Starting phenix.real_space_refine on Thu Feb 5 13:01:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l2i_62776/02_2026/9l2i_62776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l2i_62776/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/9l2i_62776/02_2026/9l2i_62776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l2i_62776/02_2026/9l2i_62776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l2i_62776/02_2026/9l2i_62776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l2i_62776/02_2026/9l2i_62776.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 2 Unusual residues: {' FE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 5.09, per 1000 atoms: 0.30 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: 1.67 Conformation dependent library (CDL) restraints added in 706.7 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: 0.38 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: 2.37 Time building geometry restraints manager: 2.16 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 2.260 nonbonded pdb=" ND1 HIS D 246 " pdb="FE FE D 602 " model vdw 1.977 2.340 nonbonded pdb=" OE1 GLU A 144 " pdb="FE FE A 601 " model vdw 1.987 2.260 nonbonded pdb="FE FE A 601 " pdb=" O HOH A 701 " model vdw 2.028 2.260 nonbonded pdb=" OE2 GLU A 243 " pdb="FE FE A 601 " model vdw 2.031 2.260 ... (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: 0.02 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: 2.040 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 covalent geometry : bond 0.00373 (17566) covalent geometry : angle 0.66052 (23858) hydrogen bonds : bond 0.12924 ( 1012) hydrogen bonds : angle 6.37143 ( 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 : 0.505 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: 0.1206 time to fit residues: 43.9831 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 : 0.487 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 205 GLN B 62 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063096 restraints weight = 54363.229| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.53 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1378 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= 0.184 Angle : 0.571 8.154 23858 Z= 0.316 Chirality : 0.042 0.161 2466 Planarity : 0.004 0.037 3086 Dihedral : 4.915 53.228 2340 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.55 % Allowed : 7.99 % Favored : 90.46 % 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: 0.75 (0.18), residues: 2096 helix: 0.93 (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 0.003 0.000 ARG C 116 TYR 0.022 0.001 TYR A 288 PHE 0.020 0.002 PHE A 212 TRP 0.020 0.002 TRP D 301 HIS 0.009 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00405 (17566) covalent geometry : angle 0.57136 (23858) hydrogen bonds : bond 0.04814 ( 1012) hydrogen bonds : angle 5.41285 ( 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 202 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.718 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: 0.8629 (tpp) cc_final: 0.8179 (tpp) REVERT: A 188 PHE cc_start: 0.8674 (m-10) cc_final: 0.8435 (m-10) REVERT: A 203 ASN cc_start: 0.8578 (t0) cc_final: 0.7796 (t0) REVERT: A 209 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: A 247 MET cc_start: 0.8884 (mmt) cc_final: 0.8634 (mmm) REVERT: A 278 GLN cc_start: 0.9356 (mm110) cc_final: 0.8995 (mm-40) REVERT: A 330 ARG cc_start: 0.8805 (pmt170) cc_final: 0.8587 (pmt170) REVERT: B 195 MET cc_start: 0.8963 (mmt) cc_final: 0.8686 (mmp) REVERT: B 300 ASP cc_start: 0.8221 (t70) cc_final: 0.7988 (t0) REVERT: B 347 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9330 (tptp) REVERT: C 133 ASP cc_start: 0.9343 (m-30) cc_final: 0.9069 (m-30) REVERT: D 184 MET cc_start: 0.8624 (tpp) cc_final: 0.8223 (tpp) REVERT: D 188 PHE cc_start: 0.8644 (m-10) cc_final: 0.8398 (m-10) REVERT: D 203 ASN cc_start: 0.8603 (t0) cc_final: 0.7627 (t0) REVERT: D 209 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: D 247 MET cc_start: 0.8884 (mmt) cc_final: 0.8619 (mmm) REVERT: D 278 GLN cc_start: 0.9350 (mm110) cc_final: 0.9058 (mm-40) REVERT: D 330 ARG cc_start: 0.8759 (pmt170) cc_final: 0.8452 (pmt170) REVERT: E 300 ASP cc_start: 0.8225 (t70) cc_final: 0.7985 (t0) REVERT: E 347 LYS cc_start: 0.9554 (tmtt) cc_final: 0.9311 (tptp) REVERT: F 96 ILE cc_start: 0.9561 (OUTLIER) cc_final: 0.9107 (pt) REVERT: F 133 ASP cc_start: 0.9347 (m-30) cc_final: 0.9111 (m-30) REVERT: F 147 ASP cc_start: 0.9267 (m-30) cc_final: 0.8901 (p0) outliers start: 27 outliers final: 20 residues processed: 191 average time/residue: 