Starting phenix.real_space_refine on Fri Jun 13 20:16:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfc_38301/06_2025/8xfc_38301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfc_38301/06_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_38301/06_2025/8xfc_38301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfc_38301/06_2025/8xfc_38301.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfc_38301/06_2025/8xfc_38301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfc_38301/06_2025/8xfc_38301.cif" } resolution = 3.89 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.28, per 1000 atoms: 0.67 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: 3.00 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.23 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: 3.68 Time building geometry restraints manager: 3.57 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: 3.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 30.950 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- 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 : 13.55 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (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 TRP 0.012 0.001 TRP C 112 HIS 0.005 0.001 HIS C 71 PHE 0.022 0.001 PHE B 95 TYR 0.008 0.001 TYR C 74 ARG 0.005 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.14830 ( 531) hydrogen bonds : angle 6.30919 ( 1527) covalent geometry : bond 0.00503 (12643) covalent geometry : angle 0.94628 (17275) *********************** 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 : 1.313 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: B 196 SER cc_start: 0.9315 (t) cc_final: 0.9095 (t) REVERT: B 266 GLN cc_start: 0.8843 (tp-100) cc_final: 0.8601 (tp40) REVERT: C 218 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8631 (tm-30) REVERT: C 269 MET cc_start: 0.8721 (ppp) cc_final: 0.8346 (tmm) REVERT: C 270 MET cc_start: 0.9203 (tmm) cc_final: 0.8494 (tmm) REVERT: D 101 MET cc_start: 0.8370 (mpp) cc_final: 0.8167 (mpp) REVERT: D 486 LEU cc_start: 0.9153 (tt) cc_final: 0.8891 (tt) REVERT: A 101 LYS cc_start: 0.9226 (mttp) cc_final: 0.9010 (mtpp) 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: 0.8789 (tp) REVERT: A 490 HIS cc_start: 0.8853 (OUTLIER) cc_final: 0.8478 (m90) outliers start: 29 outliers final: 16 residues processed: 210 average time/residue: 0.3346 time to fit residues: 97.7273 Evaluate side-chains 144 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.477 ------------------------------------------------------------------------------- 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 135 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 overall best weight: 1.2340 ------------------------------------------------------------------------------- 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 A 264 ASN A 330 GLN A 331 GLN A 404 ASN A 408 ASN A 431 ASN ** A 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.054992 restraints weight = 55712.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.056628 restraints weight = 29817.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057752 restraints weight = 19329.796| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12643 Z= 0.145 Angle : 0.674 9.396 17275 Z= 0.343 Chirality : 0.044 0.176 2010 Planarity : 0.004 0.046 2240 Dihedral : 9.196 85.992 1903 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.52 % Allowed : 12.99 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.20), residues: 1616 helix: -0.45 (0.19), residues: 743 sheet: -2.90 (0.44), residues: 114 loop : -2.87 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 285 HIS 0.004 0.001 HIS C 71 PHE 0.012 0.001 PHE B 236 TYR 0.010 0.001 TYR C 176 ARG 0.006 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.04773 ( 531) hydrogen bonds : angle 5.11949 ( 1527) covalent geometry : bond 0.00318 (12643) covalent geometry : angle 0.67396 (17275) *********************** 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 176 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 1.511 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: B 24 TYR cc_start: 0.8575 (t80) cc_final: 0.8222 (t80) REVERT: B 196 SER cc_start: 0.9308 (t) cc_final: 0.9097 (t) REVERT: B 245 MET cc_start: 0.8673 (ptp) cc_final: 0.8389 (ptp) REVERT: B 287 TYR cc_start: 0.8798 (t80) cc_final: 0.8586 (t80) REVERT: C 269 MET cc_start: 0.8558 (ppp) cc_final: 0.8179 (tmm) REVERT: C 270 MET cc_start: 0.9121 (tmm) cc_final: 0.8462 (tmm) REVERT: D 316 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8362 (mmt90) REVERT: D 486 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8990 (tt) REVERT: A 268 LEU cc_start: 0.9204 (tp) cc_final: 0.8927 (tp) outliers