Starting phenix.real_space_refine on Fri Jun 13 08:16:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9is8_60834/06_2025/9is8_60834_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9is8_60834/06_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_60834/06_2025/9is8_60834.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9is8_60834/06_2025/9is8_60834.map" model { file = "/net/cci-nas-00/data/ceres_data/9is8_60834/06_2025/9is8_60834_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9is8_60834/06_2025/9is8_60834_neut.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.27, per 1000 atoms: 0.69 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: 3.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.71 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: 5.83 Time building geometry restraints manager: 4.50 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 38.700 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:17.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.920 ------------------------------------------------------------------------------- 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 : 15.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.96 (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 TRP 0.022 0.002 TRP B 273 HIS 0.009 0.001 HIS B 219 PHE 0.031 0.002 PHE B 63 TYR 0.015 0.002 TYR D 283 ARG 0.004 0.000 ARG C 190 Details of bonding type rmsd hydrogen bonds : bond 0.20570 ( 752) hydrogen bonds : angle 7.34958 ( 2130) covalent geometry : bond 0.00998 (15169) covalent geometry : angle 0.98843 (20559) *********************** 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 : 1.685 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: 0.7104 (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: 0.6094 (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: 0.8242 (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 432 GLU cc_start: 0.7653 (pm20) cc_final: 0.7450 (pm20) REVERT: A 465 MET cc_start: 0.7165 (ttm) cc_final: 0.6924 (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: 0.6295 (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: 0.7131 (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: 0.6679 (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: 0.6880 (mp) REVERT: D 379 ASP cc_start: 0.5184 (OUTLIER) cc_final: 0.4598 (p0) REVERT: D 408 ASP cc_start: 0.5668 (OUTLIER) cc_final: 0.4684 (p0) REVERT: D 445 LEU cc_start: 0.3834 (OUTLIER) cc_final: 0.3616 (mt) REVERT: D 465 MET cc_start: 0.4808 (ttm) cc_final: 0.4332 (ttm) REVERT: D 485 MET cc_start: 0.5635 (mpp) cc_final: 0.4953 (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: 1.2133 time to fit residues: 560.7538 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 : 1.547 ------------------------------------------------------------------------------- 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 379 ASP Chi-restraints excluded: chain D residue 408 ASP Chi-restraints excluded: chain D residue 445 LEU 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 151 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 85 optimal weight: 0.0030 chunk 104 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- 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 414 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 219 HIS B 326 ASN B 352 ASN B 395 HIS 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.224819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.179394 restraints weight = 15015.233| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 1.48 r_work: 0.3388 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15169 Z= 0.189 Angle : 0.693 9.276 20559 Z= 0.369 Chirality : 0.046 0.217 2309 Planarity : 0.005 0.047 2562 Dihedral : 12.434 119.747 2242 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 8.03 % Allowed : 25.77 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.19), residues: 1788 helix: -1.08 (0.15), residues: 1050 sheet: -2.46 (0.40), residues: 121 loop : -1.95 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 246 HIS 0.008 0.001 HIS C 360 PHE 0.019 0.002 PHE B 110 TYR 0.021 0.002 TYR A 157 ARG 0.007 0.000 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 752) hydrogen bonds : angle 4.78082 ( 2130) covalent geometry : bond 0.00444 (15169) covalent geometry : angle 0.69281 (20559) *********************** 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 352 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 224 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.7243 (mmtm) cc_final: 0.6834 (mtmt) REVERT: A 78 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7830 (tp30) REVERT: A 93 ASP cc_start: 0.7375 (t0) cc_final: 0.7138 (m-30) REVERT: A 123 ASP cc_start: 0.6510 (t70) cc_final: 0.6204 (t0) REVERT: A 130 LYS cc_start: 0.7319 (tptp) cc_final: 0.7070 (tptt) REVERT: A 182 ARG cc_start: 0.7034 (mpt180) cc_final: 0.6803 (mmt-90) REVERT: A 215 ARG cc_start: 0.7700 (mtp85) cc_final: 0.6995 (ptt90) REVERT: A 238 MET cc_start: 0.8444 (tpp) cc_final: 0.7786 (tmm) REVERT: A 284 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 298 ARG cc_start: 0.7596 (ptm160) cc_final: 0.6538 (tpt170) REVERT: A 321 ARG cc_start: 0.7159 (tmm160) cc_final: 0.6714 (ttp-170) REVERT: A 342 GLN cc_start: 0.6587 (tp-100) cc_final: 0.6264 (pp30) REVERT: A 401 LEU cc_start: 0.7919 (pt) cc_final: 0.7510 (tt) REVERT: A 465 MET cc_start: 0.7553 (ttm) cc_final: 0.7339 (tpp) REVERT: A 485 MET cc_start: 0.8013 (tmm) cc_final: 0.7812 (tmm) REVERT: A 486 ASN cc_start: 0.7794 (m-40) cc_final: 0.7392 (m110) REVERT: A 488 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6414 (mm) REVERT: B 85 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7076 (tmt-80) REVERT: B 122 ASP cc_start: 0.7845 (p0) cc_final: 0.7311 (t0) REVERT: B 177 GLN cc_start: 0.6995 (mt0) cc_final: 0.6103 (tm-30) REVERT: B 307 MET cc_start: 0.9094 (ptt) cc_final: 0.8818 (ptt) REVERT: B 310 MET cc_start: 0.8956 (ptt) cc_final: 0.8253 (ptt) REVERT: B 334 ARG cc_start: 0.7384 (ppt-90) cc_final: 0.6262 (mmp-170) REVERT: B 366 MET cc_start: 0.7340 (pp-130) cc_final: 0.6766 (ppp) REVERT: B 403 GLU cc_start: 0.7040 (pp20) cc_final: 0.6486 (pp20) REVERT: B 417 GLN cc_start: 0.7350 (mm-40) cc_final: 0.6752 (tt0) REVERT: B 432 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5802 (mt-10) REVERT: B 491 ARG cc_start: 0.7020 (ptt-90) cc_final: 0.6084 (ptm-80) REVERT: B 498 ARG cc_start: 0.7539 (ttm170) cc_final: 0.7112 (ttm170) REVERT: B 507 MET cc_start: 0.6850 (ttm) cc_final: 0.6484 (ttp) REVERT: B 523 PHE cc_start: 0.6611 (OUTLIER) cc_final: 0.4790 (t80) REVERT: C 84 LYS cc_start: 0.8475 (ptpp) cc_final: 0.8104 (pttm) REVERT: C 108 PHE cc_start: 0.7079 (m-10) cc_final: 0.6858 (m-80) REVERT: C 137 LEU cc_start: 0.7562 (pt) cc_final: 0.7236 (mt) REVERT: C 162 MET cc_start: 0.8685 (tpt) cc_final: 0.8290 (tpt) REVERT: C 177 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7328 (ttm-80) REVERT: C 190 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8125 (mmm160) REVERT: C 215 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7372 (mtp180) REVERT: C 352 LYS cc_start: 0.7278 (tppp) cc_final: 0.6917 (ttpt) REVERT: C 360 HIS cc_start: 0.8177 (t70) cc_final: 0.7835 (t-90) REVERT: C 369 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7142 (mptt) REVERT: C 383 GLN cc_start: 0.8132 (tm130) cc_final: 0.7616 (tm-30) REVERT: C 387 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6395 (pp20) REVERT: D 56 LYS cc_start: 0.5944 (pptt) cc_final: 0.5326 (pttp) REVERT: D 84 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8156 (pttm) REVERT: D 105 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8532 (pp) REVERT: D 177 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7494 (ttm-80) REVERT: D 215 ARG cc_start: 0.7880 (mmt90) cc_final: 0.7605 (mmp80) REVERT: D 306 ILE cc_start: 0.7284 (OUTLIER) cc_final: 0.7071 (mp) REVERT: D 326 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5729 (ptt) REVERT: D 341 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7599 (tp) REVERT: D 450 GLN cc_start: 0.6576 (tp40) cc_final: 0.6257 (mm-40) REVERT: D 485 MET cc_start: 0.5232 (mpp) cc_final: 0.4570 (ptm) outliers start: 128 outliers final: 42 residues processed: 329 average time/residue: 1.4202 time to fit residues: 517.7864 Evaluate side-chains 254 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 201 time to evaluate : 1.669 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 488 LEU 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 388 ILE 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 B residue 523 PHE Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 190 ARG 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 105 ILE Chi-restraints excluded: chain D residue 106 MET 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 297 SER 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 372 LEU 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 171 optimal weight: 8.9990 chunk 140 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 138 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 