0.1123 time to fit residues: 33.9872 Evaluate side-chains 166 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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: 6.9990 chunk 137 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 159 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS B 62 ASN B 149 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 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 168 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 149 ASN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.058670 restraints weight = 56827.549| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 4.49 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17566 Z= 0.297 Angle : 0.636 8.105 23858 Z= 0.350 Chirality : 0.044 0.155 2466 Planarity : 0.004 0.040 3086 Dihedral : 5.102 59.302 2340 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.70 % Allowed : 11.72 % Favored : 85.57 % 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: 0.70 (0.19), residues: 2096 helix: 0.89 (0.14), residues: 1338 sheet: 0.36 (0.91), residues: 44 loop : -0.16 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 172 TYR 0.020 0.002 TYR F 149 PHE 0.013 0.002 PHE A 282 TRP 0.022 0.002 TRP D 317 HIS 0.005 0.001 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00647 (17566) covalent geometry : angle 0.63586 (23858) hydrogen bonds : bond 0.05137 ( 1012) hydrogen bonds : angle 5.48808 ( 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 201 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 MET cc_start: 0.8807 (tpp) cc_final: 0.8070 (tpp) REVERT: A 187 VAL cc_start: 0.8861 (t) cc_final: 0.8449 (p) REVERT: A 188 PHE cc_start: 0.8807 (m-10) cc_final: 0.8585 (m-10) REVERT: A 209 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7249 (mp0) REVERT: A 211 CYS cc_start: 0.8782 (t) cc_final: 0.8492 (t) REVERT: A 247 MET cc_start: 0.8971 (mmt) cc_final: 0.8683 (mmm) REVERT: A 330 ARG cc_start: 0.8889 (pmt170) cc_final: 0.8631 (pmt170) REVERT: A 367 GLU cc_start: 0.8943 (pm20) cc_final: 0.8737 (pm20) REVERT: B 300 ASP cc_start: 0.8381 (t70) cc_final: 0.8100 (t0) REVERT: B 347 LYS cc_start: 0.9585 (tmtt) cc_final: 0.9343 (tptp) REVERT: C 133 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.9075 (m-30) REVERT: D 24 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8159 (mm-30) REVERT: D 184 MET cc_start: 0.8804 (tpp) cc_final: 0.8052 (tpp) REVERT: D 187 VAL cc_start: 0.8839 (t) cc_final: 0.8499 (p) REVERT: D 188 PHE cc_start: 0.8786 (m-10) cc_final: 0.8566 (m-10) REVERT: D 209 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7135 (mp0) REVERT: D 211 CYS cc_start: 0.8832 (t) cc_final: 0.8610 (t) REVERT: D 247 MET cc_start: 0.8955 (mmt) cc_final: 0.8677 (mmm) REVERT: D 330 ARG cc_start: 0.8967 (pmt170) cc_final: 0.8718 (pmt170) REVERT: D 367 GLU cc_start: 0.8932 (pm20) cc_final: 0.8724 (pm20) REVERT: E 188 ASP cc_start: 0.9168 (m-30) cc_final: 0.8960 (m-30) REVERT: E 300 ASP cc_start: 0.8406 (t70) cc_final: 0.8109 (t0) REVERT: E 347 LYS cc_start: 0.9579 (tmtt) cc_final: 0.9337 (tptp) REVERT: F 96 ILE cc_start: 0.9632 (OUTLIER) cc_final: 0.9208 (pt) REVERT: F 133 ASP cc_start: 0.9361 (OUTLIER) cc_final: 0.9095 (m-30) REVERT: F 149 TYR cc_start: 0.7813 (m-10) cc_final: 0.7365 (m-10) outliers start: 47 outliers final: 25 residues processed: 182 average time/residue: 0.1170 time to fit residues: 33.3773 Evaluate side-chains 169 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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 209 GLU 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 164 ASN Chi-restraints excluded: chain B residue 173 CYS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 11 SER 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 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 76 THR Chi-restraints excluded: chain E residue 79 PHE Chi-restraints excluded: chain E residue 164 ASN 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 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: 4.9990 chunk 180 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 187 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** D 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** E 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.061649 restraints weight = 54406.314| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.51 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17566 Z= 0.136 Angle : 0.524 8.090 23858 Z= 0.290 Chirality : 0.040 0.146 2466 Planarity : 0.004 0.059 3086 Dihedral : 4.907 55.638 2340 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.67 % Allowed : 14.77 % Favored : 83.56 % 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: 0.80 (0.18), residues: 2096 helix: 1.01 (0.14), residues: 1342 sheet: 0.23 (0.87), residues: 44 loop : -0.20 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 116 TYR 0.014 0.001 TYR A 288 PHE 0.013 0.001 PHE E 79 TRP 0.018 0.001 TRP A 317 HIS 0.004 0.001 HIS E 80 Details of bonding type rmsd covalent geometry : bond 0.00298 (17566) covalent geometry : angle 0.52418 (23858) hydrogen bonds : bond 0.04490 ( 1012) hydrogen bonds : angle 5.27050 ( 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 188 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 0.715 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 169 ASN cc_start: 0.8151 (m110) cc_final: 0.7733 (m110) REVERT: A 184 MET cc_start: 0.8754 (tpp) cc_final: 0.7993 (tpp) REVERT: A 187 VAL cc_start: 0.8919 (t) cc_final: 0.8672 (m) REVERT: A 188 PHE cc_start: 0.8878 (m-10) cc_final: 0.8656 (m-10) REVERT: A 209 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: A 211 CYS cc_start: 0.8781 (t) cc_final: 0.8524 (t) REVERT: A 247 MET cc_start: 0.8931 (mmt) cc_final: 0.8612 (mmm) REVERT: A 330 ARG cc_start: 0.8933 (pmt170) cc_final: 0.8650 (pmt170) REVERT: B 300 ASP cc_start: 0.8132 (t70) cc_final: 0.7911 (t0) REVERT: B 347 LYS cc_start: 0.9551 (tmtt) cc_final: 0.9308 (tptp) REVERT: C 133 ASP cc_start: 0.9325 (OUTLIER) cc_final: 0.8978 (m-30) REVERT: D 169 ASN cc_start: 0.8196 (m110) cc_final: 0.7794 (m110) REVERT: D 184 MET cc_start: 0.8767 (tpp) cc_final: 0.8101 (tpp) REVERT: D 187 VAL cc_start: 0.8920 (t) cc_final: 0.8530 (p) REVERT: D 209 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: D 211 CYS cc_start: 0.8822 (t) cc_final: 0.8610 (t) REVERT: D 247 MET cc_start: 0.8915 (mmt) cc_final: 0.8586 (mmm) REVERT: D 330 ARG cc_start: 0.8950 (pmt170) cc_final: 0.8671 (pmt170) REVERT: D 367 GLU cc_start: 0.8943 (pm20) cc_final: 0.8742 (pm20) REVERT: E 290 TYR cc_start: 0.8569 (m-10) cc_final: 0.8296 (m-10) REVERT: E 300 ASP cc_start: 0.8123 (t70) cc_final: 0.7870 (t0) REVERT: E 305 CYS cc_start: 0.9098 (m) cc_final: 0.8794 (m) REVERT: E 347 LYS cc_start: 0.9544 (tmtt) cc_final: 0.9306 (tptp) REVERT: F 87 ASP cc_start: 0.9317 (t0) cc_final: 0.9107 (t0) REVERT: F 96 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9172 (pt) REVERT: F 133 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.8999 (m-30) REVERT: F 149 TYR cc_start: 0.7830 (m-80) cc_final: 0.7300 (m-10) outliers start: 29 outliers final: 18 residues processed: 174 average time/residue: 0.1401 time to fit residues: 38.0527 Evaluate side-chains 161 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 53 ASP 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 209 GLU Chi-restraints excluded: chain D residue 214 ASN 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 315 HIS 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: 0.4980 chunk 162 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 168 optimal weight: 0.5980 chunk 100 optimal weight: 0.0020 chunk 50 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 521 ASN B 54 GLN B 62 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 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 = 0.3337 r_free = 0.3337 target = 0.077414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063222 restraints weight = 53891.450| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.56 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 17566 Z= 0.116 Angle : 0.507 8.922 23858 Z= 0.278 Chirality : 0.039 0.143 2466 Planarity : 0.004 0.051 3086 Dihedral : 4.755 51.411 2340 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 15.46 % Favored : 82.36 % 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: 0.89 (0.18), residues: 2096 helix: 1.13 (0.14), residues: 1328 sheet: 0.12 (0.84), residues: 44 loop : -0.26 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 116 TYR 0.015 0.001 TYR A 288 PHE 0.020 0.001 PHE D 153 TRP 0.016 0.001 TRP A 317 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00248 (17566) covalent geometry : angle 0.50685 (23858) hydrogen bonds : bond 0.04142 ( 1012) hydrogen bonds : angle 5.17089 ( 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 203 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.807 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 76 GLU cc_start: 0.9020 (tm-30) cc_final: 0.7337 (tm-30) REVERT: A 184 MET cc_start: 0.8729 (tpp) cc_final: 0.7946 (tpp) REVERT: A 187 VAL cc_start: 0.8939 (t) cc_final: 0.8594 (m) REVERT: A 188 PHE cc_start: 0.8910 (m-10) cc_final: 0.8572 (m-10) REVERT: A 209 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7088 (mp0) REVERT: A 211 CYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8448 (t) REVERT: A 247 MET cc_start: 0.8927 (mmt) cc_final: 0.8579 (mmm) REVERT: A 330 ARG cc_start: 0.8898 (pmt170) cc_final: 0.8570 (pmt170) REVERT: B 86 TRP cc_start: 0.8798 (m-10) cc_final: 0.8406 (m-10) REVERT: B 300 ASP cc_start: 0.8058 (t70) cc_final: 0.7813 (t0) REVERT: B 305 CYS cc_start: 0.9139 (m) cc_final: 0.8815 (m) REVERT: B 347 LYS cc_start: 0.9516 (tmtt) cc_final: 0.9283 (tptp) REVERT: C 133 ASP cc_start: 0.9337 (OUTLIER) cc_final: 0.9000 (m-30) REVERT: D 76 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8315 (tp30) REVERT: D 84 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8265 (t0) REVERT: D 184 MET cc_start: 0.8724 (tpp) cc_final: 0.7895 (tpp) REVERT: D 187 VAL cc_start: 0.8945 (t) cc_final: 0.8529 (m) REVERT: D 188 PHE cc_start: 0.8927 (m-10) cc_final: 0.8504 (m-10) REVERT: D 209 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: D 211 CYS cc_start: 0.8782 (t) cc_final: 0.8526 (t) REVERT: D 247 MET cc_start: 0.8909 (mmt) cc_final: 0.8551 (mmm) REVERT: D 330 ARG cc_start: 0.8864 (pmt170) cc_final: 0.8518 (pmt170) REVERT: D 367 GLU cc_start: 0.8931 (pm20) cc_final: 0.8601 (pm20) REVERT: E 86 TRP cc_start: 0.8767 (m-10) cc_final: 0.8440 (m-10) REVERT: E 112 TYR cc_start: 0.8133 (t80) cc_final: 0.7778 (t80) REVERT: E 300 ASP cc_start: 0.8074 (t70) cc_final: 0.7839 (t0) REVERT: E 305 CYS cc_start: 0.9113 (m) cc_final: 0.8794 (m) REVERT: E 347 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9293 (tptp) REVERT: F 87 ASP cc_start: 0.9336 (t0) cc_final: 0.9102 (t0) REVERT: F 96 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9107 (pt) REVERT: F 133 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.8964 (m-30) REVERT: F 149 TYR cc_start: 0.7877 (m-80) cc_final: 0.7423 (m-10) outliers start: 38 outliers final: 23 residues processed: 185 average time/residue: 0.1283 time to fit residues: 37.8070 Evaluate side-chains 174 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 315 HIS Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 133 ASP 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 209 GLU 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 11 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 18 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 154 optimal weight: 0.0000 chunk 105 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 166 HIS D 521 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.063514 restraints weight = 54905.738| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.66 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 17566 Z= 0.115 Angle : 0.501 9.054 23858 Z= 0.275 Chirality : 0.039 0.142 2466 Planarity : 0.004 0.049 3086 Dihedral : 4.753 52.833 2340 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.18 % Allowed : 16.72 % Favored : 81.09 % 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: 0.86 (0.18), residues: 2096 helix: 1.08 (0.14), residues: 1334 sheet: 0.14 (0.83), residues: 44 loop : -0.23 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.016 0.001 TYR D 288 PHE 0.011 0.001 PHE E 79 TRP 0.050 0.001 TRP D 308 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00246 (17566) covalent geometry : angle 0.50107 (23858) hydrogen bonds : bond 0.04039 ( 1012) hydrogen bonds : angle 5.12792 ( 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 202 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 164 time to evaluate : 0.727 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 76 GLU cc_start: 0.9024 (tm-30) cc_final: 0.7355 (tm-30) REVERT: A 84 ASP cc_start: 0.8606 (m-30) cc_final: 0.8294 (t0) REVERT: A 184 MET cc_start: 0.8729 (tpp) cc_final: 0.7942 (tpp) REVERT: A 187 VAL cc_start: 0.8930 (t) cc_final: 0.8574 (m) REVERT: A 188 PHE cc_start: 0.8939 (m-10) cc_final: 0.8525 (m-10) REVERT: A 209 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 247 MET cc_start: 0.8912 (mmt) cc_final: 0.8514 (mmm) REVERT: A 330 ARG cc_start: 0.8938 (pmt170) cc_final: 0.8640 (pmt170) REVERT: A 367 GLU cc_start: 0.9047 (pm20) cc_final: 0.8799 (pm20) REVERT: B 86 TRP cc_start: 0.8772 (m-10) cc_final: 0.8366 (m-10) REVERT: B 300 ASP cc_start: 0.8062 (t70) cc_final: 0.7837 (t0) REVERT: B 347 LYS cc_start: 0.9514 (tmtt) cc_final: 0.9284 (tptp) REVERT: C 133 ASP cc_start: 0.9330 (OUTLIER) cc_final: 0.8992 (m-30) REVERT: D 76 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8307 (tp30) REVERT: D 84 ASP cc_start: 0.8558 (m-30) cc_final: 0.8263 (t0) REVERT: D 184 MET cc_start: 