Starting phenix.real_space_refine on Thu Sep 18 06:54:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834.map" model { file = "/net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9is8_60834/09_2025/9is8_60834_neut.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 4 5.49 5 S 76 5.16 5 C 9670 2.51 5 N 2459 2.21 5 O 2597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14809 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3599 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "B" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3861 Classifications: {'peptide': 474} Link IDs: {'PTRANS': 15, 'TRANS': 458} Chain: "C" Number of atoms: 3599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3599 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 14, 'TRANS': 426} Chain: "D" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3591 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 14, 'TRANS': 425} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' K': 2, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {' K': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 3.75, per 1000 atoms: 0.25 Number of scatterers: 14809 At special positions: 0 Unit cell: (124.967, 105.575, 105.575, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 76 16.00 P 4 15.00 O 2597 8.00 N 2459 7.00 C 9670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 686.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 12 sheets defined 63.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 65 through 82 Proline residue: A 76 - end of helix Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.532A pdb=" N ILE A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.756A pdb=" N ASP A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.863A pdb=" N THR A 143 " --> pdb=" O ASP A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.463A pdb=" N ARG A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.690A pdb=" N ARG A 167 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 180 removed outlier: 3.638A pdb=" N LYS A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 191 Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.664A pdb=" N ALA A 213 " --> pdb=" O TYR A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 235 through 252 Processing helix chain 'A' and resid 263 through 291 removed outlier: 3.510A pdb=" N GLY A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.600A pdb=" N ASP A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 removed outlier: 3.672A pdb=" N HIS A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 347 Processing helix chain 'A' and resid 351 through 364 removed outlier: 4.790A pdb=" N SER A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 358 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 359 " --> pdb=" O ARG A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.902A pdb=" N ASP A 368 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.924A pdb=" N ARG A 374 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.711A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 446 removed outlier: 3.535A pdb=" N VAL A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 474 Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.737A pdb=" N THR A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 60 removed outlier: 4.456A pdb=" N SER B 58 " --> pdb=" O SER B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 111 removed outlier: 3.852A pdb=" N VAL B 94 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 99 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TRP B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU B 111 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 122 removed outlier: 4.147A pdb=" N THR B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 136 removed outlier: 3.690A pdb=" N ILE B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 162 Processing helix chain 'B' and resid 163 through 173 removed outlier: 4.319A pdb=" N VAL B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 192 through 202 removed outlier: 3.708A pdb=" N ASN B 197 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 removed outlier: 4.316A pdb=" N VAL B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 251 removed outlier: 3.533A pdb=" N ARG B 226 " --> pdb=" O TYR B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.626A pdb=" N THR B 258 " --> pdb=" O PRO B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 288 removed outlier: 3.585A pdb=" N GLY B 275 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 332 removed outlier: 3.910A pdb=" N ILE B 314 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 352 removed outlier: 3.725A pdb=" N ALA B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 376 removed outlier: 3.707A pdb=" N LEU B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B 368 " --> pdb=" O ALA B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 403 removed outlier: 4.403A pdb=" N SER B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ILE B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'B' and resid 474 through 481 removed outlier: 3.968A pdb=" N VAL B 478 " --> pdb=" O GLY B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 511 Processing helix chain 'B' and resid 517 through 526 removed outlier: 3.538A pdb=" N TYR B 526 " --> pdb=" O ASN B 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 62 Processing helix chain 'C' and resid 63 through 82 removed outlier: 3.517A pdb=" N LEU C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) Proline residue: C 76 - end of helix Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 91 through 107 removed outlier: 3.665A pdb=" N ASN C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP C 103 " --> pdb=" O PHE C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 136 through 142 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.686A pdb=" N ALA C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 3.506A pdb=" N ASN C 161 " --> pdb=" O TYR C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 167 Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 186 through 215 removed outlier: 4.624A pdb=" N ALA C 192 " --> pdb=" O TRP C 188 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 213 " --> pdb=" O TYR C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.614A pdb=" N GLU C 233 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU C 234 " --> pdb=" O PHE C 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 230 through 234' Processing helix chain 'C' and resid 235 through 252 Processing helix chain 'C' and resid 263 through 296 removed outlier: 3.535A pdb=" N GLY C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 315 removed outlier: 4.781A pdb=" N PHE C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 336 removed outlier: 3.818A pdb=" N LEU C 327 " --> pdb=" O GLN C 323 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 Processing helix chain 'C' and resid 354 through 368 removed outlier: 3.854A pdb=" N SER C 359 " --> pdb=" O ARG C 355 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 363 " --> pdb=" O SER C 359 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 364 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER C 365 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 387 removed outlier: 3.661A pdb=" N SER C 386 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 467 through 475 removed outlier: 3.526A pdb=" N GLN C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.914A pdb=" N HIS C 491 " --> pdb=" O ASN C 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 81 removed outlier: 3.752A pdb=" N VAL D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Proline residue: D 76 - end of helix Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 91 through 107 removed outlier: 3.640A pdb=" N ILE D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 136 removed outlier: 3.975A pdb=" N PHE D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 142 Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.550A pdb=" N ALA D 149 " --> pdb=" O PRO D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 161 removed outlier: 3.595A pdb=" N ASN D 161 " --> pdb=" O TYR D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 167 Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 185 through 215 Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.559A pdb=" N LYS D 221 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR D 222 " --> pdb=" O PRO D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 263 through 296 removed outlier: 3.652A pdb=" N GLY D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR D 296 " --> pdb=" O VAL D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 314 removed outlier: 4.012A pdb=" N ALA D 309 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER D 310 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 342 removed outlier: 3.898A pdb=" N GLN D 325 " --> pdb=" O ARG D 321 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU D 327 " --> pdb=" O GLN D 323 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 338 " --> pdb=" O TYR D 334 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY D 340 " --> pdb=" O THR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 349 Processing helix chain 'D' and resid 354 through 363 removed outlier: 3.855A pdb=" N PHE D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 369 Processing helix chain 'D' and resid 378 through 387 Processing helix chain 'D' and resid 440 through 445 removed outlier: 4.012A pdb=" N VAL D 444 " --> pdb=" O GLY D 440 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 440 through 445' Processing helix chain 'D' and resid 467 through 476 removed outlier: 4.293A pdb=" N ALA D 476 " --> pdb=" O ASN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 393 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 400 removed outlier: 7.007A pdb=" N ASP A 398 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR A 456 " --> pdb=" O ASP A 398 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 400 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 431 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASP A 421 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE A 429 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 141 through 142 removed outlier: 3.737A pdb=" N TYR B 141 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 424 through 427 removed outlier: 3.511A pdb=" N ILE B 446 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 471 " --> pdb=" O ILE B 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 432 through 434 removed outlier: 6.313A pdb=" N GLU B 432 " --> pdb=" O THR B 490 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR B 490 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE B 434 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA B 465 " --> pdb=" O ILE B 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113 Processing sheet with id=AA7, first strand: chain 'C' and resid 389 through 393 removed outlier: 3.514A pdb=" N MET C 465 " --> pdb=" O PHE C 409 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 409 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C 410 " --> pdb=" O ILE C 439 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 397 through 398 removed outlier: 3.679A pdb=" N GLU C 397 " --> pdb=" O THR C 456 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG C 455 " --> pdb=" O ASP C 418 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C 418 " --> pdb=" O ARG C 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB1, first strand: chain 'D' and resid 113 through 114 removed outlier: 4.075A pdb=" N LEU D 119 " --> pdb=" O ASP D 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 389 through 391 Processing sheet with id=AB3, first strand: chain 'D' and resid 427 through 431 removed outlier: 6.890A pdb=" N LEU D 419 " --> pdb=" O VAL D 430 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2275 1.26 - 1.40: 4074 1.40 - 1.53: 8363 1.53 - 1.67: 328 1.67 - 1.81: 129 Bond restraints: 15169 Sorted by residual: bond pdb=" C ARG A 458 " pdb=" O ARG A 458 " ideal model delta sigma weight residual 1.235 1.122 0.113 1.08e-02 8.57e+03 1.10e+02 bond pdb="C312 POV A 901 " pdb="C313 POV A 901 " ideal model delta sigma weight residual 1.523 1.342 0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" C GLU B 215 " pdb=" O GLU B 215 " ideal model delta sigma weight residual 1.235 1.133 0.102 1.38e-02 5.25e+03 5.41e+01 bond pdb=" C ASP B 217 " pdb=" O ASP B 217 " ideal model delta sigma weight residual 1.235 1.147 0.088 1.20e-02 6.94e+03 5.38e+01 bond pdb=" C THR D 250 " pdb=" O THR D 250 " ideal model delta sigma weight residual 1.235 1.136 0.099 1.43e-02 4.89e+03 4.80e+01 ... (remaining 15164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 20362 3.91 - 7.83: 174 7.83 - 11.74: 17 11.74 - 15.65: 4 15.65 - 19.57: 2 Bond angle restraints: 20559 Sorted by residual: angle pdb=" C TYR B 222 " pdb=" CA TYR B 222 " pdb=" CB TYR B 222 " ideal model delta sigma weight residual 110.90 95.68 15.22 1.58e+00 4.01e-01 9.28e+01 angle pdb=" C GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " ideal model delta sigma weight residual 110.90 96.27 14.63 1.58e+00 4.01e-01 8.57e+01 angle pdb=" CA THR D 250 " pdb=" CB THR D 250 " pdb=" OG1 THR D 250 " ideal model delta sigma weight residual 109.60 96.70 12.90 1.50e+00 4.44e-01 7.39e+01 angle pdb=" N LYS B 216 " pdb=" CA LYS B 216 " pdb=" C LYS B 216 " ideal model delta sigma weight residual 113.88 105.02 8.86 1.23e+00 6.61e-01 5.19e+01 angle pdb=" CA ASP B 217 " pdb=" C ASP B 217 " pdb=" O ASP B 217 " ideal model delta sigma weight residual 120.81 113.23 7.58 1.15e+00 7.56e-01 4.34e+01 ... (remaining 20554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.33: 8249 27.33 - 54.66: 658 54.66 - 81.99: 58 81.99 - 109.32: 9 109.32 - 136.65: 1 Dihedral angle restraints: 8975 sinusoidal: 3669 harmonic: 5306 Sorted by residual: dihedral pdb=" CD ARG C 303 " pdb=" NE ARG C 303 " pdb=" CZ ARG C 303 " pdb=" NH1 ARG C 303 " ideal model delta sinusoidal sigma weight residual 0.00 -83.02 83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" C GLU A 78 " pdb=" N GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " ideal model delta harmonic sigma weight residual -122.60 -102.74 -19.86 0 2.50e+00 1.60e-01 6.31e+01 dihedral pdb=" C TYR B 222 " pdb=" N TYR B 222 " pdb=" CA TYR B 222 " pdb=" CB TYR B 222 " ideal model delta harmonic sigma weight residual -122.60 -107.74 -14.86 0 2.50e+00 1.60e-01 3.53e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2099 0.085 - 0.170: 171 0.170 - 0.255: 23 0.255 - 0.340: 10 0.340 - 0.425: 6 Chirality restraints: 2309 Sorted by residual: chirality pdb=" CA GLU A 78 " pdb=" N GLU A 78 " pdb=" C GLU A 78 " pdb=" CB GLU A 78 " both_signs ideal model delta sigma weight residual False 2.51 2.94 -0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CA ARG A 458 " pdb=" N ARG A 458 " pdb=" C ARG A 458 " pdb=" CB ARG A 458 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA ALA B 218 " pdb=" N ALA B 218 " pdb=" C ALA B 218 " pdb=" CB ALA B 218 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 2306 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV B 801 " 0.090 2.00e-02 2.50e+03 2.04e-01 4.14e+02 pdb=" C29 POV B 801 " -0.269 2.00e-02 2.50e+03 pdb="C210 POV B 801 " 0.275 2.00e-02 2.50e+03 pdb="C211 POV B 801 " -0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 303 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG C 303 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG C 303 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 303 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 303 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 901 " -0.116 2.00e-02 2.50e+03 1.16e-01 1.34e+02 pdb=" C29 POV D 901 " 0.117 2.00e-02 2.50e+03 pdb="C210 POV D 901 " 0.115 2.00e-02 2.50e+03 pdb="C211 POV D 901 " -0.115 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 4052 2.78 - 3.37: 16629 3.37 - 3.96: 27169 3.96 - 4.55: 38730 4.55 - 5.14: 57104 Nonbonded interactions: 143684 Sorted by model distance: nonbonded pdb=" O GLY C 425 " pdb=" OG1 THR C 426 " model vdw 2.190 3.040 nonbonded pdb=" O GLY D 481 " pdb=" OG1 THR D 482 " model vdw 2.191 3.040 nonbonded pdb=" O GLN A 383 " pdb=" OG SER A 386 " model vdw 2.199 3.040 nonbonded pdb=" OD1 ASP C 139 " pdb=" NE1 TRP C 166 " model vdw 2.208 3.120 nonbonded pdb=" O VAL A 293 " pdb=" NH1 ARG D 300 " model vdw 2.212 3.120 ... (remaining 143679 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 52 through 491) selection = (chain 'C' and resid 52 through 491) selection = (chain 'D' and resid 52 through 491) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.980 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 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 : 0.010 0.181 15169 Z= 0.521 Angle : 0.988 19.567 20559 Z= 0.592 Chirality : 0.059 0.425 2309 Planarity : 0.012 0.492 2562 Dihedral : 18.278 136.654 5545 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.23 % Favored : 90.66 % Rotamer: Outliers : 10.09 % Allowed : 24.26 % Favored : 65.64 % Cbeta Deviations : 0.