 5.724A pdb=" N ASN D 268 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N THR D 269 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 300 through 310 Processing helix chain 'D' and resid 313 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 331 through 353 removed outlier: 3.732A pdb=" N THR D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TRP D 341 " --> pdb=" O THR D 337 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS D 343 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N HIS D 344 " --> pdb=" O TYR D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 376 Processing helix chain 'D' and resid 378 through 393 removed outlier: 3.832A pdb=" N HIS D 382 " --> pdb=" O GLY D 378 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N LYS D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE D 386 " --> pdb=" O HIS D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 411 Processing helix chain 'D' and resid 450 through 460 Processing helix chain 'D' and resid 468 through 473 Processing helix chain 'D' and resid 477 through 485 Processing helix chain 'D' and resid 508 through 516 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 50 through 57 Processing helix chain 'E' and resid 108 through 134 Processing helix chain 'E' and resid 135 through 139 Processing helix chain 'E' and resid 140 through 166 removed outlier: 4.551A pdb=" N LEU E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASN E 149 " --> pdb=" O ASP E 145 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLY E 153 " --> pdb=" O ASN E 149 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU E 156 " --> pdb=" O TYR E 152 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.863A pdb=" N ARG E 171 " --> pdb=" O SER E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 207 Processing helix chain 'E' and resid 214 through 224 removed outlier: 3.556A pdb=" N ASP E 224 " --> pdb=" O ILE E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 240 removed outlier: 3.664A pdb=" N GLN E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 253 Processing helix chain 'E' and resid 253 through 266 removed outlier: 4.459A pdb=" N GLN E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 274 removed outlier: 4.373A pdb=" N ALA E 272 " --> pdb=" O PHE E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 306 removed outlier: 3.966A pdb=" N PHE E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 339 Processing helix chain 'E' and resid 339 through 345 removed outlier: 4.144A pdb=" N ALA E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 372 Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 381 through 391 removed outlier: 3.810A pdb=" N LYS E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 21 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 53 through 69 removed outlier: 3.554A pdb=" N ILE F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 81 Processing helix chain 'F' and resid 87 through 101 Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 125 through 145 Processing helix chain 'F' and resid 152 through 161 Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 448 removed outlier: 6.982A pdb=" N VAL A 438 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 163 " --> pdb=" O GLU A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 444 through 448 removed outlier: 6.989A pdb=" N VAL D 438 " --> pdb=" O LEU F 165 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS F 163 " --> pdb=" O GLU D 440 " (cutoff:3.500A) 1012 hydrogen bonds defined for protein. 3000 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3871 1.33 - 1.45: 4242 1.45 - 1.57: 9393 1.57 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 17566 Sorted by residual: bond pdb=" N TYR F 149 " pdb=" CA TYR F 149 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.28e-02 6.10e+03 8.59e+00 bond pdb=" N ARG C 144 " pdb=" CA ARG C 144 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.28e-02 6.10e+03 8.53e+00 bond pdb=" N TYR C 149 " pdb=" CA TYR C 149 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.28e-02 6.10e+03 8.30e+00 bond pdb=" N ARG F 144 " pdb=" CA ARG F 144 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.28e-02 6.10e+03 8.24e+00 bond pdb=" N THR F 146 " pdb=" CA THR F 146 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.22e-02 6.72e+03 7.77e+00 ... (remaining 17561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 22433 1.24 - 2.48: 1029 2.48 - 3.72: 323 3.72 - 4.96: 57 4.96 - 6.20: 16 Bond angle restraints: 23858 Sorted by residual: angle pdb=" N GLU E 118 " pdb=" CA GLU E 118 " pdb=" C GLU E 118 " ideal model delta sigma weight residual 111.07 106.81 4.26 1.07e+00 8.73e-01 1.59e+01 angle pdb=" N GLU B 118 " pdb=" CA GLU B 118 " pdb=" C GLU B 118 " ideal model delta sigma weight residual 111.07 106.82 4.25 1.07e+00 8.73e-01 1.58e+01 angle pdb=" O CYS D 200 " pdb=" C CYS D 200 " pdb=" N SER D 201 " ideal model delta sigma weight residual 122.12 126.31 -4.19 1.06e+00 8.90e-01 1.56e+01 angle pdb=" O CYS A 200 " pdb=" C CYS A 200 " pdb=" N SER A 201 " ideal model delta sigma weight residual 122.12 126.26 -4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C SER D 201 " pdb=" N VAL D 202 " pdb=" CA VAL D 202 " ideal model delta sigma weight residual 120.56 115.85 4.71 1.26e+00 6.30e-01 1.39e+01 ... (remaining 23853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 9173 17.71 - 35.43: 842 35.43 - 53.14: 161 53.14 - 70.86: 24 70.86 - 88.57: 24 Dihedral angle restraints: 10224 sinusoidal: 4082 harmonic: 6142 Sorted by residual: dihedral pdb=" CA ALA C 39 " pdb=" C ALA C 39 " pdb=" N TYR C 40 " pdb=" CA TYR C 40 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ALA F 39 " pdb=" C ALA F 39 " pdb=" N TYR F 40 " pdb=" CA TYR F 40 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP D 196 " pdb=" C ASP D 196 " pdb=" N ALA D 197 " pdb=" CA ALA D 197 " ideal model delta harmonic sigma weight residual -180.00 -163.18 -16.82 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 10221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1844 0.047 - 0.093: 482 0.093 - 0.140: 121 0.140 - 0.186: 13 0.186 - 0.233: 6 Chirality restraints: 2466 Sorted by residual: chirality pdb=" CA CYS D 200 " pdb=" N CYS D 200 " pdb=" C CYS D 200 " pdb=" CB CYS D 200 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA CYS A 200 " pdb=" N CYS A 200 " pdb=" C CYS A 200 " pdb=" CB CYS A 200 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 202 " pdb=" N VAL A 202 " pdb=" C VAL A 202 " pdb=" CB VAL A 202 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.98e-01 ... (remaining 2463 not shown) Planarity restraints: 3086 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 238 " -0.019 2.00e-02 2.50e+03 1.64e-02 6.74e+00 pdb=" CG TRP B 238 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 238 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP B 238 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 238 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 238 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 238 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 238 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 238 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 238 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 238 " -0.018 2.00e-02 2.50e+03 1.64e-02 6.71e+00 pdb=" CG TRP E 238 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP E 238 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 238 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 238 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 238 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 238 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 238 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 238 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP E 238 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 253 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.85e+00 pdb=" C ALA B 253 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA B 253 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL B 254 " -0.013 2.00e-02 2.50e+03 ... (remaining 3083 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 129 2.46 - 3.07: 12541 3.07 - 3.68: 29619 3.68 - 4.29: 41978 4.29 - 4.90: 67965 Nonbonded interactions: 152232 Sorted by model distance: nonbonded pdb=" OE1 GLU D 144 " pdb="FE FE D 601 " model vdw 1.849 3.000 nonbonded pdb=" ND1 HIS D 246 " pdb="FE FE D 602 " model vdw 1.977 3.080 nonbonded pdb=" OE1 GLU A 144 " pdb="FE FE A 601 " model vdw 1.987 3.000 nonbonded pdb="FE FE A 601 " pdb=" O HOH A 701 " model vdw 2.028 3.000 nonbonded pdb=" OE2 GLU A 243 " pdb="FE FE A 601 " model vdw 2.031 3.000 ... (remaining 152227 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 2.340 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.450 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 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 : 0.004 0.038 17566 Z= 0.252 Angle : 0.661 6.195 23858 Z= 0.440 Chirality : 0.046 0.233 2466 Planarity : 0.004 0.034 3086 Dihedral : 14.594 88.570 6292 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.80 % Allowed : 1.61 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2096 helix: 0.68 (0.14), residues: 1320 sheet: 0.15 (0.89), residues: 44 loop : -0.23 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 116 TYR 0.019 0.001 TYR F 148 PHE 0.028 0.002 PHE D 79 TRP 0.044 0.002 TRP B 238 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.25 (17566) covalent geometry : angle 0.66052 / 0.44 (23858) hydrogen bonds : bond 0.12924 / 8.65 ( 1012) hydrogen bonds : angle 6.37143 / 4.63 ( 3000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 225 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8329 (tpp) cc_final: 0.7679 (tpp) REVERT: A 187 VAL cc_start: 0.8303 (m) cc_final: 0.8056 (p) REVERT: A 188 PHE cc_start: 0.8293 (m-10) cc_final: 0.7964 (m-10) REVERT: A 203 ASN cc_start: 0.8074 (t0) cc_final: 0.7295 (t0) REVERT: B 300 ASP cc_start: 0.8102 (t70) cc_final: 0.7870 (t0) REVERT: B 347 LYS cc_start: 0.9557 (tmtt) cc_final: 0.9349 (tptp) REVERT: C 25 SER cc_start: 0.8101 (t) cc_final: 0.7143 (t) REVERT: C 149 TYR cc_start: 0.7173 (m-80) cc_final: 0.6837 (m-10) REVERT: C 156 LEU cc_start: 0.9079 (mp) cc_final: 0.8864 (mp) REVERT: D 184 MET cc_start: 0.8286 (tpp) cc_final: 0.7689 (tpp) REVERT: D 187 VAL cc_start: 0.8327 (m) cc_final: 0.8055 (p) REVERT: D 188 PHE cc_start: 0.8252 (m-10) cc_final: 0.7924 (m-10) REVERT: D 203 ASN cc_start: 0.8100 (t0) cc_final: 0.7325 (t0) REVERT: E 300 ASP cc_start: 0.8110 (t70) cc_final: 0.7873 (t0) REVERT: E 347 LYS cc_start: 0.9555 (tmtt) cc_final: 0.9348 (tptp) REVERT: F 25 SER cc_start: 0.8173 (t) cc_final: 0.7266 (t) REVERT: F 149 TYR cc_start: 0.7133 (m-80) cc_final: 0.6847 (m-80) outliers start: 14 outliers final: 2 residues processed: 237 average time/residue: 0.1201 time to fit residues: 43.9281 Evaluate side-chains 159 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain D residue 204 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 HIS A 205 GLN ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 29 HIS D 205 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 269 GLN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063267 restraints weight = 53881.613| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.50 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17566 Z= 0.183 Angle : 0.573 7.986 23858 Z= 0.316 Chirality : 0.042 0.159 2466 Planarity : 0.004 0.037 3086 Dihedral : 4.911 53.668 2340 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.61 % Allowed : 8.10 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.18), residues: 2096 helix: 0.94 (0.14), residues: 1326 sheet: 0.26 (0.86), residues: 44 loop : -0.12 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.022 0.001 TYR D 288 PHE 0.024 0.002 PHE A 212 TRP 0.019 0.002 TRP A 301 HIS 0.010 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (17566) covalent geometry : angle 0.57254 / 0.32 (23858) hydrogen bonds : bond 0.04864 / 3.22 ( 1012) hydrogen bonds : angle 5.41955 / 3.99 ( 3000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8624 (tpp) cc_final: 0.8177 (tpp) REVERT: A 188 PHE cc_start: 0.8678 (m-10) cc_final: 0.8443 (m-10) REVERT: A 203 ASN cc_start: 0.8567 (t0) cc_final: 0.7778 (t0) REVERT: A 209 GLU cc_start: 0.6374 (OUTLIER) cc_final: 0.6118 (mp0) REVERT: A 247 MET cc_start: 0.8902 (mmt) cc_final: 0.8685 (mmm) REVERT: A 278 GLN cc_start: 0.9350 (mm110) cc_final: 0.8987 (mm-40) REVERT: A 330 ARG cc_start: 0.8798 (pmt170) cc_final: 0.8586 (pmt170) REVERT: B 195 MET cc_start: 0.8970 (mmt) cc_final: 0.8707 (mmp) REVERT: B 300 ASP cc_start: 0.8229 (t70) cc_final: 0.7998 (t0) REVERT: B 347 LYS cc_start: 0.9561 (tmtt) cc_final: 0.9333 (tptp) REVERT: C 133 ASP cc_start: 0.9354 (m-30) cc_final: 0.9082 (m-30) REVERT: D 184 MET cc_start: 0.8622 (tpp) cc_final: 0.8222 (tpp) REVERT: D 188 PHE cc_start: 0.8640 (m-10) cc_final: 0.8394 (m-10) REVERT: D 203 ASN cc_start: 0.8588 (t0) cc_final: 0.7590 (t0) REVERT: D 209 GLU cc_start: 0.6201 (OUTLIER) cc_final: 0.5944 (mp0) REVERT: D 247 MET cc_start: 0.8925 (mmt) cc_final: 0.8683 (mmm) REVERT: D 278 GLN cc_start: 0.9334 (mm110) cc_final: 0.8999 (mm-40) REVERT: D 330 ARG cc_start: 0.8750 (pmt170) cc_final: 0.8431 (pmt170) REVERT: E 290 TYR cc_start: 0.8484 (m-10) cc_final: 0.8262 (m-10) REVERT: E 300 ASP cc_start: 0.8232 (t70) cc_final: 0.7994 (t0) REVERT: E 347 LYS cc_start: 0.9550 (tmtt) cc_final: 0.9312 (tptp) REVERT: F 96 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9105 (pt) REVERT: F 133 ASP cc_start: 0.9344 (m-30) cc_final: 0.9109 (m-30) REVERT: F 147 ASP cc_start: 0.9275 (m-30) cc_final: 0.8907 (p0) outliers start: 28 outliers final: 20 residues processed: 186 average time/residue: 0.1078 time to fit residues: 31.7700 Evaluate side-chains 169 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 89 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 24 optimal weight: 0.0370 chunk 159 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN B 149 ASN B 245 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 149 ASN E 245 ASN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.077873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.063581 