Starting phenix.real_space_refine on Thu Sep 18 08:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfc_38301/09_2025/8xfc_38301.cif" } resolution = 3.89 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3593 atoms to isotropic. 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 P 6 5.49 5 S 26 5.16 5 C 7880 2.51 5 N 2212 2.21 5 O 2247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12371 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2302 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 292} Chain: "C" Number of atoms: 2133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2133 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 270} Chain: "D" Number of atoms: 3913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3913 Classifications: {'peptide': 517} Link IDs: {'PTRANS': 26, 'TRANS': 490} Chain breaks: 1 Chain: "A" Number of atoms: 3961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 3961 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 475} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.31, per 1000 atoms: 0.27 Number of scatterers: 12371 At special positions: 0 Unit cell: (92.66, 85.28, 170.56, 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) S 26 16.00 P 6 15.00 O 2247 8.00 N 2212 7.00 C 7880 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: 1.18 Conformation dependent library (CDL) restraints added in 589.9 milliseconds Enol-peptide restraints added in 1.4 microseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2958 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 10 sheets defined 51.7% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 1 through 11 removed outlier: 3.921A pdb=" N ARG B 7 " --> pdb=" O TRP B 3 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 30 removed outlier: 3.564A pdb=" N VAL B 27 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B 28 " --> pdb=" O TYR B 24 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 30 " --> pdb=" O MET B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 38 removed outlier: 4.213A pdb=" N ALA B 37 " --> pdb=" O ASP B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 86 through 122 removed outlier: 3.609A pdb=" N VAL B 90 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 126 through 142 removed outlier: 3.552A pdb=" N ALA B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 171 through 202 removed outlier: 5.217A pdb=" N LEU B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 4.732A pdb=" N MET B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 189 " --> pdb=" O MET B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.585A pdb=" N ARG B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 Processing helix chain 'B' and resid 229 through 245 removed outlier: 4.187A pdb=" N VAL B 233 " --> pdb=" O SER B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 254 removed outlier: 4.064A pdb=" N THR B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 Processing helix chain 'B' and resid 273 through 302 removed outlier: 4.336A pdb=" N SER B 278 " --> pdb=" O PRO B 274 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 17 removed outlier: 3.775A pdb=" N ASP C 10 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP C 12 " --> pdb=" O TRP C 8 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG C 13 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 Processing helix chain 'C' and resid 38 through 41 Processing helix chain 'C' and resid 72 through 110 removed outlier: 3.589A pdb=" N ARG C 76 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR C 79 " --> pdb=" O SER C 75 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR C 109 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 128 through 137 Processing helix chain 'C' and resid 144 through 172 removed outlier: 3.513A pdb=" N VAL C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Proline residue: C 158 - end of helix Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.590A pdb=" N LYS C 181 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 196 removed outlier: 3.566A pdb=" N LEU C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 225 removed outlier: 4.515A pdb=" N VAL C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 204 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 212 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.645A pdb=" N GLN C 243 " --> pdb=" O ASN C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 279 removed outlier: 3.892A pdb=" N ILE C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.757A pdb=" N ALA C 284 " --> pdb=" O ALA C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 54 Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 110 through 116 removed outlier: 3.582A pdb=" N GLU D 116 " --> pdb=" O PHE D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 removed outlier: 4.213A pdb=" N VAL D 132 " --> pdb=" O ARG D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 155 through 168 removed outlier: 4.169A pdb=" N ARG D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.519A pdb=" N SER D 182 " --> pdb=" O GLN D 179 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA D 183 " --> pdb=" O