start: 32 outliers final: 21 residues processed: 167 average time/residue: 0.2472 time to fit residues: 60.4659 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 : 1.584 ------------------------------------------------------------------------------- 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 129 ASP Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain C residue 63 TRP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 148 VAL 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 459 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 300 THR 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 102 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 121 optimal weight: 0.0470 chunk 73 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 91 optimal weight: 0.0870 overall best weight: 0.5656 ------------------------------------------------------------------------------- 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** C 53 GLN ** 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 = 0.3123 r_free = 0.3123 target = 0.065500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.055982 restraints weight = 55674.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.057598 restraints weight = 29819.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058737 restraints weight = 19555.919| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12643 Z= 0.120 Angle : 0.635 9.636 17275 Z= 0.321 Chirality : 0.044 0.185 2010 Planarity : 0.004 0.046 2240 Dihedral : 7.934 78.204 1876 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 2.68 % Allowed : 15.20 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.20), residues: 1616 helix: -0.01 (0.19), residues: 742 sheet: -2.37 (0.47), residues: 115 loop : -2.59 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 285 HIS 0.004 0.001 HIS A 490 PHE 0.012 0.001 PHE B 28 TYR 0.019 0.001 TYR B 69 ARG 0.006 0.000 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 531) hydrogen bonds : angle 4.73784 ( 1527) covalent geometry : bond 0.00254 (12643) covalent geometry : angle 0.63535 (17275) *********************** 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 180 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 1.384 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: B 24 TYR cc_start: 0.8477 (t80) cc_final: 0.8136 (t80) REVERT: B 91 LEU cc_start: 0.9705 (mm) cc_final: 0.9402 (mt) REVERT: B 109 GLU cc_start: 0.8862 (tt0) cc_final: 0.8459 (tt0) REVERT: B 186 SER cc_start: 0.9122 (p) cc_final: 0.8520 (p) REVERT: B 196 SER cc_start: 0.9230 (t) cc_final: 0.9021 (t) REVERT: B 245 MET cc_start: 0.8602 (ptp) cc_final: 0.8333 (ptp) REVERT: C 183 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8441 (pp) REVERT: C 269 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8090 (tmm) REVERT: C 270 MET cc_start: 0.9076 (tmm) cc_final: 0.8473 (tmm) REVERT: D 486 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9036 (tt) REVERT: A 268 LEU cc_start: 0.9118 (tp) cc_final: 0.8835 (tp) REVERT: A 300 THR cc_start: 0.9214 (OUTLIER) cc_final: 0.9013 (m) REVERT: A 397 ASP cc_start: 0.8999 (p0) cc_final: 0.8753 (p0) REVERT: A 511 ASP cc_start: 0.8523 (p0) cc_final: 0.8308 (p0) outliers start: 34 outliers final: 17 residues processed: 169 average time/residue: 0.2231 time to fit residues: 57.2619 Evaluate side-chains 147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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 181 VAL Chi-restraints excluded: chain B residue 244 LEU 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 216 VAL 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 486 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 300 THR 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 134 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 72 optimal weight: 8.9990 chunk 78 optimal weight: 0.0570 chunk 22 optimal weight: 0.4980 chunk 121 optimal weight: 8.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 291 ASN ** D 247 HIS ** 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 = 0.3129 r_free = 0.3129 target = 0.065736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056313 restraints weight = 55215.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.057970 restraints weight = 29661.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059048 restraints weight = 19206.544| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12643 Z= 0.113 Angle : 0.630 9.762 17275 Z= 0.313 Chirality : 0.043 0.165 2010 Planarity : 0.004 0.048 2240 Dihedral : 7.335 74.935 1868 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.13 % Allowed : 17.