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.96 (0.17), residues: 1788 helix: -2.42 (0.13), residues: 1041 sheet: -2.88 (0.41), residues: 112 loop : -2.62 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.015 0.002 TYR D 283 PHE 0.031 0.002 PHE B 63 TRP 0.022 0.002 TRP B 273 HIS 0.009 0.001 HIS B 219 Details of bonding type rmsd covalent geometry : bond 0.00998 (15169) covalent geometry : angle 0.98843 (20559) hydrogen bonds : bond 0.20570 ( 752) hydrogen bonds : angle 7.34958 ( 2130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 278 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7215 (mmtm) cc_final: 0.6752 (mtmt) REVERT: A 93 ASP cc_start: 0.6954 (t0) cc_final: 0.6574 (m-30) REVERT: A 123 ASP cc_start: 0.6246 (t70) cc_final: 0.6033 (t70) REVERT: A 130 LYS cc_start: 0.7265 (tptp) cc_final: 0.6989 (tptt) REVERT: A 137 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7543 (tp) REVERT: A 160 PHE cc_start: 0.7370 (t80) cc_final: 0.7105 (t80) REVERT: A 182 ARG cc_start: 0.6666 (mpt180) cc_final: 0.6243 (mmt-90) REVERT: A 215 ARG cc_start: 0.7024 (mtp85) cc_final: 0.6333 (ptt90) REVERT: A 238 MET cc_start: 0.7060 (tpp) cc_final: 0.6255 (tmm) REVERT: A 298 ARG cc_start: 0.7491 (ptm160) cc_final: 0.6147 (tpt170) REVERT: A 342 GLN cc_start: 0.6357 (tp-100) cc_final: 0.6038 (pp30) REVERT: A 401 LEU cc_start: 0.7628 (pt) cc_final: 0.7261 (tt) REVERT: A 406 PRO cc_start: 0.8548 (Cg_endo) cc_final: 0.8245 (Cg_exo) REVERT: A 423 ASP cc_start: 0.4851 (OUTLIER) cc_final: 0.4649 (p0) REVERT: A 427 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 465 MET cc_start: 0.7165 (ttm) cc_final: 0.6950 (ttm) REVERT: A 485 MET cc_start: 0.7997 (tmm) cc_final: 0.7794 (tmm) REVERT: A 486 ASN cc_start: 0.7217 (m-40) cc_final: 0.6854 (m110) REVERT: B 80 LEU cc_start: 0.7685 (mp) cc_final: 0.7459 (mt) REVERT: B 85 ARG cc_start: 0.7614 (mtp180) cc_final: 0.6638 (ptt90) REVERT: B 91 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7202 (tp) REVERT: B 122 ASP cc_start: 0.7329 (p0) cc_final: 0.6640 (t0) REVERT: B 138 PHE cc_start: 0.7975 (m-80) cc_final: 0.7722 (m-80) REVERT: B 177 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.5924 (tm-30) REVERT: B 180 TYR cc_start: 0.5693 (OUTLIER) cc_final: 0.4439 (m-80) REVERT: B 280 MET cc_start: 0.7902 (mmp) cc_final: 0.7464 (mmp) REVERT: B 285 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7438 (t) REVERT: B 310 MET cc_start: 0.8552 (ptt) cc_final: 0.7664 (ptt) REVERT: B 334 ARG cc_start: 0.7202 (ppt-90) cc_final: 0.5999 (mmp-170) REVERT: B 366 MET cc_start: 0.6731 (pp-130) cc_final: 0.6076 (ppp) REVERT: B 417 GLN cc_start: 0.7281 (mm-40) cc_final: 0.6820 (tt0) REVERT: B 432 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5349 (mt-10) REVERT: B 485 PRO cc_start: 0.7961 (Cg_endo) cc_final: 0.7752 (Cg_exo) REVERT: B 491 ARG cc_start: 0.6554 (ptt-90) cc_final: 0.5631 (ptm-80) REVERT: B 523 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5579 (t80) REVERT: C 84 LYS cc_start: 0.8055 (ptpp) cc_final: 0.7559 (pttm) REVERT: C 89 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7173 (mt) REVERT: C 108 PHE cc_start: 0.6925 (m-10) cc_final: 0.6664 (m-80) REVERT: C 137 LEU cc_start: 0.7312 (pt) cc_final: 0.6709 (mt) REVERT: C 153 SER cc_start: 0.7694 (OUTLIER) cc_final: 0.7468 (p) REVERT: C 177 ARG cc_start: 0.7294 (mtm110) cc_final: 0.7077 (ttm-80) REVERT: C 215 ARG cc_start: 0.6540 (mtm180) cc_final: 0.6201 (mtp180) REVERT: C 244 MET cc_start: 0.8120 (tpt) cc_final: 0.7670 (tpp) REVERT: C 343 GLN cc_start: 0.6809 (mt0) cc_final: 0.6294 (mm-40) REVERT: C 352 LYS cc_start: 0.7008 (tppp) cc_final: 0.6734 (ttpt) REVERT: C 383 GLN cc_start: 0.8142 (tm130) cc_final: 0.7538 (tm-30) REVERT: C 387 GLU cc_start: 0.6678 (tm-30) cc_final: 0.6346 (pp20) REVERT: C 403 ASN cc_start: 0.7707 (m110) cc_final: 0.7138 (m-40) REVERT: C 462 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5473 (mp) REVERT: C 467 ARG cc_start: 0.6904 (ttp80) cc_final: 0.6680 (ttp80) REVERT: D 56 LYS cc_start: 0.5315 (pptt) cc_final: 0.4972 (pttp) REVERT: D 215 ARG cc_start: 0.6828 (mmt90) cc_final: 0.6444 (mmp80) REVERT: D 252 THR cc_start: 0.8450 (m) cc_final: 0.8130 (p) REVERT: D 288 MET cc_start: 0.8200 (mmt) cc_final: 0.7992 (mmm) REVERT: D 306 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6829 (mp) REVERT: D 363 PHE cc_start: 0.6518 (OUTLIER) cc_final: 0.6309 (p90) REVERT: D 379 ASP cc_start: 0.5184 (OUTLIER) cc_final: 0.4599 (p0) REVERT: D 408 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.4684 (p0) REVERT: D 465 MET cc_start: 0.4808 (ttm) cc_final: 0.4319 (ttm) REVERT: D 485 MET cc_start: 0.5635 (mpp) cc_final: 0.4959 (ptp) REVERT: D 487 ASN cc_start: 0.4927 (OUTLIER) cc_final: 0.4719 (t0) outliers start: 161 outliers final: 53 residues processed: 417 average time/residue: 0.5852 time to fit residues: 268.9848 Evaluate side-chains 285 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 423 ASP Chi-restraints excluded: chain A residue 427 GLU Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 458 ARG Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 66 PHE Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 84 ARG Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 219 HIS Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 90 SER Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 458 ARG Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 461 GLN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 468 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 379 ASP Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 487 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 323 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 251 HIS B 352 ASN B 421 GLN B 462 GLN B 495 GLN ** B 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 ASN C 94 ASN C 185 ASN C 216 ASN C 227 ASN C 290 ASN C 301 ASN C 307 GLN C 323 GLN C 342 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN C 378 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN C 450 GLN D 185 ASN D 218 ASN D 294 HIS D 314 HIS D 316 ASN D 487 ASN D 490 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.226827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178001 restraints weight = 15105.392| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.63 r_work: 0.3396 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15169 Z= 0.155 Angle : 0.667 8.532 20559 Z= 0.355 Chirality : 0.044 0.217 2309 Planarity : 0.005 0.045 2562 Dihedral : 12.283 118.240 2242 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.71 % Allowed : 25.89 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.19), residues: 1788 helix: -0.92 (0.15), residues: 1053 sheet: -2.46 (0.40), residues: 121 loop : -1.91 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 303 TYR 0.021 0.002 TYR A 157 PHE 0.014 0.001 PHE B 110 TRP 0.016 0.002 TRP B 273 HIS 0.007 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00333 (15169) covalent geometry : angle 0.66662 (20559) hydrogen bonds : bond 0.04938 ( 752) hydrogen bonds : angle 4.68930 ( 2130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 236 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6855 (mtmt) REVERT: A 78 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7903 (tp30) REVERT: A 93 ASP cc_start: 0.7406 (t0) cc_final: 0.7171 (m-30) REVERT: A 123 ASP cc_start: 0.6513 (t70) cc_final: 0.6205 (t0) REVERT: A 130 LYS cc_start: 0.7307 (tptp) cc_final: 0.7072 (tptt) REVERT: A 215 ARG cc_start: 0.7761 (mtp85) cc_final: 0.6990 (ptt90) REVERT: A 238 MET cc_start: 0.8449 (tpp) cc_final: 0.7785 (tmm) REVERT: A 284 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8738 (mp) REVERT: A 298 ARG cc_start: 0.7614 (ptm160) cc_final: 0.6557 (tpt170) REVERT: A 321 ARG cc_start: 0.7183 (tmm160) cc_final: 0.6769 (ttp-170) REVERT: A 401 