PRO D 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 179 through 183' Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.926A pdb=" N ASP D 201 " --> pdb=" O GLN D 197 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU D 202 " --> pdb=" O GLY D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 221 Processing helix chain 'D' and resid 238 through 244 Processing helix chain 'D' and resid 247 through 256 Processing helix chain 'D' and resid 330 through 338 Processing helix chain 'D' and resid 362 through 368 Processing helix chain 'D' and resid 387 through 399 removed outlier: 3.559A pdb=" N ILE D 392 " --> pdb=" O VAL D 388 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 394 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Proline residue: D 395 - end of helix removed outlier: 3.971A pdb=" N HIS D 399 " --> pdb=" O PRO D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 418 removed outlier: 3.956A pdb=" N ASP D 416 " --> pdb=" O ARG D 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL D 418 " --> pdb=" O LEU D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 425 removed outlier: 4.101A pdb=" N LEU D 425 " --> pdb=" O SER D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 432 Processing helix chain 'D' and resid 433 through 446 removed outlier: 3.745A pdb=" N ARG D 437 " --> pdb=" O SER D 433 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN D 438 " --> pdb=" O GLY D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 482 Processing helix chain 'D' and resid 516 through 521 Processing helix chain 'D' and resid 525 through 533 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.893A pdb=" N THR A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 109 through 121 removed outlier: 3.694A pdb=" N PHE A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 128 through 134 removed outlier: 4.610A pdb=" N HIS A 131 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.841A pdb=" N VAL A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.619A pdb=" N GLY A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 193 removed outlier: 4.013A pdb=" N PHE A 193 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 252 through 262 removed outlier: 3.919A pdb=" N ALA A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 308 through 322 Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.757A pdb=" N VAL A 360 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 421 through 431 removed outlier: 3.962A pdb=" N ILE A 429 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 removed outlier: 3.649A pdb=" N PHE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 485 through 501 removed outlier: 3.627A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 17 through 18 removed outlier: 3.555A pdb=" N THR D 17 " --> pdb=" O ARG D 64 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG D 64 " --> pdb=" O THR D 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 209 through 211 removed outlier: 6.391A pdb=" N VAL D 38 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR D 211 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL D 40 " --> pdb=" O THR D 211 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 224 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER D 235 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 226 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'D' and resid 304 through 310 removed outlier: 6.879A pdb=" N LYS D 289 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP D 308 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU D 287 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 310 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER D 285 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N GLU D 286 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR D 347 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 488 through 489 removed outlier: 8.351A pdb=" N SER D 489 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE D 322 " --> pdb=" O SER D 489 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 512 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ARG D 506 " --> pdb=" O VAL D 510 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N VAL D 510 " --> pdb=" O ARG D 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 371 through 374 removed outlier: 3.599A pdb=" N LEU D 453 " --> pdb=" O THR D 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 36 through 39 removed outlier: 6.586A pdb=" N VAL A 37 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 81 through 86 removed outlier: 6.431A pdb=" N THR A 95 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE A 84 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 93 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER A 86 " --> pdb=" O ASN A 91 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ASN A 91 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 161 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 166 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL A 159 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.663A pdb=" N SER A 338 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU A 298 " --> pdb=" O PRO A 508 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP A 510 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE A 294 " --> pdb=" O TYR A 512 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N SER A 514 " --> pdb=" O ALA A 292 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A 292 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL A 516 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N GLY A 290 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASN A 295 " --> pdb=" O TRP A 442 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP A 442 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 386 through 390 removed outlier: 5.641A pdb=" N ILE A 387 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 419 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR A 389 " --> pdb=" O GLN A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 531 hydrogen bonds defined for protein. 1527 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: 2.01 Time building geometry restraints manager: 1.54 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: 2880 1.33 - 1.45: 2541 1.45 - 1.57: 7165 1.57 - 1.69: 10 1.69 - 1.81: 47 Bond restraints: 12643 Sorted by residual: bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.61e+01 bond pdb=" C5 ATP D 602 " pdb=" C6 ATP D 602 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C8 ATP D 602 " pdb=" N7 ATP D 602 " ideal model delta sigma weight residual 1.310 1.357 -0.047 1.00e-02 1.00e+04 2.17e+01 bond pdb=" C5 ATP D 602 " pdb=" N7 ATP D 602 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.93e+01 bond pdb=" C4 ATP D 602 " pdb=" N9 ATP D 602 " ideal model delta sigma weight residual 1.374 1.335 0.039 1.00e-02 1.00e+04 1.56e+01 ... (remaining 12638 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 17137 4.04 - 8.09: 124 8.09 - 12.13: 12 12.13 - 16.18: 0 16.18 - 20.22: 2 Bond angle restraints: 17275 Sorted by residual: angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 119.65 20.22 1.00e+00 1.00e+00 4.09e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 120.20 16.63 1.00e+00 1.00e+00 2.77e+02 angle pdb=" C5 ATP D 602 " pdb=" C4 ATP D 602 " pdb=" N3 ATP D 602 " ideal model delta sigma weight residual 126.80 118.75 8.05 1.00e+00 1.00e+00 6.47e+01 angle pdb=" C ASP A 352 " pdb=" CA ASP A 352 " pdb=" CB ASP A 352 " ideal model delta sigma weight residual 110.17 119.08 -8.91 1.11e+00 8.12e-01 6.44e+01 angle pdb=" C LEU A 348 " pdb=" CA LEU A 348 " pdb=" CB LEU A 348 " ideal model delta sigma weight residual 109.85 118.72 -8.87 1.14e+00 7.69e-01 6.05e+01 ... (remaining 17270 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 6760 17.86 - 35.72: 603 35.72 - 53.57: 119 53.57 - 71.43: 32 71.43 - 89.29: 10 Dihedral angle restraints: 7524 sinusoidal: 2901 harmonic: 4623 Sorted by residual: dihedral pdb=" C SER A 262 " pdb=" N SER A 262 " pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta harmonic sigma weight residual -122.60 -137.43 14.83 0 2.50e+00 1.60e-01 3.52e+01 dihedral pdb=" CA LEU B 226 " pdb=" C LEU B 226 " pdb=" N ARG B 227 " pdb=" CA ARG B 227 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA GLY C 237 " pdb=" C GLY C 237 " pdb=" N ASP C 238 " pdb=" CA ASP C 238 " ideal model delta harmonic sigma weight residual 180.00 152.90 27.10 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 7521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1952 0.127 - 0.255: 48 0.255 - 0.382: 4 0.382 - 0.509: 4 0.509 - 0.637: 2 Chirality restraints: 2010 Sorted by residual: chirality pdb=" CA SER A 262 " pdb=" N SER A 262 " pdb=" C SER A 262 " pdb=" CB SER A 262 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA ASN A 530 " pdb=" N ASN A 530 " pdb=" C ASN A 530 " pdb=" CB ASN A 530 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.53 2.00e-01 2.50e+01 6.89e+00 chirality pdb=" CA ALA A 391 " pdb=" N ALA A 391 " pdb=" C ALA A 391 " pdb=" CB ALA A 391 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.53e+00 ... (remaining 2007 not shown) Planarity restraints: 2240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 220 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C TRP A 220 " 0.042 2.00e-02 2.50e+03 pdb=" O TRP A 220 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 221 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 490 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C HIS A 490 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS A 490 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 491 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 335 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ARG D 335 " -0.038 2.00e-02 2.50e+03 pdb=" O ARG D 335 " 0.014 2.00e-02 2.50e+03 pdb=" N MET D 336 " 0.013 2.00e-02 2.50e+03 ... (remaining 2237 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 217 2.64 - 3.21: 12267 3.21 - 3.77: 18491 3.77 - 4.34: 24520 4.34 - 4.90: 39872 Nonbonded interactions: 95367 Sorted by model distance: nonbonded pdb=" N ASP A 352 " pdb=" OD1 ASP A 352 " model vdw 2.081 3.120 nonbonded pdb=" OG SER C 52 " pdb=" OE1 GLN C 53 " model vdw 2.107 3.040 nonbonded pdb=" O SER A 