restraints weight = 54274.171| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 4.58 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17566 Z= 0.137 Angle : 0.526 8.790 23858 Z= 0.288 Chirality : 0.040 0.152 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.926 59.442 2340 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.78 % Allowed : 11.72 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2096 helix: 1.04 (0.14), residues: 1342 sheet: 0.05 (0.83), residues: 44 loop : -0.12 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.019 0.001 TYR F 149 PHE 0.012 0.001 PHE A 282 TRP 0.021 0.001 TRP D 317 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (17566) covalent geometry : angle 0.52601 / 0.29 (23858) hydrogen bonds : bond 0.04401 / 2.92 ( 1012) hydrogen bonds : angle 5.24336 / 3.87 ( 3000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8791 (tpp) cc_final: 0.8022 (tpp) REVERT: A 187 VAL cc_start: 0.8851 (t) cc_final: 0.8463 (p) REVERT: A 188 PHE cc_start: 0.8792 (m-10) cc_final: 0.8575 (m-10) REVERT: A 211 CYS cc_start: 0.8756 (t) cc_final: 0.8509 (t) REVERT: A 247 MET cc_start: 0.8899 (mmt) cc_final: 0.8624 (mmm) REVERT: A 330 ARG cc_start: 0.8811 (pmt170) cc_final: 0.8550 (pmt170) REVERT: A 367 GLU cc_start: 0.8922 (pm20) cc_final: 0.8721 (pm20) REVERT: B 290 TYR cc_start: 0.8540 (m-10) cc_final: 0.8317 (m-10) REVERT: B 300 ASP cc_start: 0.8168 (t70) cc_final: 0.7942 (t0) REVERT: B 347 LYS cc_start: 0.9537 (tmtt) cc_final: 0.9299 (tptp) REVERT: B 371 ASP cc_start: 0.8150 (t70) cc_final: 0.7627 (t70) REVERT: B 372 TYR cc_start: 0.8271 (m-80) cc_final: 0.7845 (m-80) REVERT: C 133 ASP cc_start: 0.9356 (OUTLIER) cc_final: 0.8978 (m-30) REVERT: D 184 MET cc_start: 0.8784 (tpp) cc_final: 0.8027 (tpp) REVERT: D 187 VAL cc_start: 0.8844 (t) cc_final: 0.8467 (p) REVERT: D 211 CYS cc_start: 0.8801 (t) cc_final: 0.8585 (t) REVERT: D 247 MET cc_start: 0.8908 (mmt) cc_final: 0.8631 (mmm) REVERT: D 367 GLU cc_start: 0.8911 (pm20) cc_final: 0.8709 (pm20) REVERT: E 188 ASP cc_start: 0.9068 (m-30) cc_final: 0.8865 (m-30) REVERT: E 290 TYR cc_start: 0.8407 (m-10) cc_final: 0.8188 (m-10) REVERT: E 300 ASP cc_start: 0.8181 (t70) cc_final: 0.7952 (t0) REVERT: E 347 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9306 (tptp) REVERT: F 96 ILE cc_start: 0.9546 (OUTLIER) cc_final: 0.9065 (pt) REVERT: F 133 ASP cc_start: 0.9352 (OUTLIER) cc_final: 0.9011 (m-30) outliers start: 31 outliers final: 19 residues processed: 181 average time/residue: 0.1096 time to fit residues: 31.9702 Evaluate side-chains 163 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 7.9990 chunk 180 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 HIS E 180 GLN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 HIS ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.073891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.059589 restraints weight = 56066.614| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 4.54 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17566 Z= 0.228 Angle : 0.583 7.235 23858 Z= 0.320 Chirality : 0.042 0.180 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.926 53.516 2340 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.41 % Allowed : 13.68 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 2096 helix: 0.98 (0.14), residues: 1344 sheet: 0.35 (0.90), residues: 44 loop : -0.05 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 37 TYR 0.020 0.002 TYR F 149 PHE 0.019 0.002 PHE D 153 TRP 0.018 0.002 TRP A 317 HIS 0.004 0.001 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.23 (17566) covalent geometry : angle 0.58317 / 0.32 (23858) hydrogen bonds : bond 0.04868 / 3.24 ( 1012) hydrogen bonds : angle 5.32387 / 3.95 ( 3000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8774 (tpp) cc_final: 0.8018 (tpp) REVERT: A 187 VAL cc_start: 0.8959 (t) cc_final: 0.8709 (m) REVERT: A 188 PHE cc_start: 0.8898 (m-10) cc_final: 0.8690 (m-10) REVERT: A 211 CYS cc_start: 0.8845 (t) cc_final: 0.8604 (t) REVERT: A 247 MET cc_start: 0.8965 (mmt) cc_final: 0.8656 (mmm) REVERT: A 330 ARG cc_start: 0.8986 (pmt170) cc_final: 0.8739 (pmt170) REVERT: A 367 GLU cc_start: 0.8948 (pm20) cc_final: 0.8652 (pm20) REVERT: B 300 ASP cc_start: 0.8216 (t70) cc_final: 0.7962 (t0) REVERT: B 347 LYS cc_start: 0.9571 (tmtt) cc_final: 0.9333 (tptp) REVERT: C 133 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.9021 (m-30) REVERT: D 184 MET cc_start: 0.8828 (tpp) cc_final: 0.8100 (tpp) REVERT: D 187 VAL cc_start: 0.9027 (t) cc_final: 0.8786 (m) REVERT: D 211 CYS cc_start: 0.8814 (t) cc_final: 0.8591 (t) REVERT: D 247 MET cc_start: 0.8941 (mmt) cc_final: 0.8621 (mmm) REVERT: D 367 GLU cc_start: 0.8948 (pm20) cc_final: 0.8654 (pm20) REVERT: E 112 TYR cc_start: 