HIS B 417 GLN C 343 GLN C 383 GLN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 461 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.228367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.179936 restraints weight = 15045.718| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.64 r_work: 0.3401 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15169 Z= 0.125 Angle : 0.602 8.306 20559 Z= 0.317 Chirality : 0.042 0.247 2309 Planarity : 0.004 0.042 2562 Dihedral : 10.787 105.528 2165 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.77 % Allowed : 27.02 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1788 helix: -0.33 (0.16), residues: 1055 sheet: -2.30 (0.40), residues: 119 loop : -1.65 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 246 HIS 0.006 0.001 HIS C 360 PHE 0.017 0.001 PHE B 138 TYR 0.021 0.001 TYR A 157 ARG 0.008 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 752) hydrogen bonds : angle 4.26289 ( 2130) covalent geometry : bond 0.00274 (15169) covalent geometry : angle 0.60235 (20559) *********************** 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: 92 poor density : 224 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 56 LYS cc_start: 0.7349 (mmtm) cc_final: 0.6814 (mtmt) REVERT: A 93 ASP cc_start: 0.7360 (t0) cc_final: 0.7117 (m-30) REVERT: A 119 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7281 (pt) REVERT: A 123 ASP cc_start: 0.6476 (t70) cc_final: 0.6100 (t0) REVERT: A 130 LYS cc_start: 0.7272 (tptp) cc_final: 0.7025 (tptt) REVERT: A 215 ARG cc_start: 0.7720 (mtp85) cc_final: 0.6799 (ptt90) REVERT: A 238 MET cc_start: 0.8400 (tpp) cc_final: 0.7859 (tmm) REVERT: A 284 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8535 (mt) REVERT: A 298 ARG cc_start: 0.7681 (ptm160) cc_final: 0.6585 (tpt170) REVERT: A 401 LEU cc_start: 0.7951 (pt) cc_final: 0.7534 (tp) REVERT: A 448 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7487 (mtp85) REVERT: A 485 MET cc_start: 0.8027 (tmm) cc_final: 0.7812 (tmm) REVERT: A 486 ASN cc_start: 0.7636 (m-40) cc_final: 0.7285 (m110) REVERT: B 85 ARG cc_start: 0.7834 (mtp180) cc_final: 0.6987 (tmt-80) REVERT: B 122 ASP cc_start: 0.7788 (p0) cc_final: 0.7192 (t0) REVERT: B 177 GLN cc_start: 0.7057 (mt0) cc_final: 0.6314 (mm-40) REVERT: B 180 TYR cc_start: 0.5762 (OUTLIER) cc_final: 0.5170 (t80) REVERT: B 221 ASN cc_start: 0.8202 (t0) cc_final: 0.7703 (t0) REVERT: B 228 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8074 (mt) REVERT: B 230 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7834 (mt) REVERT: B 307 MET cc_start: 0.8860 (ptt) cc_final: 0.8616 (ptt) REVERT: B 310 MET cc_start: 0.8905 (ptt) cc_final: 0.8375 (ptt) REVERT: B 334 ARG cc_start: 0.7405 (ppt-90) cc_final: 0.6284 (mmp-170) REVERT: B 366 MET cc_start: 0.7141 (pp-130) cc_final: 0.6864 (ppp) REVERT: B 403 GLU cc_start: 0.6966 (pp20) cc_final: 0.6427 (pp20) REVERT: B 417 GLN cc_start: 0.7422 (mm110) cc_final: 0.6824 (tt0) REVERT: B 491 ARG cc_start: 0.7029 (ptt-90) cc_final: 0.6146 (ptm-80) REVERT: B 498 ARG cc_start: 0.7548 (ttm170) cc_final: 0.7153 (ttm170) REVERT: C 83 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8119 (mmm-85) REVERT: C 84 LYS cc_start: 0.8493 (ptpp) cc_final: 0.8090 (pttm) REVERT: C 160 PHE cc_start: 0.8624 (t80) cc_final: 0.8417 (t80) REVERT: C 177 ARG cc_start: 0.7464 (mtm110) cc_final: 0.7153 (ttm-80) REVERT: C 190 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7888 (mmm160) REVERT: C 215 ARG cc_start: 0.7735 (mtm180) cc_final: 0.7375 (mtp180) REVERT: C 244 MET cc_start: 0.9026 (tpp) cc_final: 0.8656 (mmm) REVERT: C 326 MET cc_start: 0.8253 (ttm) cc_final: 0.7718 (ttp) REVERT: C 339 GLU cc_start: 0.7521 (tt0) cc_final: 0.7212 (mt-10) REVERT: C 352 LYS cc_start: 0.7043 (tppp) cc_final: 0.6663 (ttpt) REVERT: C 383 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7598 (tm-30) REVERT: C 384 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6151 (tt) REVERT: C 387 GLU cc_start: 0.6519 (tm-30) cc_final: 0.6258 (pp20) REVERT: C 452 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6789 (m-80) REVERT: D 155 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7313 (pt0) REVERT: D 177 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7452 (ttm-80) REVERT: D 215 ARG cc_start: 0.7832 (mmt90) cc_final: 0.7501 (mmp80) REVERT: D 326 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5249 (ptt) REVERT: D 350 LEU cc_start: 0.4903 (OUTLIER) cc_final: 0.4495 (tp) REVERT: D 485 MET cc_start: 0.5302 (mpp) cc_final: 0.4632 (ptm) outliers