0.8700 (tpp) cc_final: 0.7886 (tpp) REVERT: D 187 VAL cc_start: 0.8944 (t) cc_final: 0.8519 (m) REVERT: D 188 PHE cc_start: 0.8943 (m-10) cc_final: 0.8500 (m-10) REVERT: D 209 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: D 247 MET cc_start: 0.8908 (mmt) cc_final: 0.8506 (mmm) REVERT: D 330 ARG cc_start: 0.8855 (pmt170) cc_final: 0.8497 (pmt170) REVERT: E 86 TRP cc_start: 0.8745 (m-10) cc_final: 0.8332 (m-10) REVERT: E 93 LEU cc_start: 0.9446 (mt) cc_final: 0.9078 (mt) REVERT: E 112 TYR cc_start: 0.8050 (t80) cc_final: 0.7776 (t80) REVERT: E 300 ASP cc_start: 0.8058 (t70) cc_final: 0.7847 (t0) REVERT: E 347 LYS cc_start: 0.9512 (tmtt) cc_final: 0.9273 (tptp) REVERT: F 55 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8639 (mm-40) REVERT: F 87 ASP cc_start: 0.9344 (t0) cc_final: 0.9130 (t0) REVERT: F 99 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8897 (tpp) REVERT: F 133 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8966 (m-30) REVERT: F 149 TYR cc_start: 0.7918 (m-80) cc_final: 0.7413 (m-10) outliers start: 38 outliers final: 19 residues processed: 186 average time/residue: 0.1269 time to fit residues: 37.8428 Evaluate side-chains 173 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 209 GLU 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 315 HIS 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 209 GLU Chi-restraints excluded: chain D residue 389 GLU 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 99 MET 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: 3.9990 chunk 179 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 206 optimal weight: 1.9990 chunk 27 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 HIS ** 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 = 0.3285 r_free = 0.3285 target = 0.075003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.060800 restraints weight = 55374.775| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.57 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17566 Z= 0.175 Angle : 0.533 9.143 23858 Z= 0.293 Chirality : 0.040 0.145 2466 Planarity : 0.004 0.049 3086 Dihedral : 4.766 52.316 2340 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.47 % Allowed : 17.13 % Favored : 80.40 % 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: 1.13 (0.14), residues: 1330 sheet: 0.15 (0.86), residues: 44 loop : -0.13 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.018 0.001 TYR B 372 PHE 0.020 0.001 PHE D 212 TRP 0.045 0.002 TRP A 308 HIS 0.003 0.001 HIS B 39 Details of bonding type rmsd covalent geometry : bond 0.00384 (17566) covalent geometry : angle 0.53291 (23858) hydrogen bonds : bond 0.04347 ( 1012) hydrogen bonds : angle 5.16534 ( 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 198 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 155 time to evaluate : 0.725 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 24 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7725 (mp0) REVERT: A 76 GLU cc_start: 0.9006 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 184 MET cc_start: 0.8765 (tpp) cc_final: 0.7986 (tpp) REVERT: A 187 VAL cc_start: 0.8976 (t) cc_final: 0.8609 (m) REVERT: A 188 PHE cc_start: 0.9019 (m-10) cc_final: 0.8553 (m-10) REVERT: A 209 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: A 247 MET cc_start: 0.8914 (mmt) cc_final: 0.8511 (mmm) REVERT: A 330 ARG cc_start: 0.8953 (pmt170) cc_final: 0.8626 (pmt170) REVERT: A 367 GLU cc_start: 0.9043 (pm20) cc_final: 0.8757 (pm20) REVERT: B 86 TRP cc_start: 0.8897 (m-10) cc_final: 0.8651 (m-10) REVERT: B 300 ASP cc_start: 0.8159 (t70) cc_final: 0.7918 (t0) REVERT: B 347 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9304 (tptp) REVERT: C 133 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.9021 (m-30) REVERT: D 76 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8271 (tp30) REVERT: D 84 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8354 (t0) REVERT: D 184 MET cc_start: 0.8779 (tpp) cc_final: 0.7968 (tpp) REVERT: D 187 VAL cc_start: 0.8989 (t) cc_final: 0.8559 (m) REVERT: D 188 PHE cc_start: 0.9011 (m-10) cc_final: 0.8518 (m-10) REVERT: D 209 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7342 (mp0) REVERT: D 247 MET cc_start: 0.8910 (mmt) cc_final: 0.8502 (mmm) REVERT: D 330 ARG cc_start: 0.8913 (pmt170) cc_final: 0.8567 (pmt170) REVERT: E 86 TRP cc_start: 0.8859 (m-10) cc_final: 0.8529 (m-10) REVERT: E 112 TYR cc_start: 0.8130 (t80) cc_final: 0.7817 (t80) REVERT: E 300 ASP cc_start: 0.8176 (t70) cc_final: 0.7934 (t0) REVERT: E 347 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9296 (tptp) REVERT: F 87 ASP cc_start: 0.9358 (t0) cc_final: 0.9144 (t0) REVERT: F 133 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8997 (m-30) REVERT: F 141 MET cc_start: 0.9195 (mmp) cc_final: 0.8906 (mmt) REVERT: F 149 TYR cc_start: 0.8034 (m-80) cc_final: 0.7623 (m-10) outliers start: 43 outliers final: 31 residues processed: 179 average time/residue: 0.1283 time to fit residues: 36.7703 Evaluate side-chains 186 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 163 PHE Chi-restraints excluded: chain B residue 211 ASP 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 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 209 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 389 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 182 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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** ** C 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** 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 = 0.076789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.062540 restraints weight = 55126.634| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.64 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17566 Z= 0.121 Angle : 0.508 10.749 23858 Z= 0.277 Chirality : 0.039 0.142 2466 Planarity : 0.004 0.046 3086 Dihedral : 4.716 52.524 2340 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.18 % Allowed : 17.82 % Favored : 80.00 % 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: 0.93 (0.18), residues: 2096 helix: 1.15 (0.14), residues: 1334 sheet: 0.09 (0.84), residues: 44 loop : -0.22 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.028 0.001 TYR B 372 PHE 0.021 0.001 PHE A 153 TRP 0.053 0.001 TRP D 308 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00263 (17566) covalent geometry : angle 0.50777 (23858) hydrogen bonds : bond 0.04099 ( 1012) hydrogen bonds : angle 5.14995 ( 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 200 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.716 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 76 GLU cc_start: 0.9040 (tm-30) cc_final: 0.7379 (tm-30) REVERT: A 184 MET cc_start: 0.8744 (tpp) cc_final: 0.7946 (tpp) REVERT: A 187 VAL cc_start: 0.8898 (t) cc_final: 0.8460 (m) REVERT: A 188 PHE cc_start: 0.8975 (m-10) cc_final: 0.8447 (m-10) REVERT: A 209 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: A 247 MET cc_start: 0.8894 (mmt) cc_final: 0.8475 (mmm) REVERT: A 330 ARG cc_start: 0.8987 (pmt170) cc_final: 0.8702 (pmt170) REVERT: A 367 GLU cc_start: 0.9051 (pm20) cc_final: 0.8834 (pm20) REVERT: B 86 TRP cc_start: 0.8795 (m-10) cc_final: 0.8336 (m-10) REVERT: B 300 ASP cc_start: 0.8097 (t70) cc_final: 0.7871 (t0) REVERT: B 347 LYS cc_start: 0.9517 (tmtt) cc_final: 0.9280 (tptp) REVERT: C 99 MET cc_start: 0.9151 (tpt) cc_final: 0.8874 (tpp) REVERT: C 133 ASP cc_start: 0.9310 (OUTLIER) cc_final: 0.8974 (m-30) REVERT: D 76 GLU cc_start: 0.9167 (mm-30) cc_final: 0.8289 (tp30) REVERT: D 84 ASP cc_start: 0.8572 (m-30) cc_final: 0.8280 (t0) REVERT: D 184 MET cc_start: 0.8732 (tpp) cc_final: 0.7947 (tpp) REVERT: D 187 VAL cc_start: 0.8931 (t) cc_final: 0.8548 (m) REVERT: D 188 PHE cc_start: 0.8982 (m-10) cc_final: 0.8451 (m-10) REVERT: D 209 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7205 (mp0) REVERT: D 247 MET cc_start: 0.8883 (mmt) cc_final: 0.8462 (mmm) REVERT: D 330 ARG cc_start: 0.8909 (pmt170) cc_final: 0.8546 (pmt170) REVERT: D 367 GLU cc_start: 0.9000 (mp0) cc_final: 0.8767 (pm20) REVERT: E 86 TRP cc_start: 0.8762 (m-10) cc_final: 0.8301 (m-10) REVERT: E 93 LEU cc_start: 0.9432 (mt) cc_final: 0.9083 (mt) REVERT: E 112 TYR cc_start: 0.7974 (t80) cc_final: 0.7770 (t80) REVERT: E 300 ASP cc_start: 0.8096 (t70) cc_final: 0.7871 (t0) REVERT: E 347 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9276 (tptp) REVERT: F 87 ASP cc_start: 0.9369 (t0) cc_final: 0.9145 (t0) REVERT: F 133 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.8985 (m-30) REVERT: F 141 MET cc_start: 0.9106 (mmp) cc_final: 0.8839 (mmt) REVERT: F 149 TYR cc_start: 0.8003 (m-80) cc_final: 0.7575 (m-10) outliers start: 38 outliers final: 27 residues processed: 184 average time/residue: 0.1279 time to fit residues: 37.6075 Evaluate side-chains 186 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 211 CYS Chi-restraints excluded: chain A residue 389 GLU 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 315 HIS Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 143 LEU 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 211 CYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 