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.21), residues: 1616 helix: 0.29 (0.20), residues: 747 sheet: -1.95 (0.49), residues: 114 loop : -2.40 (0.21), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 PHE 0.010 0.001 PHE D 487 TYR 0.017 0.001 TYR B 69 ARG 0.004 0.000 ARG D 427 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 531) hydrogen bonds : angle 4.56919 ( 1527) covalent geometry : bond 0.00247 (12643) covalent geometry : angle 0.62996 (17275) *********************** 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 167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8758 (tpt90) cc_final: 0.8449 (tpm170) REVERT: B 24 TYR cc_start: 0.8438 (t80) cc_final: 0.8133 (t80) REVERT: B 91 LEU cc_start: 0.9709 (mm) cc_final: 0.9400 (mt) REVERT: B 109 GLU cc_start: 0.8800 (tt0) cc_final: 0.8457 (tt0) REVERT: B 186 SER cc_start: 0.9044 (p) cc_final: 0.8607 (t) REVERT: B 196 SER cc_start: 0.9209 (t) cc_final: 0.8990 (t) REVERT: C 269 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.8047 (tmm) REVERT: C 270 MET cc_start: 0.9075 (tmm) cc_final: 0.8452 (tmm) REVERT: D 486 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8972 (tt) REVERT: A 268 LEU cc_start: 0.9126 (tp) cc_final: 0.8807 (tp) REVERT: A 397 ASP cc_start: 0.9008 (p0) cc_final: 0.8762 (p0) outliers start: 27 outliers final: 19 residues processed: 160 average time/residue: 0.2554 time to fit residues: 61.7775 Evaluate side-chains 146 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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 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 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 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 300 THR 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 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 120 optimal weight: 0.0000 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 144 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 B 291 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 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 = 0.3131 r_free = 0.3131 target = 0.065670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056278 restraints weight = 55253.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.057920 restraints weight = 29627.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059040 restraints weight = 19262.473| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12643 Z= 0.117 Angle : 0.615 9.694 17275 Z= 0.306 Chirality : 0.042 0.169 2010 Planarity : 0.004 0.054 2240 Dihedral : 6.983 76.848 1868 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.83 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.21), residues: 1616 helix: 0.44 (0.20), residues: 750 sheet: -1.69 (0.53), residues: 108 loop : -2.29 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 PHE 0.021 0.001 PHE C 188 TYR 0.021 0.001 TYR D 354 ARG 0.007 0.000 ARG A 443 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 531) hydrogen bonds : angle 4.51472 ( 1527) covalent geometry : bond 0.00257 (12643) covalent geometry : angle 0.61460 (17275) *********************** 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 167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 131 time to evaluate : 1.304 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: B 24 TYR cc_start: 0.8427 (t80) cc_final: 0.8160 (t80) REVERT: B 91 LEU cc_start: 0.9708 (mm) cc_final: 0.9409 (mt) REVERT: B 196 SER cc_start: 0.9210 (t) cc_final: 0.8994 (t) REVERT: C 183 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8409 (pp) REVERT: C 269 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8073 (tmm) REVERT: C 270 MET cc_start: 0.9066 (tmm) cc_final: 0.8447 (tmm) REVERT: D 486 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9007 (tt) REVERT: A 268 LEU cc_start: 0.9097 (tp) cc_final: 0.8785 (tp) REVERT: A 397 ASP cc_start: 0.9027 (p0) cc_final: 0.8790 (p0) outliers start: 36 outliers final: 23 residues processed: 158 average time/residue: 0.2186 time to fit residues: 52.9320 Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.419 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain B residue 296 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 415 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 74 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 151 optimal weight: 0.0970 chunk 21 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.0000 overall best weight: 0.4782 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.066616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.057180 restraints weight = 55876.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.058859 restraints weight = 29793.