start: 92 outliers final: 29 residues processed: 292 average time/residue: 1.4073 time to fit residues: 453.5273 Evaluate side-chains 240 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 1.524 ------------------------------------------------------------------------------- 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 105 ILE Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 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 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 C residue 58 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 341 LEU 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 452 PHE Chi-restraints excluded: chain C residue 465 MET 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 326 MET Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 356 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 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 170 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.225185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.174495 restraints weight = 15115.240| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 1.68 r_work: 0.3395 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15169 Z= 0.125 Angle : 0.585 8.891 20559 Z= 0.309 Chirality : 0.041 0.233 2309 Planarity : 0.004 0.042 2562 Dihedral : 9.757 92.995 2142 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 6.02 % Allowed : 25.71 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1788 helix: -0.01 (0.16), residues: 1062 sheet: -1.97 (0.43), residues: 112 loop : -1.36 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 246 HIS 0.004 0.001 HIS C 360 PHE 0.022 0.001 PHE C 187 TYR 0.026 0.001 TYR C 371 ARG 0.007 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 752) hydrogen bonds : angle 4.05254 ( 2130) covalent geometry : bond 0.00283 (15169) covalent geometry : angle 0.58506 (20559) *********************** 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 316 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 220 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7676 (OUTLIER) cc_final: 0.6692 (t80) REVERT: A 56 LYS cc_start: 0.7321 (mmtm) cc_final: 0.6763 (mtmt) REVERT: A 93 ASP cc_start: 0.7337 (t0) cc_final: 0.7110 (m-30) REVERT: A 119 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7344 (pt) REVERT: A 123 ASP cc_start: 0.6507 (t70) cc_final: 0.6127 (t0) REVERT: A 130 LYS cc_start: 0.7324 (tptp) cc_final: 0.7089 (tptt) REVERT: A 215 ARG cc_start: 0.7692 (mtp85) cc_final: 0.6771 (ptt90) REVERT: A 238 MET cc_start: 0.8396 (tpp) cc_final: 0.7852 (tmm) REVERT: A 284 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 298 ARG cc_start: 0.7715 (ptm160) cc_final: 0.6563 (tpt170) REVERT: A 369 LYS cc_start: 0.8200 (mppt) cc_final: 0.7986 (mptt) REVERT: A 401 LEU cc_start: 0.7947 (pt) cc_final: 0.7538 (tp) REVERT: A 448 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7475 (mtp85) REVERT: A 486 ASN cc_start: 0.7658 (m-40) cc_final: 0.7325 (m110) REVERT: A 488 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6488 (mm) REVERT: B 85 ARG cc_start: 0.7778 (mtp180) cc_final: 0.6918 (tmt-80) REVERT: B 122 ASP cc_start: 0.7956 (p0) cc_final: 0.7232 (t0) REVERT: B 177 GLN cc_start: 0.7074 (mt0) cc_final: 0.6406 (mm-40) REVERT: B 180 TYR cc_start: 0.5907 (OUTLIER) cc_final: 0.5361 (t80) REVERT: B 221 ASN cc_start: 0.8176 (t0) cc_final: 0.7689 (t0) REVERT: B 228 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7867 (mt) REVERT: B 307 MET cc_start: 0.8901 (ptt) cc_final: 0.8631 (ptt) REVERT: B 310 MET cc_start: 0.8894 (ptt) cc_final: 0.8102 (ptt) REVERT: B 334 ARG cc_start: 0.7430 (ppt-90) cc_final: 0.6355 (mmp-170) REVERT: B 366 MET cc_start: 0.7090 (OUTLIER) cc_final: 0.6832 (ppp) REVERT: B 403 GLU cc_start: 0.6894 (pp20) cc_final: 0.6375 (pp20) REVERT: B 417 GLN cc_start: 0.7212 (mm110) cc_final: 0.6768 (tt0) REVERT: B 432 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5946 (mt-10) REVERT: B 491 ARG cc_start: 0.6904 (ptt-90) cc_final: 0.6114 (ptm-80) REVERT: B 498 ARG cc_start: 0.7579 (ttm170) cc_final: 0.7097 (ttp-110) REVERT: C 83 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8112 (mmm-85) REVERT: C 84 LYS cc_start: 0.8489 (ptpp) cc_final: 0.8102 (pttm) REVERT: C 160 PHE cc_start: 0.8644 (t80) cc_final: 0.8434 (t80) REVERT: C 177 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7244 (ttm-80) REVERT: C 190 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7730 (mmm160) REVERT: C 215 ARG cc_start: 0.7824 (mtm180) cc_final: 0.6965 (mmt90) REVERT: C 244 MET cc_start: 