LEU cc_start: 0.7926 (pt) cc_final: 0.7518 (tt) REVERT: A 465 MET cc_start: 0.7569 (ttm) cc_final: 0.7287 (tpp) REVERT: A 486 ASN cc_start: 0.7781 (m-40) cc_final: 0.7398 (m110) REVERT: A 488 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6376 (mm) REVERT: B 85 ARG cc_start: 0.7899 (mtp180) cc_final: 0.7027 (tmt-80) REVERT: B 122 ASP cc_start: 0.7798 (p0) cc_final: 0.7278 (t0) REVERT: B 177 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6085 (tm-30) REVERT: B 228 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8154 (mt) REVERT: B 230 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 280 MET cc_start: 0.9161 (mmp) cc_final: 0.8622 (mmp) REVERT: B 307 MET cc_start: 0.9034 (ptt) cc_final: 0.8727 (ptt) REVERT: B 310 MET cc_start: 0.8948 (ptt) cc_final: 0.8423 (ptt) REVERT: B 334 ARG cc_start: 0.7380 (ppt-90) cc_final: 0.6294 (mmp-170) REVERT: B 366 MET cc_start: 0.7231 (pp-130) cc_final: 0.6816 (ppp) REVERT: B 403 GLU cc_start: 0.6996 (pp20) cc_final: 0.6452 (pp20) REVERT: B 417 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6914 (tt0) REVERT: B 432 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5789 (mt-10) REVERT: B 491 ARG cc_start: 0.7050 (ptt-90) cc_final: 0.6197 (ptm-80) REVERT: B 498 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7086 (ttm170) REVERT: C 84 LYS cc_start: 0.8458 (ptpp) cc_final: 0.8124 (pttm) REVERT: C 108 PHE cc_start: 0.7022 (m-10) cc_final: 0.6809 (m-80) REVERT: C 137 LEU cc_start: 0.7557 (pt) cc_final: 0.7216 (mt) REVERT: C 177 ARG cc_start: 0.7545 (mtm110) cc_final: 0.7302 (ttm-80) REVERT: C 215 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7415 (mtp180) REVERT: C 352 LYS cc_start: 0.7288 (tppp) cc_final: 0.6849 (ttpt) REVERT: C 360 HIS cc_start: 0.8169 (t70) cc_final: 0.7837 (t-90) REVERT: C 369 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.7065 (mptt) REVERT: C 383 GLN cc_start: 0.8137 (tm130) cc_final: 0.7639 (tm-30) REVERT: C 387 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6405 (pp20) REVERT: D 56 LYS cc_start: 0.5914 (pptt) cc_final: 0.4942 (mttm) REVERT: D 84 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.7930 (pttm) REVERT: D 150 MET cc_start: 0.7825 (mmm) cc_final: 0.7443 (mmm) REVERT: D 177 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7507 (ttm-80) REVERT: D 215 ARG cc_start: 0.7889 (mmt90) cc_final: 0.7575 (mmp80) REVERT: D 326 MET cc_start: 0.6229 (OUTLIER) cc_final: 0.5736 (ptt) REVERT: D 341 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7720 (tp) REVERT: D 450 GLN cc_start: 0.6622 (tp40) cc_final: 0.6307 (mm-40) REVERT: D 485 MET cc_start: 0.5263 (mpp) cc_final: 0.4545 (ptm) outliers start: 123 outliers final: 32 residues processed: 332 average time/residue: 0.6053 time to fit residues: 221.4814 Evaluate side-chains 252 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 177 GLN Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 134 optimal weight: 8.9990 chunk 141 optimal weight: 0.0060 chunk 85 optimal weight: 9.9990 chunk 174 optimal weight: 30.0000 chunk 59 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 125 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 overall best weight: 2.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 395 HIS ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 402 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 = 0.4367 r_free = 0.4367 target = 0.221740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.170312 restraints weight = 15241.083| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.89 r_work: 0.3275 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15169 Z= 0.196 Angle : 0.665 10.875 20559 Z= 0.351 Chirality : 0.046 0.249 2309 Planarity : 0.004 0.046 2562 Dihedral : 10.966 108.829 2158 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 6.52 % Allowed : 26.52 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.19), residues: 1788 helix: -0.57 (0.16), residues: 1049 sheet: -2.37 (0.41), residues: 119 loop : -1.70 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 467 TYR 0.021 0.002 TYR A 157 PHE 0.020 0.002 PHE B 110 TRP 0.021 0.002 TRP D 246 HIS 0.005 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00471 (15169) covalent geometry : angle 0.66479 (20559) hydrogen bonds : bond 0.05002 ( 752) hydrogen bonds : angle 4.45300 ( 2130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 212 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.6572 (t80) REVERT: A 56 LYS cc_start: 0.7357 (mmtm) cc_final: 0.6813 (mtmt) REVERT: A 93 ASP cc_start: 0.7470 (t0) cc_final: 0.7216 (m-30) REVERT: A 123 ASP cc_start: 0.6528 (t70) cc_final: 0.6145 (t0) REVERT: A 130 LYS cc_start: 0.7355 (tptp) cc_final: 0.7104 (tptt) REVERT: A 215 ARG cc_start: 0.7740 (mtp85) cc_final: 0.6985 (ptt90) REVERT: A 238 MET cc_start: 0.8542 (tpp) cc_final: 0.7819 (tmm) REVERT: A 284 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8618 (mp) REVERT: A 298 ARG cc_start: 0.7645 (ptm160) cc_final: 0.6548 (tpt170) REVERT: A 321 ARG cc_start: 0.7109 (tmm160) cc_final: 0.6901 (ttt-90) REVERT: A 401 LEU cc_start: 0.7965 (pt) cc_final: 0.7540 (tt) REVERT: A 488 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6327 (mm) REVERT: B 85 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7074 (tmt-80) REVERT: B 122 ASP cc_start: 0.7877 (p0) cc_final: 0.7286 (t0) REVERT: B 123 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 177 GLN cc_start: 0.6951 (mt0) cc_final: 0.6287 (mm-40) REVERT: B 180 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5215 (t80) REVERT: B 230 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7936 (mt) REVERT: B 307 MET cc_start: 0.9052 (ptt) cc_final: 0.8787 (ptt) REVERT: B 310 MET cc_start: 0.8956 (ptt) cc_final: 0.8366 (ptt) REVERT: B 334 ARG cc_start: 0.7411 (ppt-90) cc_final: 0.6271 (mmp-170) REVERT: B 362 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: B 366 MET cc_start: 0.7292 (pp-130) cc_final: 0.6868 (ppp) REVERT: B 403 GLU cc_start: 0.7101 (pp20) cc_final: 0.6582 (pp20) REVERT: B 417 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6773 (tt0) REVERT: B 432 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5879 (mt-10) REVERT: B 491 ARG cc_start: 0.6932 (ptt-90) cc_final: 0.6134 (ptm-80) REVERT: B 498 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7191 (ttm170) REVERT: C 83 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8136 (mmm-85) REVERT: C 84 LYS cc_start: 0.8514 (ptpp) cc_final: 0.8110 (pttm) REVERT: C 177 ARG cc_start: 0.7538 (mtm110) cc_final: 0.7216 (ttm-80) REVERT: C 215 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7501 (mtp180) REVERT: C 326 MET cc_start: 0.8288 (ttm) cc_final: 0.7677 (ttp) REVERT: C 352 LYS cc_start: 0.7029 (tppp) cc_final: 0.6628 (ttpt) REVERT: C 383 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7603 (tm-30) REVERT: C 384 LEU cc_start: 0.6683 (OUTLIER) cc_final: 0.6162 (tt) REVERT: C 387 GLU cc_start: 0.6583 (tm-30) cc_final: 0.6329 (pp20) REVERT: C 439 ILE cc_start: 0.8084 (OUTLIER) cc_final: 0.7748 (pp) REVERT: D 56 LYS cc_start: 0.5877 (pptt) cc_final: 0.4839 (mttm) REVERT: D 152 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7697 (mp) REVERT: D 155 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7387 (pt0) REVERT: D 177 ARG cc_start: 0.8101 (ttp80) cc_final: 0.7542 (ttm-80) REVERT: D 215 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7570 (mmp80) REVERT: D 350 LEU cc_start: 0.5169 (OUTLIER) cc_final: 0.4733 (tp) REVERT: D 450 GLN cc_start: 0.6522 (tp40) cc_final: 0.6311 (mm-40) REVERT: D 485 MET cc_start: 0.5320 (mpp) cc_final: 0.4564 (ptm) outliers start: 104 outliers final: 43 residues processed: 289 average time/residue: 0.5940 time to fit residues: 188.8973 Evaluate side-chains 252 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 453 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 306 ILE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 127 optimal weight: 6.9990 chunk 158 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 168 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 486 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.225501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176723 restraints weight = 15060.598| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 1.59 r_work: 0.3335 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15169 