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.059976 restraints weight = 19144.960| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12643 Z= 0.109 Angle : 0.612 10.068 17275 Z= 0.303 Chirality : 0.042 0.176 2010 Planarity : 0.004 0.051 2240 Dihedral : 6.655 76.324 1868 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.28 % Allowed : 19.29 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.21), residues: 1616 helix: 0.51 (0.20), residues: 750 sheet: -1.68 (0.51), residues: 114 loop : -2.17 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 285 HIS 0.003 0.001 HIS C 71 PHE 0.016 0.001 PHE C 188 TYR 0.019 0.001 TYR B 69 ARG 0.006 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 531) hydrogen bonds : angle 4.43232 ( 1527) covalent geometry : bond 0.00234 (12643) covalent geometry : angle 0.61160 (17275) *********************** 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 167 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8832 (tpp-160) cc_final: 0.8184 (tpt90) REVERT: B 12 MET cc_start: 0.8730 (mtt) cc_final: 0.7112 (mtt) REVERT: B 24 TYR cc_start: 0.8387 (t80) cc_final: 0.8173 (t80) REVERT: B 83 SER cc_start: 0.9204 (m) cc_final: 0.8671 (p) REVERT: B 91 LEU cc_start: 0.9706 (mm) cc_final: 0.9409 (mt) REVERT: B 109 GLU cc_start: 0.8636 (tt0) cc_final: 0.8422 (tt0) REVERT: B 186 SER cc_start: 0.9149 (p) cc_final: 0.8647 (t) REVERT: B 196 SER cc_start: 0.9178 (t) cc_final: 0.8958 (t) REVERT: B 295 ASP cc_start: 0.8887 (t0) cc_final: 0.8649 (t0) REVERT: C 183 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8436 (pp) REVERT: C 269 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7998 (tmm) REVERT: C 270 MET cc_start: 0.9071 (tmm) cc_final: 0.8482 (tmm) REVERT: D 486 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8952 (tt) REVERT: A 268 LEU cc_start: 0.9049 (tp) cc_final: 0.8750 (tp) REVERT: A 397 ASP cc_start: 0.8998 (p0) cc_final: 0.8753 (p0) outliers start: 29 outliers final: 20 residues processed: 157 average time/residue: 0.2199 time to fit residues: 52.9602 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 : 1.550 ------------------------------------------------------------------------------- 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 296 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 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 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 434 ILE 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 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 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 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.065828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.056326 restraints weight = 56368.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.057979 restraints weight = 30371.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.059105 restraints weight = 19701.897| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12643 Z= 0.127 Angle : 0.629 10.667 17275 Z= 0.310 Chirality : 0.042 0.169 2010 Planarity : 0.004 0.050 2240 Dihedral : 6.252 77.070 1862 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.28 % Allowed : 20.39 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1616 helix: 0.54 (0.20), residues: 762 sheet: -1.49 (0.54), residues: 108 loop : -2.10 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 285 HIS 0.004 0.001 HIS B 55 PHE 0.014 0.001 PHE C 188 TYR 0.018 0.001 TYR B 69 ARG 0.008 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 531) hydrogen bonds : angle 4.46066 ( 1527) covalent geometry : bond 0.00285 (12643) covalent geometry : angle 0.62889 (17275) *********************** 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 156 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 ARG cc_start: 0.8847 (tpp-160) cc_final: 0.8635 (tpp-160) REVERT: B 91 LEU cc_start: 0.9717 (mm) cc_final: 0.9419 (mt) REVERT: B 109 GLU cc_start: 0.8657 (tt0) cc_final: 0.8453 (tt0) REVERT: B 186 SER cc_start: 0.9220 (p) cc_final: 0.8881 (t) REVERT: B 196 SER cc_start: 0.9220 (t) cc_final: 0.9011 (t) REVERT: B 205 ASP cc_start: 0.8897 (m-30) cc_final: 0.8469 (t70) REVERT: C 183 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8463 (pp) REVERT: C 269 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7944 (tmm) REVERT: C 270 MET cc_start: 0.9073 (tmm) cc_final: 0.8473 (tmm) REVERT: D 486 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8969 (tt) REVERT: A 268 LEU cc_start: 0.9134 (tp) cc_final: 0.8890 (tp) REVERT: A 397 ASP cc_start: 0.9005 (p0) cc_final: 0.8741 (p0) outliers start: 29 outliers final: 21 residues processed: 147 average time/residue: 0.2125 time to fit residues: 47.7438 Evaluate side-chains 148 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 296 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 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 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 421 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 8.9990 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 59 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 156 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 55 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.064598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.055126 restraints weight = 57029.