347 " pdb=" OG SER A 347 " model vdw 2.132 3.040 nonbonded pdb=" O GLU D 15 " pdb=" OG1 THR D 66 " model vdw 2.223 3.040 nonbonded pdb=" OG SER D 244 " pdb=" OE1 GLN D 246 " model vdw 2.224 3.040 ... (remaining 95362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.780 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.005 0.081 12643 Z= 0.304 Angle : 0.946 20.221 17275 Z= 0.618 Chirality : 0.061 0.637 2010 Planarity : 0.004 0.043 2240 Dihedral : 14.649 89.290 4566 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 9.03 % Favored : 90.59 % Rotamer: Outliers : 2.28 % Allowed : 5.83 % Favored : 91.89 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.18), residues: 1616 helix: -1.61 (0.17), residues: 734 sheet: -3.47 (0.40), residues: 112 loop : -3.47 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.008 0.001 TYR C 74 PHE 0.022 0.001 PHE B 95 TRP 0.012 0.001 TRP C 112 HIS 0.005 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00503 (12643) covalent geometry : angle 0.94628 (17275) hydrogen bonds : bond 0.14830 ( 531) hydrogen bonds : angle 6.30919 ( 1527) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.517 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: symmetry clash revert: symmetry clash REVERT: B 196 SER cc_start: 0.9315 (t) cc_final: 0.9095 (t) REVERT: B 205 ASP cc_start: 0.8836 (m-30) cc_final: 0.8488 (t70) REVERT: B 266 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8601 (tp40) REVERT: C 53 GLN cc_start: 0.8343 (pm20) cc_final: 0.8143 (pm20) REVERT: C 136 LEU cc_start: 0.9695 (tp) cc_final: 0.9454 (tp) REVERT: C 218 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8628 (tm-30) REVERT: C 269 MET cc_start: 0.8721 (ppp) cc_final: 0.8347 (tmm) REVERT: C 270 MET cc_start: 0.9203 (tmm) cc_final: 0.8494 (tmm) REVERT: D 486 LEU cc_start: 0.9153 (tt) cc_final: 0.8890 (tt) REVERT: A 243 LYS cc_start: 0.9162 (tppt) cc_final: 0.8835 (tppt) REVERT: A 268 LEU cc_start: 0.9114 (tp) cc_final: 0.8788 (tp) REVERT: A 490 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8477 (m90) outliers start: 29 outliers final: 16 residues processed: 210 average time/residue: 0.1366 time to fit residues: 39.3306 Evaluate side-chains 146 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 497 GLN Chi-restraints excluded: chain D residue 524 ARG Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 490 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 201 ASN B 228 ASN B 256 ASN C 138 GLN C 142 HIS D 105 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN A 82 GLN A 125 ASN A 131 HIS ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 404 ASN A 408 ASN A 431 ASN A 464 ASN A 497 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.055579 restraints weight = 55401.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.057261 restraints weight = 29112.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058392 restraints weight = 18709.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.059172 restraints weight = 13538.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059749 restraints weight = 10672.902| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12643 Z= 0.133 Angle : 0.673 10.064 17275 Z= 0.340 Chirality : 0.044 0.176 2010 Planarity : 0.005 0.048 2240 Dihedral : 9.136 86.947 1903 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.28 % Allowed : 12.68 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.20), residues: 1616 helix: -0.41 (0.19), residues: 745 sheet: -2.64 (0.44), residues: 126 loop : -2.89 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 295 TYR 0.010 0.001 TYR C 176 PHE 0.011 0.001 PHE B 236 TRP 0.018 0.001 TRP C 285 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00277 (12643) covalent geometry : angle 0.67270 (17275) hydrogen bonds : bond 0.04563 ( 531) hydrogen bonds : angle 5.03070 ( 1527) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.510 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: B 24 TYR cc_start: 0.8553 (t80) cc_final: 0.8168 (t80) REVERT: B 91 LEU cc_start: 0.9716 (mm) cc_final: 0.9382 (mt) REVERT: B 196 SER cc_start: 0.9253 (t) cc_final: 0.9041 (t) REVERT: B 302 ASP cc_start: 0.8741 (t0) cc_final: 0.8515 (t0) REVERT: C 137 MET cc_start: 0.9108 (tpp) cc_final: 0.8892 (tpp) REVERT: C 218 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8664 (tm-30) REVERT: C 269 MET cc_start: 0.8521 (ppp) cc_final: 0.8130 (tmm) REVERT: C 270 MET cc_start: 0.9118 (tmm) cc_final: 0.8461 (tmm) REVERT: D 316 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8361 (mmt90) REVERT: D 486 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8999 (tt) REVERT: A 268 LEU cc_start: 0.9164 (tp) cc_final: 0.8907 (tp) outliers start: 29 outliers final: 16 residues processed: 172 average time/residue: 0.1162 time to fit residues: 29.0468 Evaluate side-chains 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 316 ARG Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 507 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 8 optimal weight: 0.0970 chunk 156 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 75 optimal weight: 0.0570 chunk 59 optimal weight: 0.0870 chunk 79 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.065803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056246 restraints weight = 55943.