Z= 0.188 Angle : 0.649 10.407 20559 Z= 0.340 Chirality : 0.045 0.246 2309 Planarity : 0.004 0.048 2562 Dihedral : 10.418 98.472 2149 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 7.08 % Allowed : 25.33 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.19), residues: 1788 helix: -0.41 (0.16), residues: 1061 sheet: -2.17 (0.42), residues: 119 loop : -1.49 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 467 TYR 0.020 0.002 TYR A 157 PHE 0.021 0.002 PHE B 110 TRP 0.020 0.002 TRP D 246 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00449 (15169) covalent geometry : angle 0.64870 (20559) hydrogen bonds : bond 0.04691 ( 752) hydrogen bonds : angle 4.25620 ( 2130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 208 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6573 (t80) REVERT: A 56 LYS cc_start: 0.7338 (mmtm) cc_final: 0.6773 (mtmt) REVERT: A 93 ASP cc_start: 0.7377 (t0) cc_final: 0.7123 (m-30) REVERT: A 123 ASP cc_start: 0.6493 (t70) cc_final: 0.6080 (t0) REVERT: A 238 MET cc_start: 0.8433 (tpp) cc_final: 0.7848 (tmm) REVERT: A 284 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 298 ARG cc_start: 0.7651 (ptm160) cc_final: 0.6707 (ttp80) REVERT: A 401 LEU cc_start: 0.7928 (pt) cc_final: 0.7525 (tp) REVERT: A 431 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.7004 (ttm-80) REVERT: A 465 MET cc_start: 0.7872 (ttm) cc_final: 0.7544 (ttp) REVERT: B 85 ARG cc_start: 0.7892 (mtp180) cc_final: 0.7085 (tmt-80) REVERT: B 122 ASP cc_start: 0.7940 (p0) cc_final: 0.7714 (p0) REVERT: B 177 GLN cc_start: 0.7123 (mt0) cc_final: 0.6249 (mm-40) REVERT: B 228 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7954 (mt) REVERT: B 230 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7874 (mt) REVERT: B 285 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8250 (t) REVERT: B 307 MET cc_start: 0.9058 (ptt) cc_final: 0.8790 (ptt) REVERT: B 334 ARG cc_start: 0.7436 (ppt-90) cc_final: 0.6290 (mmp-170) REVERT: B 362 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: B 366 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6859 (ppp) REVERT: B 403 GLU cc_start: 0.7054 (pp20) cc_final: 0.6526 (pp20) REVERT: B 417 GLN cc_start: 0.7385 (mm-40) cc_final: 0.6817 (tt0) REVERT: B 491 ARG cc_start: 0.6987 (ptt-90) cc_final: 0.6125 (ptm-80) REVERT: B 498 ARG cc_start: 0.7581 (ttm170) cc_final: 0.7203 (ttm170) REVERT: C 83 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8091 (mmm-85) REVERT: C 84 LYS cc_start: 0.8476 (ptpp) cc_final: 0.8094 (pttm) REVERT: C 162 MET cc_start: 0.8781 (tpt) cc_final: 0.8505 (tpt) REVERT: C 167 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (mtt180) REVERT: C 177 ARG cc_start: 0.7508 (mtm110) cc_final: 0.7230 (ttm-80) REVERT: C 215 ARG cc_start: 0.7799 (mtm180) cc_final: 0.7092 (mmt90) REVERT: C 339 GLU cc_start: 0.7518 (tt0) cc_final: 0.7285 (mt-10) REVERT: C 352 LYS cc_start: 0.6986 (tppp) cc_final: 0.6592 (ttpt) REVERT: C 369 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6913 (ttpt) REVERT: C 383 GLN cc_start: 0.8132 (tm-30) cc_final: 0.7576 (tm-30) REVERT: C 384 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6259 (tt) REVERT: C 451 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7521 (tt) REVERT: D 84 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8188 (pttm) REVERT: D 155 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7414 (pt0) REVERT: D 177 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7533 (ttm-80) REVERT: D 215 ARG cc_start: 0.7834 (mmt90) cc_final: 0.7559 (mmp80) REVERT: D 350 LEU cc_start: 0.5201 (OUTLIER) cc_final: 0.4730 (tp) REVERT: D 355 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6895 (mtm-85) REVERT: D 485 MET cc_start: 0.5172 (mpp) cc_final: 0.4434 (ptm) outliers start: 113 outliers final: 48 residues processed: 297 average time/residue: 0.5762 time to fit residues: 188.7081 Evaluate side-chains 259 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 194 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 167 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 147 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 167 optimal weight: 20.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN C 161 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.226329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.183207 restraints weight = 15034.390| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 1.41 r_work: 0.3391 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15169 Z= 0.159 Angle : 0.618 9.460 20559 Z= 0.324 Chirality : 0.043 0.207 2309 Planarity : 0.004 0.047 2562 Dihedral : 9.824 93.155 2137 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.71 % Allowed : 25.83 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.20), residues: 1788 helix: -0.20 (0.16), residues: 1065 sheet: -1.85 (0.44), residues: 112 loop : -1.45 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 467 TYR 0.021 0.002 TYR A 157 PHE 0.020 0.002 PHE C 187 TRP 0.018 0.002 TRP D 246 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd covalent geometry : bond 0.00375 (15169) covalent geometry : angle 0.61832 (20559) hydrogen bonds : bond 0.04384 ( 752) hydrogen bonds : angle 4.12289 ( 2130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 198 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.6522 (t80) REVERT: A 56 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6694 (mtmt) REVERT: A 93 ASP cc_start: 0.7287 (t0) cc_final: 0.7067 (m-30) REVERT: A 123 ASP cc_start: 0.6528 (t70) cc_final: 0.6133 (t0) REVERT: A 238 MET cc_start: 0.8375 (tpp) cc_final: 0.7868 (tmm) REVERT: A 284 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8583 (mp) REVERT: A 292 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8419 (t) REVERT: A 298 ARG cc_start: 0.7648 (ptm160) cc_final: 0.6707 (ttp80) REVERT: A 401 LEU cc_start: 0.7903 (pt) cc_final: 0.7497 (tp) REVERT: A 431 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6849 (ttm-80) REVERT: A 465 MET cc_start: 0.7724 (ttm) cc_final: 0.7441 (ttp) REVERT: A 486 ASN cc_start: 0.7326 (m-40) cc_final: 0.7024 (m110) REVERT: B 85 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7088 (tmt-80) REVERT: B 122 ASP cc_start: 0.7920 (p0) cc_final: 0.7666 (p0) REVERT: B 177 GLN cc_start: 0.7312 (mt0) cc_final: 0.6542 (mm-40) REVERT: B 228 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 307 MET cc_start: 0.9000 (ptt) cc_final: 0.8708 (ptt) REVERT: B 310 MET cc_start: 0.8971 (ptt) cc_final: 0.8472 (ptt) REVERT: B 334 ARG cc_start: 0.7453 (ppt-90) cc_final: 0.6402 (mmp-170) REVERT: B 362 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: B 366 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6831 (ppp) REVERT: B 394 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6599 (tm-30) REVERT: B 417 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6795 (tt0) REVERT: B 491 ARG cc_start: 0.6989 (ptt-90) cc_final: 0.6139 (ptm-80) REVERT: B 498 ARG cc_start: 0.7602 (ttm170) cc_final: 0.7246 (ttm170) REVERT: C 83 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8047 (mmm-85) REVERT: C 84 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8107 (pttm) REVERT: C 162 MET cc_start: 0.8753 (tpt) cc_final: 0.8534 (tpt) REVERT: C 177 ARG cc_start: 0.7565 (mtm110) cc_final: 0.7282 (ttm-80) REVERT: C 215 ARG cc_start: 0.7780 (mtm180) cc_final: 0.7058 (mmt90) REVERT: C 352 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6590 (ttpt) REVERT: C 365 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7879 (t) REVERT: C 383 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7513 (tm-30) REVERT: C 384 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6303 (tp) REVERT: C 388 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6413 (mtt) REVERT: C 412 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7551 (mp) REVERT: C 439 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7850 (pp) REVERT: C 451 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7475 (tp) REVERT: C 465 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7391 (tpt) REVERT: D 84 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8142 (pttm) REVERT: D 155 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7344 (pt0) REVERT: D 177 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7473 (ttm-80) REVERT: D 215 