0.8128 (t80) cc_final: 0.7699 (t80) REVERT: E 300 ASP cc_start: 0.8262 (t70) cc_final: 0.8004 (t0) REVERT: E 347 LYS cc_start: 0.9563 (tmtt) cc_final: 0.9317 (tptp) REVERT: F 96 ILE cc_start: 0.9612 (OUTLIER) cc_final: 0.9177 (pt) REVERT: F 133 ASP cc_start: 0.9348 (OUTLIER) cc_final: 0.9061 (m-30) outliers start: 42 outliers final: 25 residues processed: 170 average time/residue: 0.1241 time to fit residues: 34.1623 Evaluate side-chains 164 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 173 CYS Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 211 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 34 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 0.0980 chunk 155 optimal weight: 0.5980 chunk 168 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 HIS ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 ASN ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 HIS ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 467 HIS D 521 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062730 restraints weight = 53744.874| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 4.55 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17566 Z= 0.119 Angle : 0.505 8.676 23858 Z= 0.278 Chirality : 0.039 0.148 2466 Planarity : 0.004 0.041 3086 Dihedral : 4.761 49.448 2340 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 15.75 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2096 helix: 1.09 (0.14), residues: 1344 sheet: 0.13 (0.86), residues: 44 loop : -0.06 (0.23), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.015 0.001 TYR D 288 PHE 0.015 0.001 PHE D 188 TRP 0.017 0.001 TRP A 317 HIS 0.004 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (17566) covalent geometry : angle 0.50518 / 0.28 (23858) hydrogen bonds : bond 0.04264 / 2.85 ( 1012) hydrogen bonds : angle 5.16481 / 3.83 ( 3000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8676 (tm-30) REVERT: A 184 MET cc_start: 0.8738 (tpp) cc_final: 0.7966 (tpp) REVERT: A 187 VAL cc_start: 0.8956 (t) cc_final: 0.8633 (m) REVERT: A 188 PHE cc_start: 0.8919 (m-10) cc_final: 0.8612 (m-10) REVERT: A 211 CYS cc_start: 0.8804 (t) cc_final: 0.8473 (t) REVERT: A 247 MET cc_start: 0.8899 (mmt) cc_final: 0.8663 (mmm) REVERT: A 330 ARG cc_start: 0.8903 (pmt170) cc_final: 0.8614 (pmt170) REVERT: B 86 TRP cc_start: 0.8781 (m-10) cc_final: 0.8401 (m-10) REVERT: B 300 ASP cc_start: 0.8109 (t70) cc_final: 0.7860 (t0) REVERT: B 305 CYS cc_start: 0.9102 (m) cc_final: 0.8795 (m) REVERT: B 347 LYS cc_start: 0.9523 (tmtt) cc_final: 0.9285 (tptp) REVERT: C 133 ASP cc_start: 0.9327 (OUTLIER) cc_final: 0.8992 (m-30) REVERT: D 184 MET cc_start: 0.8756 (tpp) cc_final: 0.8085 (tpp) REVERT: D 187 VAL cc_start: 0.8986 (t) cc_final: 0.8714 (m) REVERT: D 211 CYS cc_start: 0.8821 (t) cc_final: 0.8556 (t) REVERT: D 247 MET cc_start: 0.8869 (mmt) cc_final: 0.8664 (mmt) REVERT: E 86 TRP cc_start: 0.8755 (m-10) cc_final: 0.8451 (m-10) REVERT: E 93 LEU cc_start: 0.9460 (mt) cc_final: 0.9109 (mt) REVERT: E 112 TYR cc_start: 0.8000 (t80) cc_final: 0.7784 (t80) REVERT: E 300 ASP cc_start: 0.8100 (t70) cc_final: 0.7851 (t0) REVERT: E 305 CYS cc_start: 0.9103 (m) cc_final: 0.8790 (m) REVERT: E 347 LYS cc_start: 0.9525 (tmtt) cc_final: 0.9303 (tptp) REVERT: F 96 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9124 (pt) REVERT: F 133 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.8979 (m-30) outliers start: 37 outliers final: 22 residues processed: 180 average time/residue: 0.1164 time to fit residues: 33.9600 Evaluate side-chains 167 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 53 ASP Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 154 optimal weight: 0.0980 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** 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 = 0.3297 r_free = 0.3297 target = 0.075700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.061607 restraints weight = 54514.873| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.52 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17566 Z= 0.150 Angle : 0.524 9.013 23858 Z= 0.287 Chirality : 0.040 0.146 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.759 47.611 2340 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.41 % Allowed : 16.32 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2096 helix: 1.06 (0.14), residues: 1348 sheet: 0.13 (0.87), residues: 44 loop : 0.01 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 37 TYR 0.019 0.001 TYR F 149 PHE 0.012 0.001 PHE B 79 TRP 0.044 0.001 TRP D 308 HIS 0.003 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (17566) covalent geometry : angle 0.52403 / 0.29 (23858) hydrogen bonds : bond 0.04318 / 2.88 ( 1012) hydrogen bonds : angle 5.18992 / 3.84 ( 