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057883 restraints weight = 29906.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059019 restraints weight = 19472.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.059752 restraints weight = 14197.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.060331 restraints weight = 11329.844| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12643 Z= 0.122 Angle : 0.646 10.161 17275 Z= 0.326 Chirality : 0.043 0.203 2010 Planarity : 0.004 0.048 2240 Dihedral : 8.028 82.105 1876 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.05 % Allowed : 14.57 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.20), residues: 1616 helix: -0.04 (0.19), residues: 741 sheet: -2.36 (0.46), residues: 121 loop : -2.59 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 427 TYR 0.017 0.001 TYR B 69 PHE 0.009 0.001 PHE A 193 TRP 0.021 0.001 TRP C 285 HIS 0.004 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00255 (12643) covalent geometry : angle 0.64623 (17275) hydrogen bonds : bond 0.04070 ( 531) hydrogen bonds : angle 4.73622 ( 1527) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8465 (t80) cc_final: 0.8126 (t80) REVERT: B 91 LEU cc_start: 0.9708 (mm) cc_final: 0.9386 (mt) REVERT: B 109 GLU cc_start: 0.8779 (tt0) cc_final: 0.8516 (tt0) REVERT: B 186 SER cc_start: 0.9107 (p) cc_final: 0.8585 (t) REVERT: B 196 SER cc_start: 0.9237 (t) cc_final: 0.9024 (t) REVERT: B 291 ASN cc_start: 0.9179 (m-40) cc_final: 0.8899 (m-40) REVERT: B 295 ASP cc_start: 0.8934 (t0) cc_final: 0.8729 (t0) REVERT: C 183 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 269 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8070 (tmm) REVERT: C 270 MET cc_start: 0.9062 (tmm) cc_final: 0.8463 (tmm) REVERT: D 486 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9013 (tt) REVERT: A 268 LEU cc_start: 0.9107 (tp) cc_final: 0.8837 (tp) REVERT: A 346 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.7644 (mpt90) REVERT: A 511 ASP cc_start: 0.8422 (p0) cc_final: 0.7480 (p0) outliers start: 26 outliers final: 13 residues processed: 163 average time/residue: 0.1013 time to fit residues: 24.3606 Evaluate side-chains 142 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 73 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 133 optimal weight: 0.0570 chunk 138 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.054927 restraints weight = 56007.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.056550 restraints weight = 30243.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.057648 restraints weight = 19625.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.058399 restraints weight = 14339.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.058967 restraints weight = 11396.742| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12643 Z= 0.159 Angle : 0.648 9.728 17275 Z= 0.327 Chirality : 0.043 0.223 2010 Planarity : 0.004 0.046 2240 Dihedral : 7.559 73.371 1872 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.52 % Allowed : 16.69 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.21), residues: 1616 helix: 0.30 (0.20), residues: 741 sheet: -2.15 (0.49), residues: 115 loop : -2.40 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 208 TYR 0.017 0.001 TYR B 69 PHE 0.011 0.001 PHE B 236 TRP 0.021 0.001 TRP C 285 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00358 (12643) covalent geometry : angle 0.64847 (17275) hydrogen bonds : bond 0.04174 ( 531) hydrogen bonds : angle 4.69595 ( 1527) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 134 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 TYR cc_start: 0.8485 (t80) cc_final: 0.8139 (t80) REVERT: B 196 SER cc_start: 0.9250 (t) cc_final: 0.9044 (t) REVERT: B 205 ASP cc_start: 0.8887 (m-30) cc_final: 0.8401 (t70) REVERT: B 266 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8325 (tp-100) REVERT: C 183 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8442 (pp) REVERT: C 269 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8086 (tmm) REVERT: C 270 MET cc_start: 0.9118 (tmm) cc_final: 0.8473 (tmm) REVERT: D 486 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9006 (tt) REVERT: A 196 MET cc_start: 0.8898 (mmm) cc_final: 0.8638 (mmt) REVERT: A 268 LEU cc_start: 0.9225 (tp) cc_final: 0.8931 (tp) REVERT: A 346 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7945 (mpt90) REVERT: A 511 ASP cc_start: 0.8511 (p0) cc_final: 0.8111 (p0) outliers start: 32 outliers final: 21 residues processed: 156 average time/residue: 0.0976 time to fit residues: 23.5970 Evaluate side-chains 152 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 0.0030 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 ASN ** D 247 HIS ** 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 = 0.3118 r_free = 0.3118 target = 0.065171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055647 restraints weight = 56085.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.057289 restraints weight = 30019.