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7566 (mmp80) REVERT: D 350 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4627 (tp) REVERT: D 355 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6909 (mtm-85) REVERT: D 465 MET cc_start: 0.6947 (ttm) cc_final: 0.6610 (ttm) REVERT: D 485 MET cc_start: 0.5111 (mpp) cc_final: 0.4408 (ptm) outliers start: 107 outliers final: 41 residues processed: 280 average time/residue: 0.6195 time to fit residues: 190.3524 Evaluate side-chains 253 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 448 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 366 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 167 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.224648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.173371 restraints weight = 15077.572| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.69 r_work: 0.3369 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15169 Z= 0.123 Angle : 0.575 9.268 20559 Z= 0.302 Chirality : 0.041 0.175 2309 Planarity : 0.004 0.045 2562 Dihedral : 9.487 89.459 2134 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 5.52 % Allowed : 26.27 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.20), residues: 1788 helix: 0.08 (0.16), residues: 1071 sheet: -1.74 (0.45), residues: 112 loop : -1.28 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 467 TYR 0.021 0.001 TYR A 157 PHE 0.022 0.001 PHE C 187 TRP 0.014 0.002 TRP D 246 HIS 0.009 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00279 (15169) covalent geometry : angle 0.57526 (20559) hydrogen bonds : bond 0.03922 ( 752) hydrogen bonds : angle 3.97059 ( 2130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 204 time to evaluate : 0.447 Fit side-chains REVERT: A 53 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.6429 (t80) REVERT: A 56 LYS cc_start: 0.7261 (mmtm) cc_final: 0.6682 (mtmt) REVERT: A 93 ASP cc_start: 0.7336 (t0) cc_final: 0.7094 (m-30) REVERT: A 123 ASP cc_start: 0.6509 (t70) cc_final: 0.6112 (t0) REVERT: A 137 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7851 (tm) REVERT: A 146 SER cc_start: 0.8141 (OUTLIER) cc_final: 0.7569 (m) REVERT: A 238 MET cc_start: 0.8372 (tpp) cc_final: 0.7861 (tmm) REVERT: A 292 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8218 (t) REVERT: A 298 ARG cc_start: 0.7671 (ptm160) cc_final: 0.6700 (ttp80) REVERT: A 401 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 431 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6846 (ttm-80) REVERT: A 465 MET cc_start: 0.7740 (ttm) cc_final: 0.7524 (ttp) REVERT: A 486 ASN cc_start: 0.7318 (m-40) cc_final: 0.7039 (m110) REVERT: A 488 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6397 (mm) REVERT: B 85 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7022 (tmt-80) REVERT: B 122 ASP cc_start: 0.7869 (p0) cc_final: 0.7594 (p0) REVERT: B 177 GLN cc_start: 0.7271 (mt0) cc_final: 0.6489 (mm-40) REVERT: B 180 TYR cc_start: 0.5778 (OUTLIER) cc_final: 0.5222 (t80) REVERT: B 228 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7696 (mt) REVERT: B 280 MET cc_start: 0.9072 (mmp) cc_final: 0.8838 (mmp) REVERT: B 307 MET cc_start: 0.8943 (ptt) cc_final: 0.8673 (ptt) REVERT: B 310 MET cc_start: 0.8953 (ptt) cc_final: 0.8449 (ptt) REVERT: B 334 ARG cc_start: 0.7441 (ppt-90) cc_final: 0.6375 (mmp-170) REVERT: B 362 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: B 394 GLN cc_start: 0.7186 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 417 GLN cc_start: 0.7334 (mm-40) cc_final: 0.6788 (tt0) REVERT: B 432 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.5992 (mt-10) REVERT: B 491 ARG cc_start: 0.6761 (ptt-90) cc_final: 0.6062 (ptm-80) REVERT: B 498 ARG cc_start: 0.7560 (ttm170) cc_final: 0.7012 (ttm170) REVERT: C 83 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8015 (mmm-85) REVERT: C 84 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8103 (pttm) REVERT: C 177 ARG cc_start: 0.7494 (mtm110) cc_final: 0.7205 (ttm-80) REVERT: C 215 ARG cc_start: 0.7796 (mtm180) cc_final: 0.7008 (mmt90) REVERT: C 326 MET cc_start: 0.8003 (ttm) cc_final: 0.7524 (ttp) REVERT: C 352 LYS cc_start: 0.6901 (OUTLIER) cc_final: 0.6507 (ttpt) REVERT: C 383 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 387 GLU cc_start: 0.6702 (tp30) cc_final: 0.6491 (tp30) REVERT: C 412 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7331 (mp) REVERT: C 439 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7875 (pp) REVERT: D 84 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8145 (pttm) REVERT: D 155 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7292 (pt0) REVERT: D 177 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7464 (ttm-80) REVERT: D 215 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7506 (mmp80) REVERT: D 350 LEU cc_start: 0.4685 (OUTLIER) cc_final: 0.4160 (tp) REVERT: D 355 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6930 (mtm-85) REVERT: D 485 MET cc_start: 0.5101 (mpp) cc_final: 0.4510 (ptp) outliers start: 88 outliers final: 37 residues processed: 269 average time/residue: 0.6222 time to fit residues: 183.1010 Evaluate side-chains 248 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 394 GLN Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 23 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 177 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 495 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.223497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.171896 restraints weight = 15021.475| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.74 r_work: 0.3310 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15169 Z= 0.159 Angle : 0.610 12.053 20559 Z= 0.318 Chirality : 0.043 0.215 2309 Planarity : 0.004 0.045 2562 Dihedral : 9.301 89.510 2129 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 4.95 % Allowed : 27.40 % Favored : 67.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.20), residues: 1788 helix: 0.06 (0.16), residues: 1076 sheet: -1.71 (0.45), residues: 112 loop : -1.19 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 467 TYR 0.022 0.002 TYR A 157 PHE 0.033 0.002 PHE A 409 TRP 0.018 0.002 TRP D 246 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00378 (15169) covalent geometry : angle 0.61032 (20559) hydrogen bonds : bond 0.04261 ( 752) hydrogen bonds : angle 4.01474 ( 2130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.6532 (t80) REVERT: A 56 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6595 (mtmt) REVERT: A 93 ASP cc_start: 0.7305 (t0) cc_final: 0.7063 (m-30) REVERT: A 123 ASP cc_start: 0.6490 (t70) cc_final: 0.6069 (t0) REVERT: A 146 SER cc_start: 0.8122 (OUTLIER) cc_final: 0.7524 (m) REVERT: A 238 MET cc_start: 0.8409 (tpp) cc_final: 0.7867 (tmm) REVERT: A 292 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8237 (t) REVERT: A 298 ARG cc_start: 0.7508 (ptm160) cc_final: 0.6464 (ttp80) REVERT: A 401 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7548 (tp) REVERT: A 431 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6780 (ttm-80) REVERT: A 465 MET cc_start: 0.7828 (ttm) cc_final: 0.7585 (ttp) REVERT: A 488 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6344 (mm) REVERT: B 85 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7095 (ptt90) REVERT: B 122 ASP cc_start: 0.7761 (p0) cc_final: 0.7504 (p0) REVERT: B 177 GLN cc_start: 0.7276 (mt0) cc_final: 0.6478 (mm-40) REVERT: B 180 TYR cc_start: 0.5673 (OUTLIER) cc_final: 0.5152 (t80) REVERT: B 307 MET cc_start: 0.9031 (ptt) cc_final: 0.8814 (ptt) REVERT: B 310 MET cc_start: 0.9009 (ptt) cc_final: 0.8475 (ptt) REVERT: B 334 ARG cc_start: 0.7463 (ppt-90) cc_final: 0.6304 (mmp-170) REVERT: B 362 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7484 (mtm) REVERT: B 382 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6858 (pm20) REVERT: B 417 GLN cc_start: 0.7366 (mm-40) cc_final: 0.6798 (tt0) REVERT: B 432 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5978 (mt-10) REVERT: B 491 ARG cc_start: 0.6706 (ptt-90) cc_final: 0.5978 (ptm-80) REVERT: B 498 ARG cc_start: 0.7595 (ttm170) cc_final: 0.7216 (ttm170) REVERT: C 83 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8068 (mmm-85) REVERT: C 84 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8091 (pttm) REVERT: C 177 ARG cc_start: 0.7443 (mtm110) cc_final: 0.7153 (ttm-80) REVERT: C 215 ARG cc_start: 0.7833 (mtm180) cc_final: 0.7005 (mmt90) REVERT: C 326 MET cc_start: 0.8102 (ttm) cc_final: 0.7643 (ttp) REVERT: C 352 LYS cc_start: 0.6900 (OUTLIER) cc_final: 0.6508 (ttpt) REVERT: C 383 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7437 (tm-30) REVERT: C 412 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7471 (mp) REVERT: C 421 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6329 (m-30) REVERT: C 439 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7795 (pp) REVERT: C 451 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7383 (tp) REVERT: D 84 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8117 (pttm) REVERT: D 155 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7418 (pt0) REVERT: D 177 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7482 (ttm-80) REVERT: D 215 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7517 (mmp80) REVERT: D 350 LEU cc_start: 0.4749 (OUTLIER) cc_final: 0.4267 (tp) REVERT: D 355 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7021 (mtm-85) REVERT: D 434 LYS cc_start: 0.3656 (OUTLIER) cc_final: 0.3166 (ttpt) REVERT: D 485 MET cc_start: 0.5082 (mpp) cc_final: 0.4441 (ptp) outliers start: 79 outliers final: 41 residues processed: 262 average time/residue: 0.6413 time to fit residues: 184.0589 Evaluate side-chains 254 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 382 GLN Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 421 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 122 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 173 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.228459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.187746 restraints weight = 14984.955| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.40 r_work: 0.3402 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15169 Z= 0.128 Angle : 0.586 12.188 20559 Z= 0.304 Chirality : 0.041 0.183 2309 Planarity : 0.004 0.045 2562 Dihedral : 9.013 89.145 2127 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.58 % Allowed : 27.96 % Favored : 67.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.20), residues: 1788 helix: 0.23 (0.16), residues: 1080 sheet: -1.67 (0.45), residues: 112 loop : -1.20 (0.27), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 467 TYR 0.021 0.001 TYR A 157 PHE 0.032 0.001 PHE A 409 TRP 0.016 0.002 TRP D 246 HIS 0.003 0.001 HIS C 260 Details of bonding type rmsd covalent geometry : bond 0.00295 (15169) covalent geometry : angle 0.58566 (20559) hydrogen bonds : bond 0.03884 ( 752) hydrogen bonds : angle 3.91451 ( 2130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 204 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7643 (OUTLIER) cc_final: 0.6521 (t80) REVERT: A 56 LYS cc_start: 0.7173 (mmtm) cc_final: 0.6535 (mtmt) REVERT: A 93 ASP cc_start: 0.7191 (t0) cc_final: 0.6991 (m-30) REVERT: A 123 ASP cc_start: 0.6477 (t70) cc_final: 0.6109 (t0) REVERT: A 137 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7905 (tm) REVERT: A 146 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7529 (m) REVERT: A 238 MET cc_start: 0.8278 (tpp) cc_final: 0.7826 (tmm) REVERT: A 292 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8198 (t) REVERT: A 298 ARG cc_start: 0.7491 (ptm160) cc_final: 0.6438 (ttp80) REVERT: A 401 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7575 (tp) REVERT: A 431 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6904 (ttm-80) REVERT: A 465 MET cc_start: 0.7819 (ttm) cc_final: 0.7563 (ttp) REVERT: A 488 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.6343 (mm) REVERT: B 75 LYS cc_start: 0.5194 (OUTLIER) cc_final: 0.4591 (tttm) REVERT: B 85 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7088 (ptt90) REVERT: B 122 ASP cc_start: 0.7610 (p0) cc_final: 0.7344 (p0) REVERT: B 177 GLN cc_start: 0.7180 (mt0) cc_final: 0.6505 (mm-40) REVERT: B 180 TYR cc_start: 0.5735 (OUTLIER) cc_final: 0.5208 (t80) REVERT: B 307 MET cc_start: 0.8930 (ptt) cc_final: 0.8654 (ptt) REVERT: B 310 MET cc_start: 0.8979 (ptt) cc_final: 0.8281 (ptt) REVERT: B 334 ARG cc_start: 0.7432 (ppt-90) cc_final: 0.6366 (mmp-170) REVERT: B 362 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7456 (mtm) REVERT: B 417 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6790 (tt0) REVERT: B 432 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5983 (mt-10) REVERT: B 491 ARG cc_start: 0.6775 (ptt-90) cc_final: 0.6079 (ptm-80) REVERT: B 498 ARG cc_start: 0.7566 (ttm170) cc_final: 0.7003 (ttm170) REVERT: C 83 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7971 (mmm-85) REVERT: C 84 LYS cc_start: 0.8449 (ptpp) cc_final: 0.8102 (pttm) REVERT: C 177 ARG cc_start: 0.7447 (mtm110) cc_final: 0.7162 (ttm-80) REVERT: C 215 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6997 (mmt90) REVERT: C 326 MET cc_start: 0.8065 (ttm) cc_final: 0.7649 (ttp) REVERT: C 352 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6371 (ttpt) REVERT: C 383 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 412 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (mp) REVERT: C 439 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7732 (pp) REVERT: C 451 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7377 (tp) REVERT: D 84 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8031 (pttm) REVERT: D 155 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7390 (pt0) REVERT: D 177 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7481 (ttm-80) REVERT: D 215 ARG cc_start: 0.7740 (mmt90) cc_final: 0.7496 (mmp80) REVERT: D 355 ARG cc_start: 0.7270 (OUTLIER) cc_final: 0.7001 (mtm-85) REVERT: D 434 LYS cc_start: 0.3741 (OUTLIER) cc_final: 0.3242 (ttpt) REVERT: D 450 GLN cc_start: 0.6775 (tp40) cc_final: 0.6512 (mm-40) REVERT: D 485 MET cc_start: 0.5142 (mpp) cc_final: 0.4533 (ptp) outliers start: 73 outliers final: 43 residues processed: 263 average time/residue: 0.6469 time to fit residues: 185.8186 Evaluate side-chains 255 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 431 ARG Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 98 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 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 = 0.4423 r_free = 0.4423 target = 0.227923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.187408 restraints weight = 15043.644| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.43 r_work: 0.3482 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15169 Z= 0.139 Angle : 0.597 12.737 20559 Z= 0.309 Chirality : 0.042 0.194 2309 Planarity : 0.004 0.045 2562 Dihedral : 8.956 89.054 2125 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.08 % Allowed : 27.77 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1788 helix: 0.23 (0.16), residues: 1083 sheet: -1.58 (0.45), residues: 112 loop : -1.21 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 467 TYR 0.017 0.001 TYR A 57 PHE 0.033 0.001 PHE A 409 TRP 0.016 0.002 TRP D 246 HIS 0.003 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00324 (15169) covalent geometry : angle 0.59682 (20559) hydrogen bonds : bond 0.04008 ( 752) hydrogen bonds : angle 3.91537 ( 2130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 197 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.6435 (t80) REVERT: A 56 LYS cc_start: 0.7147 (mmtm) cc_final: 0.6540 (mtmt) REVERT: A 123 ASP cc_start: 0.6532 (t70) cc_final: 0.6221 (t0) REVERT: A 137 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7855 (tm) REVERT: A 146 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7519 (m) REVERT: A 180 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7815 (mttp) REVERT: A 238 MET cc_start: 0.8301 (tpp) cc_final: 0.7930 (tmm) REVERT: A 292 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (t) REVERT: A 298 ARG cc_start: 0.7492 (ptm160) cc_final: 0.6435 (ttp80) REVERT: A 401 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7676 (tp) REVERT: A 465 MET cc_start: 0.7819 (ttm) cc_final: 0.7568 (ttp) REVERT: A 485 MET cc_start: 0.7642 (tmm) cc_final: 0.7116 (mmp) REVERT: A 488 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6408 (mm) REVERT: B 75 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4725 (tttm) REVERT: B 85 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7104 (ptt90) REVERT: B 122 ASP cc_start: 0.7609 (p0) cc_final: 0.7334 (p0) REVERT: B 177 GLN