3000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8680 (tm-30) REVERT: A 84 ASP cc_start: 0.8683 (OUTLIER) cc_final: 0.8372 (t0) REVERT: A 184 MET cc_start: 0.8724 (tpp) cc_final: 0.7966 (tpp) REVERT: A 187 VAL cc_start: 0.8939 (t) cc_final: 0.8588 (m) REVERT: A 188 PHE cc_start: 0.8953 (m-10) cc_final: 0.8583 (m-10) REVERT: A 247 MET cc_start: 0.8929 (mmt) cc_final: 0.8724 (mmt) REVERT: A 330 ARG cc_start: 0.8935 (pmt170) cc_final: 0.8600 (pmt170) REVERT: B 86 TRP cc_start: 0.8836 (m-10) cc_final: 0.8580 (m-10) REVERT: B 112 TYR cc_start: 0.8141 (t80) cc_final: 0.7779 (t80) REVERT: B 300 ASP cc_start: 0.8128 (t70) cc_final: 0.7897 (t0) REVERT: B 347 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9306 (tptp) REVERT: C 133 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.9001 (m-30) REVERT: D 84 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8320 (t0) REVERT: D 184 MET cc_start: 0.8742 (tpp) cc_final: 0.7909 (tpp) REVERT: D 187 VAL cc_start: 0.8954 (t) cc_final: 0.8585 (m) REVERT: D 188 PHE cc_start: 0.8997 (m-10) cc_final: 0.8469 (m-10) REVERT: D 247 MET cc_start: 0.8918 (mmt) cc_final: 0.8704 (mmt) REVERT: E 86 TRP cc_start: 0.8802 (m-10) cc_final: 0.8474 (m-10) REVERT: E 112 TYR cc_start: 0.8103 (t80) cc_final: 0.7734 (t80) REVERT: E 300 ASP cc_start: 0.8121 (t70) cc_final: 0.7894 (t0) REVERT: E 347 LYS cc_start: 0.9527 (tmtt) cc_final: 0.9304 (tptp) REVERT: F 133 ASP cc_start: 0.9320 (OUTLIER) cc_final: 0.9007 (m-30) outliers start: 42 outliers final: 24 residues processed: 172 average time/residue: 0.1180 time to fit residues: 33.0443 Evaluate side-chains 173 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 206 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** 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 = 0.3312 r_free = 0.3312 target = 0.076423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.062246 restraints weight = 54748.649| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 4.61 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17566 Z= 0.131 Angle : 0.513 9.484 23858 Z= 0.281 Chirality : 0.039 0.143 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.710 46.715 2340 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.41 % Allowed : 16.84 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.18), residues: 2096 helix: 1.06 (0.14), residues: 1346 sheet: 0.03 (0.85), residues: 44 loop : -0.01 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.016 0.001 TYR A 288 PHE 0.021 0.001 PHE A 153 TRP 0.044 0.001 TRP D 308 HIS 0.002 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17566) covalent geometry : angle 0.51273 / 0.28 (23858) hydrogen bonds : bond 0.04231 / 2.83 ( 1012) hydrogen bonds : angle 5.19439 / 3.85 ( 3000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 84 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.8341 (t0) REVERT: A 184 MET cc_start: 0.8691 (tpp) cc_final: 0.7948 (tpp) REVERT: A 187 VAL cc_start: 0.8896 (t) cc_final: 0.8534 (m) REVERT: A 188 PHE cc_start: 0.8975 (m-10) cc_final: 0.8575 (m-10) REVERT: A 247 MET cc_start: 0.8837 (mmt) cc_final: 0.8474 (mmt) REVERT: A 330 ARG cc_start: 0.8965 (pmt170) cc_final: 0.8617 (pmt170) REVERT: B 86 TRP cc_start: 0.8781 (m-10) cc_final: 0.8352 (m-10) REVERT: B 112 TYR cc_start: 0.7991 (t80) cc_final: 0.7615 (t80) REVERT: B 172 ASP cc_start: 0.8645 (m-30) cc_final: 0.8306 (m-30) REVERT: B 300 ASP cc_start: 0.8100 (t70) cc_final: 0.7867 (t0) REVERT: B 347 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9297 (tptp) REVERT: C 133 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.8999 (m-30) REVERT: C 141 MET cc_start: 0.9164 (mmp) cc_final: 0.8883 (mmt) REVERT: D 84 ASP cc_start: 0.8585 (m-30) cc_final: 0.8290 (t0) REVERT: D 184 MET cc_start: 0.8732 (tpp) cc_final: 0.7926 (tpp) REVERT: D 187 VAL cc_start: 0.8911 (t) cc_final: 0.8521 (m) REVERT: D 188 PHE cc_start: 0.9013 (m-10) cc_final: 0.8445 (m-10) REVERT: D 247 MET cc_start: 0.8792 (mmt) cc_final: 0.8435 (mmt) REVERT: E 86 TRP cc_start: 0.8742 (m-10) cc_final: 0.8298 (m-10) REVERT: E 118 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8582 (mm-30) REVERT: E 172 ASP cc_start: 0.8659 (m-30) cc_final: 0.8318 (m-30) REVERT: E 300 ASP cc_start: 0.8093 (t70) cc_final: 0.7864 (t0) REVERT: E 347 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9303 (tptp) REVERT: F 133 ASP cc_start: 0.9304 (OUTLIER) cc_final: 0.8986 (m-30) outliers start: 42 outliers final: 26 residues processed: 177 average time/residue: 0.1149 time to fit residues: 32.9592 Evaluate side-chains 175 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 0.0470 chunk 89 optimal weight: 10.0000 chunk 182 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 11 optimal weight: 5.9990 