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.058405 restraints weight = 19416.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.059173 restraints weight = 14127.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059734 restraints weight = 11192.067| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12643 Z= 0.122 Angle : 0.625 10.015 17275 Z= 0.313 Chirality : 0.043 0.169 2010 Planarity : 0.004 0.050 2240 Dihedral : 7.213 76.652 1872 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.99 % Allowed : 18.27 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.21), residues: 1616 helix: 0.43 (0.20), residues: 750 sheet: -2.00 (0.50), residues: 115 loop : -2.30 (0.21), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 162 TYR 0.018 0.001 TYR B 69 PHE 0.009 0.001 PHE B 236 TRP 0.021 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00268 (12643) covalent geometry : angle 0.62517 (17275) hydrogen bonds : bond 0.03907 ( 531) hydrogen bonds : angle 4.56053 ( 1527) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8762 (tpt90) cc_final: 0.8421 (tpm170) REVERT: B 24 TYR cc_start: 0.8438 (t80) cc_final: 0.8144 (t80) REVERT: B 91 LEU cc_start: 0.9716 (mm) cc_final: 0.9406 (mt) REVERT: B 109 GLU cc_start: 0.8673 (tt0) cc_final: 0.8212 (tt0) REVERT: B 186 SER cc_start: 0.9090 (p) cc_final: 0.8520 (p) REVERT: B 196 SER cc_start: 0.9250 (t) cc_final: 0.9043 (t) REVERT: B 205 ASP cc_start: 0.8822 (m-30) cc_final: 0.8319 (t70) REVERT: C 183 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8408 (pp) REVERT: C 269 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8059 (tmm) REVERT: C 270 MET cc_start: 0.9064 (tmm) cc_final: 0.8455 (tmm) REVERT: D 486 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9020 (tt) REVERT: A 268 LEU cc_start: 0.9114 (tp) cc_final: 0.8814 (tp) outliers start: 38 outliers final: 25 residues processed: 159 average time/residue: 0.0989 time to fit residues: 24.0573 Evaluate side-chains 154 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 105 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.065793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.056309 restraints weight = 56024.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.057947 restraints weight = 29997.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059068 restraints weight = 19400.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.059841 restraints weight = 14113.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.060375 restraints weight = 11181.612| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12643 Z= 0.113 Angle : 0.618 9.781 17275 Z= 0.308 Chirality : 0.042 0.186 2010 Planarity : 0.004 0.051 2240 Dihedral : 6.730 75.846 1868 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.60 % Allowed : 18.90 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.21), residues: 1616 helix: 0.57 (0.20), residues: 744 sheet: -1.51 (0.53), residues: 108 loop : -2.14 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 162 TYR 0.019 0.001 TYR B 69 PHE 0.009 0.001 PHE D 487 TRP 0.016 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00248 (12643) covalent geometry : angle 0.61771 (17275) hydrogen bonds : bond 0.03686 ( 531) hydrogen bonds : angle 4.46587 ( 1527) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8694 (tpt90) cc_final: 0.8485 (tpm170) REVERT: B 91 LEU cc_start: 0.9712 (mm) cc_final: 0.9418 (mt) REVERT: B 196 SER cc_start: 0.9233 (t) cc_final: 0.9020 (t) REVERT: B 205 ASP cc_start: 0.8801 (m-30) cc_final: 0.8277 (t70) REVERT: C 183 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8432 (pp) REVERT: C 269 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: C 270 MET cc_start: 0.9072 (tmm) cc_final: 0.8460 (tmm) REVERT: D 486 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8987 (tt) REVERT: A 268 LEU cc_start: 0.9113 (tp) cc_final: 0.8818 (tp) outliers start: 33 outliers final: 20 residues processed: 154 average time/residue: 0.0964 time to fit residues: 23.2575 Evaluate side-chains 145 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 103 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN B 55 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 247 HIS ** 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 = 0.3036 r_free = 0.3036 target = 0.062134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.052646 restraints weight = 57507.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.054176 restraints weight = 31417.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055217 restraints weight = 20728.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.055966 restraints weight = 15394.