12 optimal weight: 0.2980 chunk 202 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 168 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 = 0.3326 r_free = 0.3326 target = 0.077041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062823 restraints weight = 55347.569| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.65 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17566 Z= 0.121 Angle : 0.515 11.136 23858 Z= 0.280 Chirality : 0.040 0.268 2466 Planarity : 0.004 0.047 3086 Dihedral : 4.691 52.402 2340 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.13 % Allowed : 18.33 % Favored : 79.54 % 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: 0.97 (0.18), residues: 2096 helix: 1.17 (0.14), residues: 1334 sheet: 0.06 (0.84), residues: 44 loop : -0.18 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 333 TYR 0.017 0.001 TYR D 288 PHE 0.013 0.001 PHE B 163 TRP 0.060 0.001 TRP D 308 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00267 (17566) covalent geometry : angle 0.51532 (23858) hydrogen bonds : bond 0.04038 ( 1012) hydrogen bonds : angle 5.13158 ( 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 193 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7643 (mp0) REVERT: A 76 GLU cc_start: 0.9065 (tm-30) cc_final: 0.7416 (tm-30) REVERT: A 84 ASP cc_start: 0.8638 (m-30) cc_final: 0.8341 (t0) REVERT: A 184 MET cc_start: 0.8755 (tpp) cc_final: 0.7953 (tpp) REVERT: A 187 VAL cc_start: 0.8893 (t) cc_final: 0.8436 (m) REVERT: A 188 PHE cc_start: 0.9002 (m-10) cc_final: 0.8438 (m-10) REVERT: A 209 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7271 (mp0) REVERT: A 247 MET cc_start: 0.8853 (mmt) cc_final: 0.8429 (mmm) REVERT: A 330 ARG cc_start: 0.8974 (pmt170) cc_final: 0.8675 (pmt170) REVERT: A 367 GLU cc_start: 0.9038 (pm20) cc_final: 0.8744 (pm20) REVERT: B 86 TRP cc_start: 0.8788 (m-10) cc_final: 0.8329 (m-10) REVERT: B 300 ASP cc_start: 0.8099 (t70) cc_final: 0.7878 (t0) REVERT: B 347 LYS cc_start: 0.9509 (tmtt) cc_final: 0.9276 (tptp) REVERT: C 99 MET cc_start: 0.9158 (tpt) cc_final: 0.8904 (tpp) REVERT: C 133 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.9006 (m-30) REVERT: C 149 TYR cc_start: 0.8542 (m-80) cc_final: 0.8260 (m-10) REVERT: D 76 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8279 (tp30) REVERT: D 84 ASP cc_start: 0.8588 (m-30) cc_final: 0.8297 (t0) REVERT: D 184 MET cc_start: 0.8742 (tpp) cc_final: 0.7964 (tpp) REVERT: D 187 VAL cc_start: 0.8929 (t) cc_final: 0.8513 (m) REVERT: D 188 PHE cc_start: 0.8990 (m-10) cc_final: 0.8442 (m-10) REVERT: D 209 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: D 247 MET cc_start: 0.8847 (mmt) cc_final: 0.8420 (mmm) REVERT: D 330 ARG cc_start: 0.8909 (pmt170) cc_final: 0.8525 (pmt170) REVERT: D 367 GLU cc_start: 0.8970 (mp0) cc_final: 0.8688 (pm20) REVERT: E 86 TRP cc_start: 0.8759 (m-10) cc_final: 0.8449 (m-10) REVERT: E 93 LEU cc_start: 0.9449 (mt) cc_final: 0.9109 (mt) REVERT: E 112 TYR cc_start: 0.7999 (t80) cc_final: 0.7635 (t80) REVERT: E 118 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8560 (mm-30) REVERT: E 300 ASP cc_start: 0.8100 (t70) cc_final: 0.7885 (t0) REVERT: E 347 LYS cc_start: 0.9511 (tmtt) cc_final: 0.9273 (tptp) REVERT: F 87 ASP cc_start: 0.9356 (t0) cc_final: 0.9127 (t0) REVERT: F 133 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.8974 (m-30) REVERT: F 141 MET cc_start: 0.9098 (mmp) cc_final: 0.8851 (mmt) REVERT: F 149 TYR cc_start: 0.8093 (m-80) cc_final: 0.7694 (m-10) outliers start: 37 outliers final: 26 residues processed: 178 average time/residue: 0.1262 time to fit residues: 36.2725 Evaluate side-chains 185 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 209 GLU Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 389 GLU 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 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 209 GLU Chi-restraints excluded: chain D residue 211 CYS Chi-restraints excluded: chain D residue 389 GLU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 115 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 206 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 168 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 = 0.3324 r_free = 0.3324 target = 0.076872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.062750 restraints weight = 54472.914| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 4.61 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17566 Z= 0.128 Angle : 0.517 10.871 23858 Z= 0.282 Chirality : 0.040 0.297 2466 Planarity : 0.004 0.047 3086 Dihedral : 4.695 52.360 2340 