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.076788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062772 restraints weight = 54586.491| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 4.59 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17566 Z= 0.123 Angle : 0.512 9.987 23858 Z= 0.278 Chirality : 0.039 0.140 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.676 46.537 2340 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.95 % Allowed : 17.82 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2096 helix: 1.07 (0.14), residues: 1348 sheet: 0.06 (0.85), residues: 44 loop : -0.02 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 116 TYR 0.016 0.001 TYR D 288 PHE 0.017 0.001 PHE D 212 TRP 0.053 0.001 TRP A 308 HIS 0.002 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (17566) covalent geometry : angle 0.51249 / 0.28 (23858) hydrogen bonds : bond 0.04165 / 2.78 ( 1012) hydrogen bonds : angle 5.20474 / 3.84 ( 3000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 84 ASP cc_start: 0.8673 (m-30) cc_final: 0.8361 (t0) REVERT: A 184 MET cc_start: 0.8697 (tpp) cc_final: 0.7913 (tpp) REVERT: A 187 VAL cc_start: 0.8924 (t) cc_final: 0.8486 (m) REVERT: A 188 PHE cc_start: 0.9009 (m-10) cc_final: 0.8497 (m-10) REVERT: A 330 ARG cc_start: 0.8949 (pmt170) cc_final: 0.8671 (pmt170) REVERT: B 86 TRP cc_start: 0.8793 (m-10) cc_final: 0.8383 (m-10) REVERT: B 300 ASP cc_start: 0.8106 (t70) cc_final: 0.7880 (t0) REVERT: B 347 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9298 (tptp) REVERT: C 133 ASP cc_start: 0.9316 (OUTLIER) cc_final: 0.8984 (m-30) REVERT: D 84 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8297 (t0) REVERT: D 184 MET cc_start: 0.8725 (tpp) cc_final: 0.8110 (tpp) REVERT: D 187 VAL cc_start: 0.8924 (t) cc_final: 0.8634 (m) REVERT: D 247 MET cc_start: 0.8687 (mmt) cc_final: 0.8396 (mmt) REVERT: E 86 TRP cc_start: 0.8769 (m-10) cc_final: 0.8325 (m-10) REVERT: E 300 ASP cc_start: 0.8093 (t70) cc_final: 0.7868 (t0) REVERT: E 347 LYS cc_start: 0.9513 (tmtt) cc_final: 0.9288 (tptp) REVERT: F 55 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8656 (mm-40) REVERT: F 133 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.9002 (m-30) outliers start: 34 outliers final: 26 residues processed: 180 average time/residue: 0.1101 time to fit residues: 32.4265 Evaluate side-chains 180 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 47 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** 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 = 0.3287 r_free = 0.3287 target = 0.075090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.061071 restraints weight = 55478.671| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.57 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17566 Z= 0.168 Angle : 0.552 10.043 23858 Z= 0.301 Chirality : 0.041 0.146 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.723 46.509 2340 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.07 % Allowed : 18.45 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2096 helix: 1.14 (0.14), residues: 1330 sheet: 0.20 (0.88), residues: 44 loop : -0.12 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 330 TYR 0.022 0.001 TYR E 290 PHE 0.021 0.001 PHE D 212 TRP 0.060 0.002 TRP D 308 HIS 0.003 0.001 HIS E 315 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (17566) covalent geometry : angle 0.55166 / 0.30 (23858) hydrogen bonds : bond 0.04402 / 2.95 ( 1012) hydrogen bonds : angle 5.26074 / 3.89 ( 3000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9078 (tm-30) cc_final: 0.7410 (tm-30) REVERT: A 84 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8343 (t0) REVERT: A 184 MET cc_start: 0.8743 (tpp) cc_final: 0.7933 (tpp) REVERT: A 187 VAL cc_start: 0.8878 (t) cc_final: 0.8429 (m) REVERT: A 188 PHE cc_start: 0.9008 (m-10) cc_final: 0.8471 (m-10) REVERT: A 247 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8722 (mmm) REVERT: A 330 ARG cc_start: 0.8999 (pmt170) cc_final: 0.8694 (pmt170) REVERT: B 86 TRP cc_start: 0.8855 (m-10) cc_final: 0.8387 (m-10) REVERT: B 300 ASP cc_start: 0.8133 (t70) cc_final: 0.7900 (t0) REVERT: B 347 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9301 (tptp) REVERT: C 99 MET cc_start: 0.9192 (tpt) cc_final: 0.8849 (tpp) REVERT: C 133 ASP cc_start: 0.9320 (OUTLIER) cc_final: 0.9005 (m-30) REVERT: C 141 MET cc_start: 0.9161 (mmp) cc_final: 0.8892 (mmt) REVERT: C 149 TYR cc_start: 0.8462 (m-80) cc_final: 0.8169 (m-10) REVERT: D 76 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8361 (tp30) REVERT: D 84 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8335 (t0) REVERT: D 184 MET cc_start: 0.8781 (tpp) cc_final: 0.8146 (tpp) REVERT: D 187 VAL cc_start: 0.9014 (t) cc_final: 0.8691 (m) REVERT: E 86 TRP cc_start: 0.8812 (m-10) cc_final: 0.8482 (m-10) REVERT: E 300 ASP cc_start: 0.8131 (t70) cc_final: 0.7900 (t0) REVERT: E 347 LYS cc_start: 0.9521 (tmtt) cc_final: 0.9293 (tptp) REVERT: F 133 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.9001 (m-30) outliers start: 36 outliers final: 24 residues processed: 166 average time/residue: 0.1158 time to fit residues: 31.5269 Evaluate side-chains 177 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 3.9990 chunk 92 optimal weight: 0.0770 chunk 135 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.077032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.062971 restraints weight = 54409.789| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.62 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17566 Z= 0.127 Angle : 0.544 11.424 23858 Z= 0.294 Chirality : 0.040 0.162 2466 Planarity : 0.004 0.041 3086 Dihedral : 4.715 47.600 2340 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.61 % Allowed : 18.97 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2096 helix: 1.09 (0.14), residues: 1338 sheet: 0.07 (0.86), residues: 44 loop : -0.15 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 37 TYR 0.037 0.001 TYR E 372 PHE 0.011 0.001 PHE D 282 TRP 0.053 0.001 TRP D 308 HIS 0.003 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (17566) covalent geometry : angle 0.54406 / 0.29 (23858) hydrogen bonds : bond 0.04223 / 2.84 ( 1012) hydrogen bonds : angle 5.27519 / 3.89 ( 3000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4192 Ramachandran restraints generated. 2096 Oldfield, 0 Emsley, 2096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8723 (tm-30) REVERT: A 84 ASP cc_start: 0.8625 (m-30) cc_final: 0.8343 (t0) REVERT: A 184 MET cc_start: 0.8713 (tpp) cc_final: 0.7921 (tpp) REVERT: A 187 VAL cc_start: 0.8870 (t) cc_final: 0.8424 (m) REVERT: A 188 PHE cc_start: 0.9024 (m-10) cc_final: 0.8455 (m-10) REVERT: A 247 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8693 (mmm) REVERT: A 330 ARG cc_start: 0.8967 (pmt170) cc_final: 0.8676 (pmt170) REVERT: B 86 TRP cc_start: 0.8774 (m-10) cc_final: 0.8315 (m-10) REVERT: B 116 LYS cc_start: 0.8166 (tppp) cc_final: 0.7948 (tppp) REVERT: B 300 ASP cc_start: 0.8094 (t70) cc_final: 0.7853 (t0) REVERT: B 347 LYS cc_start: 0.9513 (tmtt) cc_final: 0.9288 (tptp) REVERT: C 55 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8651 (mm-40) REVERT: C 99 MET cc_start: 0.9165 (tpt) cc_final: 0.8919 (tpp) REVERT: C 133 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9004 (m-30) REVERT: C 149 TYR cc_start: 0.8507 (m-80) cc_final: 0.8258 (m-10) REVERT: D 84 ASP cc_start: 0.8586 (m-30) cc_final: 0.8307 (t0) REVERT: D 184 MET cc_start: 0.8778 (tpp) cc_final: 0.8235 (tpp) REVERT: D 187 VAL cc_start: 0.8958 (t) cc_final: 0.8654 (m) REVERT: E 86 TRP cc_start: 0.8739 (m-10) cc_final: 0.8285 (m-10) REVERT: E 300 ASP cc_start: 0.8095 (t70) cc_final: 0.7873 (t0) REVERT: E 347 LYS cc_start: 0.9509 (tmtt) cc_final: 0.9275 (tptp) REVERT: F 55 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8637 (mm-40) REVERT: F 99 MET cc_start: 0.9166 (tpt) cc_final: 0.8934 (tpp) REVERT: F 133 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.8964 (m-30) outliers start: 28 outliers final: 22 residues processed: 171 average time/residue: 0.1163 time to fit residues: 32.4448 Evaluate side-chains 176 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 204 LEU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 156 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 315 HIS Chi-restraints excluded: chain F residue 11 SER Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 133 ASP Chi-restraints excluded: chain F residue 143 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 189 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.061101 restraints weight = 55334.074| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.59 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17566 Z= 0.170 Angle : 0.565 9.715 23858 Z= 0.306 Chirality : 0.041 0.147 2466 Planarity : 0.004 0.040 3086 Dihedral : 4.745 46.221 2340 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.67 % Allowed : 19.14 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 2096 helix: 1.01 (0.14), residues: 1348 sheet: 0.11 (0.87), residues: 44 loop : 0.01 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 172 TYR 0.025 0.001 TYR E 290 PHE 0.017 0.001 PHE A 212 TRP 0.042 0.002 TRP D 308 HIS 0.003 0.001 HIS E 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (17566) covalent geometry : angle 0.56487 / 0.31 (23858) hydrogen bonds : bond 0.04418 / 2.96 ( 1012) hydrogen bonds : angle 5.30103 / 3.93 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.54 seconds wall clock time: 47 minutes 18.69 seconds (2838.69 seconds total)