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.056506 restraints weight = 12258.562| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 12643 Z= 0.324 Angle : 0.796 11.553 17275 Z= 0.401 Chirality : 0.047 0.171 2010 Planarity : 0.005 0.054 2240 Dihedral : 6.735 78.951 1864 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 3.78 % Allowed : 19.13 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.21), residues: 1616 helix: 0.31 (0.19), residues: 758 sheet: -2.01 (0.50), residues: 119 loop : -2.30 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 412 TYR 0.024 0.002 TYR D 354 PHE 0.016 0.002 PHE B 236 TRP 0.011 0.001 TRP A 398 HIS 0.006 0.001 HIS A 235 Details of bonding type rmsd covalent geometry : bond 0.00715 (12643) covalent geometry : angle 0.79566 (17275) hydrogen bonds : bond 0.05011 ( 531) hydrogen bonds : angle 5.05063 ( 1527) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 109 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 109 GLU cc_start: 0.8695 (tt0) cc_final: 0.8255 (tt0) REVERT: B 186 SER cc_start: 0.9274 (p) cc_final: 0.8897 (p) REVERT: B 205 ASP cc_start: 0.8946 (m-30) cc_final: 0.8566 (t70) REVERT: B 302 ASP cc_start: 0.8722 (t0) cc_final: 0.8319 (t0) REVERT: C 183 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8592 (pp) REVERT: C 269 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: C 270 MET cc_start: 0.9143 (tmm) cc_final: 0.8463 (tmm) REVERT: C 285 TRP cc_start: 0.9535 (p90) cc_final: 0.9228 (p90) REVERT: D 486 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9091 (tt) REVERT: A 268 LEU cc_start: 0.9342 (tp) cc_final: 0.9110 (tp) outliers start: 48 outliers final: 33 residues processed: 144 average time/residue: 0.0928 time to fit residues: 21.2940 Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 256 ASN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 ILE Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 22 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 0.2980 chunk 93 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 75 optimal weight: 0.0570 chunk 92 optimal weight: 3.9990 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.065273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.055714 restraints weight = 55719.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.057364 restraints weight = 30011.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.058447 restraints weight = 19444.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.059243 restraints weight = 14253.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059812 restraints weight = 11245.972| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12643 Z= 0.122 Angle : 0.677 11.757 17275 Z= 0.333 Chirality : 0.043 0.180 2010 Planarity : 0.004 0.051 2240 Dihedral : 6.451 82.575 1864 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.20 % Allowed : 21.26 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.21), residues: 1616 helix: 0.61 (0.20), residues: 744 sheet: -1.87 (0.51), residues: 116 loop : -2.03 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 162 TYR 0.019 0.001 TYR B 69 PHE 0.010 0.001 PHE B 16 TRP 0.010 0.001 TRP C 112 HIS 0.004 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00260 (12643) covalent geometry : angle 0.67701 (17275) hydrogen bonds : bond 0.04042 ( 531) hydrogen bonds : angle 4.57692 ( 1527) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8732 (tpt90) cc_final: 0.8445 (tpm170) REVERT: B 91 LEU cc_start: 0.9708 (mm) cc_final: 0.9387 (mt) REVERT: B 109 GLU cc_start: 0.8578 (tt0) cc_final: 0.8087 (tt0) REVERT: B 186 SER cc_start: 0.9135 (p) cc_final: 0.8621 (p) REVERT: B 196 SER cc_start: 0.9293 (t) cc_final: 0.9090 (t) REVERT: B 205 ASP cc_start: 0.8822 (m-30) cc_final: 0.8304 (t70) REVERT: C 137 MET cc_start: 0.8988 (tpp) cc_final: 0.8734 (tpp) REVERT: C 211 LEU cc_start: 0.9466 (tp) cc_final: 0.9236 (tp) REVERT: C 269 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7943 (tmm) REVERT: C 270 MET cc_start: 0.9054 (tmm) cc_final: 0.8457 (tmm) REVERT: D 486 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9018 (tt) REVERT: A 268 LEU cc_start: 0.9112 (tp) cc_final: 0.8141 (tp) outliers start: 28 outliers final: 21 residues processed: 146 average time/residue: 0.0951 time to fit residues: 21.6582 Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 60 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 354 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.064849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.055190 restraints weight = 56558.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.056826 restraints weight = 30644.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.057960 restraints weight = 19985.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058729 restraints weight = 14511.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059322 restraints weight = 11510.175| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12643 Z= 0.134 Angle : 0.657 11.732 17275 Z= 0.323 Chirality : 0.044 0.185 2010 Planarity : 0.004 0.049 2240 Dihedral : 6.328 87.637 1864 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 2.20 % Allowed : 21.10 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1616 helix: 0.56 (0.20), residues: 759 sheet: -1.88 (0.50), residues: 117 loop : -2.05 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.017 0.001 TYR B 69 PHE 0.011 0.001 PHE B 236 TRP 0.013 0.001 TRP C 285 HIS 0.004 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00302 (12643) covalent geometry : angle 0.65723 (17275) hydrogen bonds : bond 0.03931 ( 531) hydrogen bonds : angle 4.57868 ( 1527) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8707 (tpt90) cc_final: 0.8480 (tpm170) REVERT: B 109 GLU cc_start: 0.8589 (tt0) cc_final: 0.8112 (tt0) REVERT: B 186 SER cc_start: 0.9192 (p) cc_final: 0.8668 (p) REVERT: B 205 ASP cc_start: 0.8845 (m-30) cc_final: 0.8367 (t70) REVERT: C 211 LEU cc_start: 0.9435 (tp) cc_final: 0.9201 (tp) REVERT: C 269 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7903 (tmm) REVERT: C 270 MET cc_start: 0.9066 (tmm) cc_final: 0.8488 (tmm) REVERT: D 486 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8998 (tt) REVERT: A 268 LEU cc_start: 0.8484 (tp) cc_final: 0.8225 (tp) outliers start: 28 outliers final: 22 residues processed: 139 average time/residue: 0.0969 time to fit residues: 20.6538 Evaluate side-chains 139 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 349 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 0.2980 chunk 52 optimal weight: 0.0060 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 128 optimal weight: 0.5980 chunk 44 optimal weight: 0.0770 chunk 108 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.066344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.056794 restraints weight = 56163.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058441 restraints weight = 30373.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059556 restraints weight = 19799.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060303 restraints weight = 14476.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.060874 restraints weight = 11516.934| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12643 Z= 0.117 Angle : 0.673 12.774 17275 Z= 0.325 Chirality : 0.043 0.198 2010 Planarity : 0.004 0.060 2240 Dihedral : 6.137 87.105 1864 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.81 % Allowed : 21.81 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.21), residues: 1616 helix: 0.61 (0.20), residues: 758 sheet: -1.33 (0.53), residues: 108 loop : -2.01 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.018 0.001 TYR B 69 PHE 0.010 0.001 PHE B 16 TRP 0.013 0.001 TRP C 285 HIS 0.003 0.001 HIS B 55 Details of bonding type rmsd covalent geometry : bond 0.00252 (12643) covalent geometry : angle 0.67256 (17275) hydrogen bonds : bond 0.03579 ( 531) hydrogen bonds : angle 4.49525 ( 1527) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8872 (ptp) cc_final: 0.8527 (pmm) REVERT: B 83 SER cc_start: 0.9259 (m) cc_final: 0.8727 (p) REVERT: B 91 LEU cc_start: 0.9704 (mm) cc_final: 0.9400 (mt) REVERT: B 109 GLU cc_start: 0.8531 (tt0) cc_final: 0.8111 (tt0) REVERT: B 186 SER cc_start: 0.9186 (p) cc_final: 0.8668 (p) REVERT: B 196 SER cc_start: 0.9232 (t) cc_final: 0.9025 (t) REVERT: B 205 ASP cc_start: 0.8792 (m-30) cc_final: 0.8282 (t70) REVERT: C 155 PHE cc_start: 0.8762 (m-80) cc_final: 0.8508 (m-10) REVERT: C 211 LEU cc_start: 0.9419 (tp) cc_final: 0.9196 (tp) REVERT: C 269 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7843 (tmm) REVERT: C 270 MET cc_start: 0.9039 (tmm) cc_final: 0.8478 (tmm) REVERT: D 101 MET cc_start: 0.8411 (mpp) cc_final: 0.8103 (mpp) REVERT: D 386 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8183 (m-10) REVERT: D 486 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8963 (tt) outliers start: 23 outliers final: 18 residues processed: 142 average time/residue: 0.0932 time to fit residues: 20.5936 Evaluate side-chains 140 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 386 TYR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 486 LEU Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 452 PHE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 147 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 152 optimal weight: 0.3980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 GLN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** 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 = 0.3126 r_free = 0.3126 target = 0.065543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.056052 restraints weight = 55947.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.057683 restraints weight = 30385.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.058805 restraints weight = 19719.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.059554 restraints weight = 14375.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.060112 restraints weight = 11362.373| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12643 Z= 0.130 Angle : 0.671 12.829 17275 Z= 0.326 Chirality : 0.043 0.187 2010 Planarity : 0.004 0.053 2240 Dihedral : 6.012 84.835 1862 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.28 % Allowed : 21.81 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.22), residues: 1616 helix: 0.64 (0.20), residues: 759 sheet: -1.29 (0.53), residues: 108 loop : -1.99 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 162 TYR 0.018 0.001 TYR B 189 PHE 0.010 0.001 PHE B 236 TRP 0.012 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00295 (12643) covalent geometry : angle 0.67108 (17275) hydrogen bonds : bond 0.03712 ( 531) hydrogen bonds : angle 4.51884 ( 1527) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1858.39 seconds wall clock time: 32 minutes 56.00 seconds (1976.00 seconds total)