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.95 % Allowed : 18.51 % Favored : 79.54 % 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: 0.97 (0.18), residues: 2096 helix: 1.11 (0.14), residues: 1348 sheet: 0.09 (0.84), residues: 44 loop : -0.06 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 333 TYR 0.033 0.001 TYR E 372 PHE 0.018 0.001 PHE B 163 TRP 0.051 0.001 TRP D 308 HIS 0.002 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00283 (17566) covalent geometry : angle 0.51707 (23858) hydrogen bonds : bond 0.04037 ( 1012) hydrogen bonds : angle 5.15328 ( 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 194 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7645 (mp0) REVERT: A 76 GLU cc_start: 0.9081 (tm-30) cc_final: 0.7508 (tm-30) REVERT: A 184 MET cc_start: 0.8762 (tpp) cc_final: 0.8129 (tpp) REVERT: A 187 VAL cc_start: 0.8929 (t) cc_final: 0.8644 (m) REVERT: A 209 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 247 MET cc_start: 0.8838 (mmt) cc_final: 0.8417 (mmm) REVERT: A 330 ARG cc_start: 0.8956 (pmt170) cc_final: 0.8660 (pmt170) REVERT: A 367 GLU cc_start: 0.9032 (pm20) cc_final: 0.8729 (pm20) REVERT: B 86 TRP cc_start: 0.8831 (m-10) cc_final: 0.8375 (m-10) REVERT: B 300 ASP cc_start: 0.8125 (t70) cc_final: 0.7912 (t0) REVERT: B 347 LYS cc_start: 0.9498 (tmtt) cc_final: 0.9276 (tptp) REVERT: C 99 MET cc_start: 0.9156 (tpt) cc_final: 0.8910 (tpp) REVERT: C 133 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.8980 (m-30) REVERT: D 76 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8264 (tp30) REVERT: D 84 ASP cc_start: 0.8646 (m-30) cc_final: 0.8337 (t0) REVERT: D 184 MET cc_start: 0.8744 (tpp) cc_final: 0.8106 (tpp) REVERT: D 187 VAL cc_start: 0.8952 (t) cc_final: 0.8658 (m) REVERT: D 209 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: D 247 MET cc_start: 0.8838 (mmt) cc_final: 0.8471 (mmm) REVERT: D 330 ARG cc_start: 0.8900 (pmt170) cc_final: 0.8523 (pmt170) REVERT: D 367 GLU cc_start: 0.8962 (mp0) cc_final: 0.8738 (pm20) REVERT: E 86 TRP cc_start: 0.8781 (m-10) cc_final: 0.8470 (m-10) REVERT: E 93 LEU cc_start: 0.9456 (mt) cc_final: 0.9125 (mt) REVERT: E 112 TYR cc_start: 0.8077 (t80) cc_final: 0.7788 (t80) REVERT: E 300 ASP cc_start: 0.8114 (t70) cc_final: 0.7906 (t0) REVERT: E 347 LYS cc_start: 0.9498 (tmtt) cc_final: 0.9271 (tptp) REVERT: F 87 ASP cc_start: 0.9350 (t0) cc_final: 0.9114 (t0) REVERT: F 99 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8951 (tpp) REVERT: F 133 ASP cc_start: 0.9311 (OUTLIER) cc_final: 0.8965 (m-30) REVERT: F 141 MET cc_start: 0.9107 (mmp) cc_final: 0.8857 (mmt) REVERT: F 149 TYR cc_start: 0.8155 (m-80) cc_final: 0.7761 (m-10) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 0.1232 time to fit residues: 35.4437 Evaluate side-chains 184 residues out of total 1740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 389 GLU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 156 LEU 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 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 389 GLU Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain E residue 70 LEU 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 99 MET 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: 9.9990 chunk 105 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 128 optimal weight: 0.0770 chunk 109 optimal weight: 0.8980 chunk 180 optimal weight: 4.9990 chunk 189 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 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 = 0.3336 r_free = 0.3336 target = 0.077403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.063060 restraints weight = 54374.507| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.67 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17566 Z= 0.121 Angle : 0.528 12.399 23858 Z= 0.286 Chirality : 0.040 0.216 2466 Planarity : 0.004 0.046 3086 Dihedral : 4.683 52.388 2340 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.78 % Allowed : 18.79 % 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: 0.95 (0.18), residues: 2096 helix: 1.09 (0.14), residues: 1346 sheet: 0.08 (0.84), residues: 44 loop : -0.06 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.025 0.001 TYR E 290 PHE 0.018 0.001 PHE D 188 TRP 0.042 0.001 TRP D 308 HIS 0.003 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00268 (17566) covalent geometry : angle 0.52761 (23858) hydrogen bonds : bond 0.03986 ( 1012) hydrogen bonds : angle 5.15846 ( 3000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.77 seconds wall clock time: 48 minutes 39.68 seconds (2919.68 seconds total)