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.056734 restraints weight = 30705.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057833 restraints weight = 19924.758| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12643 Z= 0.171 Angle : 0.676 11.666 17275 Z= 0.332 Chirality : 0.043 0.174 2010 Planarity : 0.004 0.049 2240 Dihedral : 6.204 82.845 1862 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.52 % Allowed : 20.31 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1616 helix: 0.67 (0.20), residues: 755 sheet: -1.89 (0.51), residues: 115 loop : -2.10 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.005 0.001 HIS B 55 PHE 0.013 0.001 PHE C 188 TYR 0.019 0.001 TYR B 69 ARG 0.004 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 531) hydrogen bonds : angle 4.55930 ( 1527) covalent geometry : bond 0.00385 (12643) covalent geometry : angle 0.67640 (17275) *********************** 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 155 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 186 SER cc_start: 0.9309 (p) cc_final: 0.8938 (t) REVERT: B 205 ASP cc_start: 0.8887 (m-30) cc_final: 0.8485 (t70) REVERT: C 183 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8491 (pp) REVERT: C 211 LEU cc_start: 0.9519 (tp) cc_final: 0.9285 (tp) REVERT: C 269 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7997 (tmm) REVERT: C 270 MET cc_start: 0.9115 (tmm) cc_final: 0.8482 (tmm) REVERT: D 101 MET cc_start: 0.8440 (mpp) cc_final: 0.8215 (mpp) REVERT: D 486 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 154 MET cc_start: 0.8254 (mtm) cc_final: 0.8027 (mtt) REVERT: A 268 LEU cc_start: 0.9221 (tp) cc_final: 0.8953 (tp) REVERT: A 397 ASP cc_start: 0.9031 (p0) cc_final: 0.8787 (p0) outliers start: 32 outliers final: 22 residues processed: 146 average time/residue: 0.2171 time to fit residues: 48.9671 Evaluate side-chains 147 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 139 ILE 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 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 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 421 THR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 526 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 133 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.065420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.055942 restraints weight = 56271.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.057534 restraints weight = 30272.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.058657 restraints weight = 19906.922| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12643 Z= 0.126 Angle : 0.654 12.400 17275 Z= 0.319 Chirality : 0.042 0.174 2010 Planarity : 0.004 0.047 2240 Dihedral : 6.137 87.505 1862 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.20 % Allowed : 21.02 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1616 helix: 0.65 (0.20), residues: 760 sheet: -1.86 (0.51), residues: 115 loop : -1.98 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 285 HIS 0.003 0.001 HIS B 55 PHE 0.014 0.001 PHE C 188 TYR 0.020 0.001 TYR B 69 ARG 0.004 0.000 ARG C 162 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 531) hydrogen bonds : angle 4.50294 ( 1527) covalent geometry : bond 0.00284 (12643) covalent geometry : angle 0.65406 (17275) *********************** 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 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 SER cc_start: 0.9274 (m) cc_final: 0.8745 (p) REVERT: B 91 LEU cc_start: 0.9716 (mm) cc_final: 0.9404 (mt) REVERT: B 109 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8292 (tp30) REVERT: B 186 SER cc_start: 0.9438 (p) cc_final: 0.8830 (p) REVERT: B 205 ASP cc_start: 0.8878 (m-30) cc_final: 0.8428 (t70) REVERT: C 183 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8514 (pp) REVERT: C 211 LEU cc_start: 0.9422 (tp) cc_final: 0.9175 (tp) REVERT: C 269 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7963 (tmm) REVERT: C 270 MET cc_start: 0.9090 (tmm) cc_final: 0.8486 (tmm) REVERT: D 101 MET cc_start: 0.8499 (mpp) cc_final: 0.8273 (mpp) REVERT: D 486 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9001 (tt) REVERT: A 268 LEU cc_start: 0.9181 (tp) cc_final: 0.8920 (tp) REVERT: A 397 ASP cc_start: 