0.8987 (tpp) cc_final: 0.8585 (mmm) REVERT: C 326 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7803 (ttt) REVERT: C 352 LYS cc_start: 0.6882 (tppp) cc_final: 0.6569 (ttpt) REVERT: C 383 GLN cc_start: 0.8038 (tm-30) cc_final: 0.7546 (tm-30) REVERT: D 84 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8012 (pttm) REVERT: D 177 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7397 (ttm-80) REVERT: D 215 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7500 (mmp80) REVERT: D 232 LEU cc_start: 0.8645 (mt) cc_final: 0.8390 (mt) REVERT: D 326 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5506 (ptt) REVERT: D 339 GLU cc_start: 0.6570 (tm-30) cc_final: 0.6153 (mp0) REVERT: D 350 LEU cc_start: 0.4894 (OUTLIER) cc_final: 0.4548 (tp) REVERT: D 485 MET cc_start: 0.5394 (mpp) cc_final: 0.4750 (ptm) outliers start: 96 outliers final: 44 residues processed: 292 average time/residue: 1.3120 time to fit residues: 422.7536 Evaluate side-chains 274 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 216 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER 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 407 THR 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 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 264 VAL Chi-restraints excluded: chain B residue 274 LEU 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 432 GLU Chi-restraints excluded: chain B residue 446 ILE Chi-restraints excluded: chain B residue 461 GLU Chi-restraints excluded: chain B residue 518 MET Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 388 MET Chi-restraints excluded: chain C residue 399 VAL 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 454 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 78 GLU 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 297 SER Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 350 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 71 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 6 optimal weight: 0.0570 chunk 61 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 311 ASN ** 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 = 0.4400 r_free = 0.4400 target = 0.225675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.175338 restraints weight = 15279.185| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 1.83 r_work: 0.3380 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15169 Z= 0.119 Angle : 0.572 10.309 20559 Z= 0.300 Chirality : 0.041 0.180 2309 Planarity : 0.004 0.041 2562 Dihedral : 9.421 88.456 2138 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 5.83 % Allowed : 26.21 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1788 helix: 0.16 (0.16), residues: 1068 sheet: -1.87 (0.43), residues: 112 loop : -1.23 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 246 HIS 0.003 0.001 HIS B 365 PHE 0.032 0.001 PHE A 409 TYR 0.020 0.001 TYR A 157 ARG 0.008 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 752) hydrogen bonds : angle 3.95929 ( 2130) covalent geometry : bond 0.00268 (15169) covalent geometry : angle 0.57169 (20559) *********************** 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 304 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 211 time to evaluate : 1.849 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6644 (t80) REVERT: A 56 LYS cc_start: 0.7391 (mmtm) cc_final: 0.6792 (mtmt) REVERT: A 93 ASP cc_start: 0.7392 (t0) cc_final: 0.7144 (m-30) REVERT: A 119 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7226 (pt) REVERT: A 123 ASP cc_start: 0.6387 (t70) cc_final: 0.6009 (t0) REVERT: A 137 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7946 (tm) REVERT: A 215 ARG cc_start: 0.7698 (mtp85) cc_final: 0.6719 (ptt90) REVERT: A 238 MET cc_start: 0.8397 (tpp) cc_final: 0.7852 (tmm) REVERT: A 284 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8661 (mp) REVERT: A 298 ARG cc_start: 0.7776 (ptm160) cc_final: 0.6589 (tpt170) REVERT: A 401 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7516 (tp) REVERT: A 448 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7570 (mtp85) REVERT: B 122 ASP cc_start: 0.7869 (p0) cc_final: 0.7584 (p0) REVERT: B 177 GLN cc_start: 0.7231 (mt0) cc_final: 0.6389 (mm-40) REVERT: B 221 ASN cc_start: 0.8208 (t0) cc_final: 0.7687 (t0) REVERT: B 228 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7780 (mt) REVERT: B 307 MET cc_start: 0.8851 (ptt) cc_final: 0.8631 (ptt) REVERT: B 310 MET cc_start: 0.8898 (ptt) cc_final: 0.8423 (ptt) REVERT: B 334 ARG cc_start: 0.7456 (ppt-90) cc_final: 0.6287 (mmp-170) REVERT: B 394 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6467 (tm-30) REVERT: B 398 ARG cc_start: 0.6882 (tpt90) cc_final: 0.6654 (tpt90) REVERT: B 417 GLN cc_start: 0.7259 (mm110) cc_final: 0.6783 (tt0) REVERT: B 432 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: B 491 ARG cc_start: 0.6730 (ptt-90) cc_final: 0.6004 (ptm-80) REVERT: B 498 ARG cc_start: 0.7590 (ttm170) cc_final: 0.7108 (ttp-110) REVERT: C 83 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8121 (mmm-85) REVERT: C 84 LYS cc_start: 0.8487 (ptpp) cc_final: 0.8086 (pttm) REVERT: C 160 PHE cc_start: 0.8608 (t80) cc_final: 0.8391 (t80) REVERT: C 177 ARG cc_start: 0.7380 (mtm110) cc_final: 0.7076 (ttm-80) REVERT: C 190 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7725 (mmm160) REVERT: C 215 ARG cc_start: 0.7817 (mtm180) cc_final: 0.6972 (mmt90) REVERT: C 244 MET cc_start: 0.9001 (tpp) cc_final: 0.8638 (mmm) REVERT: C 326 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7730 (ttt) REVERT: C 352 LYS cc_start: 0.6738 (tppp) cc_final: 0.6406 (ttpt) REVERT: C 383 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7518 (tm-30) REVERT: C 451 LEU cc_start: 0.7768 (OUTLIER) cc_final: 0.7377 (tp) REVERT: D 84 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8009 (pttm) REVERT: D 177 ARG cc_start: 0.7978 (ttp80) cc_final: 0.7443 (ttm-80) REVERT: D 215 ARG cc_start: 0.7853 (mmt90) cc_final: 0.7496 (mmp80) REVERT: D 232 LEU cc_start: 0.8635 (mt) cc_final: 0.8379 (mt) REVERT: D 326 MET cc_start: 0.6330 (OUTLIER) cc_final: 0.5470 (ptt) REVERT: D 339 GLU cc_start: 0.6452 (tm-30) cc_final: 0.5955 (mp0) REVERT: D 434 LYS cc_start: 0.3706 (OUTLIER) cc_final: 0.3202 (pptt) REVERT: D 450 GLN cc_start: 0.6519 (tp40) cc_final: 0.5979 (mm-40) REVERT: D 485 MET cc_start: 0.5408 (mpp) cc_final: 0.4768 (ptm) outliers start: 93 outliers final: 37 residues processed: 281 average time/residue: 1.5087 time to fit residues: 469.2815 Evaluate side-chains 253 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER 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 401 LEU Chi-restraints excluded: chain A residue 407 THR 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 228 ILE Chi-restraints excluded: chain B residue 264 VAL 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 461 GLU Chi-restraints excluded: chain C residue 58 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 399 VAL 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 454 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 78 GLU 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 297 SER Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 434 LYS 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 88 optimal weight: 9.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 0.2980 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 414 ASN A 486 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.222238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171192 restraints weight = 15100.337| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.73 r_work: 0.3307 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 15169 Z= 0.205 Angle : 0.633 12.386 20559 Z= 0.333 Chirality : 0.045 0.225 2309 Planarity : 0.004 0.043 2562 Dihedral : 9.565 87.884 2134 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.64 % Allowed : 26.21 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.20), residues: 1788 helix: -0.10 (0.16), residues: 1078 sheet: -1.75 (0.45), residues: 112 loop : -1.27 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 246 HIS 0.005 0.001 HIS C 294 PHE 0.027 0.002 PHE A 409 TYR 0.021 0.002 TYR A 157 ARG 0.008 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 752) hydrogen bonds : angle 4.12234 ( 2130) covalent geometry : bond 0.00498 (15169) covalent geometry : angle 0.63250 (20559) *********************** 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: 90 poor density : 202 time to evaluate : 1.513 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7726 (OUTLIER) cc_final: 0.6768 (t80) REVERT: A 56 LYS cc_start: 0.7328 (mmtm) cc_final: 0.6739 (mtmt) REVERT: A 93 ASP cc_start: 0.7421 (t0) cc_final: 0.7164 (m-30) REVERT: A 119 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7162 (pt) REVERT: A 123 ASP cc_start: 0.6536 (t70) cc_final: 0.6144 (t0) REVERT: A 182 ARG cc_start: 0.6952 (mmt-90) cc_final: 0.6571 (mmt-90) REVERT: A 238 MET cc_start: 0.8442 (tpp) cc_final: 0.7910 (tmm) REVERT: A 284 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8622 (mp) REVERT: A 298 ARG