cc_start: 0.7131 (mt0) cc_final: 0.6545 (mm-40) REVERT: B 180 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.5325 (t80) REVERT: B 307 MET cc_start: 0.8928 (ptt) cc_final: 0.8622 (ptt) REVERT: B 310 MET cc_start: 0.8984 (ptt) cc_final: 0.8510 (ptt) REVERT: B 334 ARG cc_start: 0.7318 (ppt-90) cc_final: 0.6264 (mmp-170) REVERT: B 417 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6797 (tt0) REVERT: B 432 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6030 (mt-10) REVERT: B 491 ARG cc_start: 0.6970 (ptt-90) cc_final: 0.6295 (ptm-80) REVERT: B 498 ARG cc_start: 0.7718 (ttm170) cc_final: 0.7190 (ttm170) REVERT: C 83 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7986 (mmm-85) REVERT: C 84 LYS cc_start: 0.8437 (ptpp) cc_final: 0.8079 (pttm) REVERT: C 177 ARG cc_start: 0.7569 (mtm110) cc_final: 0.7241 (ttm-80) REVERT: C 215 ARG cc_start: 0.7881 (mtm180) cc_final: 0.7292 (mmp80) REVERT: C 326 MET cc_start: 0.8171 (ttm) cc_final: 0.7756 (ttp) REVERT: C 352 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6708 (ttpt) REVERT: C 383 GLN cc_start: 0.7801 (tm-30) cc_final: 0.7333 (tm-30) REVERT: C 412 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7585 (mp) REVERT: C 439 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7867 (pp) REVERT: C 451 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7407 (tp) REVERT: D 84 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7856 (pttm) REVERT: D 177 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7560 (ttm-80) REVERT: D 339 GLU cc_start: 0.6723 (tm-30) cc_final: 0.6123 (mp0) REVERT: D 355 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.7147 (mtm-85) REVERT: D 434 LYS cc_start: 0.3900 (OUTLIER) cc_final: 0.3341 (ttpt) REVERT: D 450 GLN cc_start: 0.6934 (tp40) cc_final: 0.6635 (mm-40) REVERT: D 485 MET cc_start: 0.4910 (mpp) cc_final: 0.4270 (ptm) outliers start: 81 outliers final: 43 residues processed: 264 average time/residue: 0.6319 time to fit residues: 183.0832 Evaluate side-chains 260 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 16 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 0.0020 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.225667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.174856 restraints weight = 15136.839| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 1.72 r_work: 0.3353 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15169 Z= 0.117 Angle : 0.582 12.200 20559 Z= 0.300 Chirality : 0.041 0.170 2309 Planarity : 0.004 0.044 2562 Dihedral : 8.765 89.439 2125 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.64 % Allowed : 29.22 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.20), residues: 1788 helix: 0.41 (0.16), residues: 1087 sheet: -1.54 (0.45), residues: 112 loop : -1.27 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 467 TYR 0.023 0.001 TYR A 157 PHE 0.033 0.001 PHE A 409 TRP 0.014 0.002 TRP A 135 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00266 (15169) covalent geometry : angle 0.58182 (20559) hydrogen bonds : bond 0.03666 ( 752) hydrogen bonds : angle 3.84180 ( 2130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3576 Ramachandran restraints generated. 1788 Oldfield, 0 Emsley, 1788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6437 (t80) REVERT: A 56 LYS cc_start: 0.7189 (mmtm) cc_final: 0.6519 (mtmt) REVERT: A 123 ASP cc_start: 0.6325 (t70) cc_final: 0.5974 (t0) REVERT: A 137 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7973 (tm) REVERT: A 146 SER cc_start: 0.7888 (OUTLIER) cc_final: 0.7381 (m) REVERT: A 180 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7616 (mtpp) REVERT: A 238 MET cc_start: 0.8297 (tpp) cc_final: 0.7763 (tmm) REVERT: A 292 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8110 (t) REVERT: A 298 ARG cc_start: 0.7569 (ptm160) cc_final: 0.6470 (ttp80) REVERT: A 367 MET cc_start: 0.7630 (mmm) cc_final: 0.7250 (tpp) REVERT: A 401 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7529 (tp) REVERT: A 465 MET cc_start: 0.7810 (ttm) cc_final: 0.7589 (ttp) REVERT: A 485 MET cc_start: 0.7869 (tmm) cc_final: 0.7105 (mmp) REVERT: A 488 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6266 (mm) REVERT: B 75 LYS cc_start: 0.5021 (OUTLIER) cc_final: 0.4444 (tttm) REVERT: B 122 ASP cc_start: 0.7565 (p0) cc_final: 0.7279 (p0) REVERT: B 177 GLN cc_start: 0.7336 (mt0) cc_final: 0.6585 (mm-40) REVERT: B 180 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5213 (t80) REVERT: B 307 MET cc_start: 0.8879 (ptt) cc_final: 0.8602 (ptt) REVERT: B 310 MET cc_start: 0.8930 (ptt) cc_final: 0.8012 (ptt) REVERT: B 334 ARG cc_start: 0.7360 (ppt-90) cc_final: 0.6182 (mmp-170) REVERT: B 417 GLN cc_start: 0.7329 (mm-40) cc_final: 0.6835 (tt0) REVERT: B 432 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6002 (mt-10) REVERT: B 491 ARG cc_start: 0.6725 (ptt-90) cc_final: 0.6025 (ptm-80) REVERT: B 498 ARG cc_start: 0.7556 (ttm170) cc_final: 0.7016 (ttm170) REVERT: C 83 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7886 (mmm-85) REVERT: C 84 LYS cc_start: 0.8419 (ptpp) cc_final: 0.8034 (pttm) REVERT: C 177 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7092 (ttm-80) REVERT: C 215 ARG cc_start: 0.7750 (mtm180) cc_final: 0.6964 (mmp80) REVERT: C 326 MET cc_start: 0.7920 (ttm) cc_final: 0.7482 (ttt) REVERT: C 335 ARG cc_start: 0.6759 (mtt-85) cc_final: 0.6420 (mtt180) REVERT: C 352 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6286 (ttpt) REVERT: C 383 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7425 (tm-30) REVERT: C 412 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7228 (mp) REVERT: C 439 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7710 (pp) REVERT: C 451 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7301 (tp) REVERT: D 84 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.7790 (pttm) REVERT: D 177 ARG cc_start: 0.7951 (ttp80) cc_final: 0.7385 (ttm-80) REVERT: D 232 LEU cc_start: 0.8587 (mt) cc_final: 0.8297 (mt) REVERT: D 339 GLU cc_start: 0.6591 (tm-30) cc_final: 0.5863 (mp0) REVERT: D 355 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.6985 (mtm-85) REVERT: D 434 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.3449 (ttpt) REVERT: D 450 GLN cc_start: 0.6712 (tp40) cc_final: 0.6404 (mm-40) REVERT: D 485 MET cc_start: 0.5234 (mpp) cc_final: 0.4466 (ptm) outliers start: 58 outliers final: 35 residues processed: 250 average time/residue: 0.6676 time to fit residues: 183.1582 Evaluate side-chains 249 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 196 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 180 TYR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ILE Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL Chi-restraints excluded: chain D residue 84 LYS Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 420 VAL Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 467 ARG Chi-restraints excluded: chain D residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 159 optimal weight: 0.0060 chunk 156 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 140 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 chunk 145 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** D 383 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 = 0.4433 r_free = 0.4433 target = 0.229421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.189392 restraints weight = 15009.340| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.44 r_work: 0.3483 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15169 Z= 0.115 Angle : 0.578 11.698 20559 Z= 0.298 Chirality : 0.041 0.166 2309 Planarity : 0.004 0.045 2562 Dihedral : 8.677 89.645 2125 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.45 % Allowed : 29.47 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.20), residues: 1788 helix: 0.49 (0.16), residues: 1087 sheet: -1.47 (0.45), residues: 112 loop : -1.22 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 467 TYR 0.016 0.001 TYR A 57 PHE 0.033 0.001 PHE A 409 TRP 0.014 0.002 TRP D 246 HIS 0.003 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00259 (15169) covalent geometry : angle 0.57756 (20559) hydrogen bonds : bond 0.03635 ( 752) hydrogen bonds : angle 3.80853 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7065.08 seconds wall clock time: 120 minutes 36.72 seconds (7236.72 seconds total)