0.9022 (p0) cc_final: 0.8746 (p0) outliers start: 28 outliers final: 23 residues processed: 140 average time/residue: 0.2051 time to fit residues: 44.7203 Evaluate side-chains 149 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.412 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain B residue 296 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 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 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 285 ASP Chi-restraints excluded: chain A residue 421 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 21 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 ** 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 = 0.3148 r_free = 0.3148 target = 0.066479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057046 restraints weight = 55627.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058646 restraints weight = 30047.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.059810 restraints weight = 19475.003| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12643 Z= 0.114 Angle : 0.662 13.114 17275 Z= 0.321 Chirality : 0.042 0.176 2010 Planarity : 0.004 0.079 2240 Dihedral : 6.010 87.681 1862 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.13 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1616 helix: 0.63 (0.20), residues: 765 sheet: -1.54 (0.52), residues: 114 loop : -1.99 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 285 HIS 0.003 0.001 HIS B 55 PHE 0.010 0.001 PHE D 487 TYR 0.020 0.001 TYR B 69 ARG 0.005 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03596 ( 531) hydrogen bonds : angle 4.43654 ( 1527) covalent geometry : bond 0.00253 (12643) covalent geometry : angle 0.66191 (17275) ********************** 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 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8733 (ptp) cc_final: 0.8434 (pmm) REVERT: B 83 SER cc_start: 0.9262 (m) cc_final: 0.8700 (p) REVERT: B 91 LEU cc_start: 0.9699 (mm) cc_final: 0.9407 (mt) REVERT: B 109 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: B 185 MET cc_start: 0.8778 (tpp) cc_final: 0.8567 (tpp) REVERT: B 186 SER cc_start: 0.9398 (p) cc_final: 0.8852 (p) REVERT: C 183 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8495 (pp) REVERT: C 211 LEU cc_start: 0.9422 (tp) cc_final: 0.9201 (tp) REVERT: C 269 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7813 (tmm) REVERT: C 270 MET cc_start: 0.9067 (tmm) cc_final: 0.8486 (tmm) REVERT: D 101 MET cc_start: 0.8511 (mpp) cc_final: 0.8288 (mpp) REVERT: D 178 ASP cc_start: 0.8942 (t0) cc_final: 0.8380 (p0) REVERT: D 486 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.8938 (tt) REVERT: A 268 LEU cc_start: 0.9127 (tp) cc_final: 0.8878 (tp) REVERT: A 397 ASP cc_start: 0.9019 (p0) cc_final: 0.8750 (p0) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.2276 time to fit residues: 49.9811 Evaluate side-chains 151 residues out of total 1270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 296 LEU 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 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 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 285 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 434 ILE 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 100 optimal weight: 0.0670 chunk 156 optimal weight: 1.9990 chunk 78 optimal weight: 0.0270 chunk 52 optimal weight: 0.4980 chunk 57 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ** 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 = 0.3147 r_free = 0.3147 target = 0.066486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.057003 restraints weight = 55888.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058673 restraints weight = 30159.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.059768 restraints weight = 19567.763| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12643 Z= 0.113 Angle : 0.655 12.792 17275 Z= 0.318 Chirality : 0.042 0.174 2010 Planarity : 0.004 0.047 2240 Dihedral : 5.860 83.606 1862 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.20 % Allowed : 21.57 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.22), residues: 1616 helix: 0.70 (0.20), residues: 761 sheet: -1.54 (0.52), residues: 114 loop : -1.94 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 285 HIS 0.003 0.001 HIS B 55 PHE 0.011 0.001 PHE D 487 TYR 0.019 0.001 TYR B 69 ARG 0.004 0.000 ARG B 304 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 531) hydrogen bonds : angle 4.42710 ( 1527) covalent geometry : bond 0.00249 (12643) covalent geometry : angle 0.65454 (17275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3808.95 seconds wall clock time: 70 minutes 11.29 seconds (4211.29 seconds total)