cc_start: 0.7697 (ptm160) cc_final: 0.6750 (ttp80) REVERT: A 401 LEU cc_start: 0.7942 (pt) cc_final: 0.7517 (tp) REVERT: A 414 ASN cc_start: 0.7591 (t0) cc_final: 0.7249 (t0) REVERT: A 448 ARG cc_start: 0.7855 (mtp85) cc_final: 0.7531 (mtp85) REVERT: A 488 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6333 (mm) REVERT: B 85 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7121 (ptt90) REVERT: B 122 ASP cc_start: 0.7908 (p0) cc_final: 0.7660 (p0) REVERT: B 123 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7748 (mp) REVERT: B 177 GLN cc_start: 0.7382 (mt0) cc_final: 0.6553 (mm-40) REVERT: B 180 TYR cc_start: 0.5707 (OUTLIER) cc_final: 0.5367 (t80) REVERT: B 228 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7779 (mt) REVERT: B 280 MET cc_start: 0.9209 (mmp) cc_final: 0.8922 (mmp) REVERT: B 307 MET cc_start: 0.9088 (ptt) cc_final: 0.8817 (ptt) REVERT: B 310 MET cc_start: 0.8993 (ptt) cc_final: 0.8496 (ptt) REVERT: B 334 ARG cc_start: 0.7438 (ppt-90) cc_final: 0.6280 (mmp-170) REVERT: B 417 GLN cc_start: 0.7270 (mm110) cc_final: 0.6783 (tt0) REVERT: B 432 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5968 (mt-10) REVERT: B 491 ARG cc_start: 0.6732 (ptt-90) cc_final: 0.5997 (ptm-80) REVERT: B 498 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7152 (ttm170) REVERT: C 83 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8098 (mmm-85) REVERT: C 84 LYS cc_start: 0.8485 (ptpp) cc_final: 0.8108 (pttm) REVERT: C 177 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7181 (ttm-80) REVERT: C 190 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7631 (mmm160) REVERT: C 215 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7030 (mmt90) REVERT: C 244 MET cc_start: 0.9037 (tpp) cc_final: 0.8693 (mmm) REVERT: C 326 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7750 (ttp) REVERT: C 352 LYS cc_start: 0.6934 (tppp) cc_final: 0.6558 (ttpt) REVERT: C 381 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6158 (mp) REVERT: C 383 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7478 (tm-30) REVERT: C 451 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7424 (tp) REVERT: D 84 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8094 (pttm) REVERT: D 177 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7454 (ttm-80) REVERT: D 215 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7547 (mmp80) REVERT: D 232 LEU cc_start: 0.8671 (mt) cc_final: 0.8376 (mt) REVERT: D 326 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5612 (ptt) REVERT: D 327 LEU cc_start: 0.6312 (mt) cc_final: 0.6097 (mp) REVERT: D 434 LYS cc_start: 0.3689 (OUTLIER) cc_final: 0.3179 (ttpt) REVERT: D 450 GLN cc_start: 0.6669 (tp40) cc_final: 0.6179 (mm-40) REVERT: D 485 MET cc_start: 0.5496 (mpp) cc_final: 0.4834 (ptm) outliers start: 90 outliers final: 43 residues processed: 271 average time/residue: 1.2118 time to fit residues: 362.1459 Evaluate side-chains 253 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 194 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER 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 407 THR Chi-restraints excluded: chain A residue 413 VAL 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 123 LEU 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 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 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 C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL 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 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 202 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 357 SER Chi-restraints excluded: chain D residue 434 LYS 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 173 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 167 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 156 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN C 161 ASN C 402 GLN D 216 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.225262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.175024 restraints weight = 15228.771| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 1.78 r_work: 0.3381 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15169 Z= 0.113 Angle : 0.563 11.555 20559 Z= 0.296 Chirality : 0.040 0.162 2309 Planarity : 0.004 0.043 2562 Dihedral : 9.179 88.274 2134 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 4.95 % Allowed : 26.65 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.20), residues: 1788 helix: 0.25 (0.16), residues: 1074 sheet: -1.75 (0.44), residues: 112 loop : -1.16 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 246 HIS 0.003 0.001 HIS D 329 PHE 0.030 0.001 PHE A 409 TYR 0.021 0.001 TYR A 157 ARG 0.010 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 752) hydrogen bonds : angle 3.92343 ( 2130) covalent geometry : bond 0.00248 (15169) covalent geometry : angle 0.56325 (20559) *********************** 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 276 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.6693 (t80) REVERT: A 56 LYS cc_start: 0.7304 (mmtm) cc_final: 0.6708 (mtmt) REVERT: A 93 ASP cc_start: 0.7386 (t0) cc_final: 0.7106 (m-30) REVERT: A 119 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7243 (pt) REVERT: A 123 ASP cc_start: 0.6381 (t70) cc_final: 0.5979 (t0) REVERT: A 137 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7904 (tm) REVERT: A 238 MET cc_start: 0.8401 (tpp) cc_final: 0.7865 (tmm) REVERT: A 284 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 298 ARG cc_start: 0.7676 (ptm160) cc_final: 0.6624 (ttp80) REVERT: A 321 ARG cc_start: 0.7010 (tmm160) cc_final: 0.6806 (ttt-90) REVERT: A 367 MET cc_start: 0.7863 (mmm) cc_final: 0.7476 (tpp) REVERT: A 401 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7554 (tp) REVERT: A 414 ASN cc_start: 0.7417 (t0) cc_final: 0.7097 (t0) REVERT: A 448 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7494 (mtp85) REVERT: A 488 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6410 (mm) REVERT: B 122 ASP cc_start: 0.7783 (p0) cc_final: 0.7468 (p0) REVERT: B 177 GLN cc_start: 0.7344 (mt0) cc_final: 0.6508 (mm-40) REVERT: B 180 TYR cc_start: 0.5629 (OUTLIER) cc_final: 0.5317 (t80) REVERT: B 280 MET cc_start: 0.9159 (mmp) cc_final: 0.8876 (mmp) REVERT: B 307 MET cc_start: 0.8886 (ptt) cc_final: 0.8614 (ptt) REVERT: B 310 MET cc_start: 0.8946 (ptt) cc_final: 0.8228 (ptt) REVERT: B 334 ARG cc_start: 0.7437 (ppt-90) cc_final: 0.6240 (mmp-170) REVERT: B 339 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6374 (mtm180) REVERT: B 394 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6427 (tm-30) REVERT: B 417 GLN cc_start: 0.7250 (mm110) cc_final: 0.6825 (tt0) REVERT: B 432 GLU cc_start: 0.6519 (OUTLIER) cc_final: 0.5952 (mt-10) REVERT: B 491 ARG cc_start: 0.6717 (ptt-90) cc_final: 0.6102 (ptm-80) REVERT: B 498 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7078 (ttp-110) REVERT: C 83 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8009 (mmm-85) REVERT: C 84 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8088 (pttm) REVERT: C 177 ARG cc_start: 0.7457 (mtm110) cc_final: 0.7166 (ttm-80) REVERT: C 215 ARG cc_start: 0.7850 (mtm180) cc_final: 0.7124 (mmp80) REVERT: C 244 MET cc_start: 0.8996 (tpp) cc_final: 0.8618 (mmm) REVERT: C 326 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7735 (ttt) REVERT: C 352 LYS cc_start: 0.6762 (tppp) cc_final: 0.6367 (ttpt) REVERT: C 381 LEU cc_start: 0.6476 (OUTLIER) cc_final: 0.6133 (mp) REVERT: C 383 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7428 (tm-30) REVERT: C 451 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7347 (tp) REVERT: D 177 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7455 (ttm-80) REVERT: D 215 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7509 (mmp80) REVERT: D 232 LEU cc_start: 0.8618 (mt) cc_final: 0.8361 (mt) REVERT: D 326 MET cc_start: 0.6397 (OUTLIER) cc_final: 0.5580 (ptt) REVERT: D 339 GLU cc_start: 0.6479 (tm-30) cc_final: 0.5847 (mp0) REVERT: D 363 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7488 (p90) REVERT: D 434 LYS cc_start: 0.3729 (OUTLIER) cc_final: 0.3228 (ttpt) REVERT: D 450 GLN cc_start: 0.6670 (tp40) cc_final: 0.6245 (mm-40) REVERT: D 485 MET cc_start: 0.5207 (mpp) cc_final: 0.4549 (ptm) outliers start: 79 outliers final: 36 residues processed: 258 average time/residue: 1.2409 time to fit residues: 354.7035 Evaluate side-chains 244 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU 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 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 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 339 ARG 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 C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL 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 451 LEU Chi-restraints excluded: chain C residue 452 PHE Chi-restraints excluded: chain C residue 454 VAL 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 326 MET Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 363 PHE Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 467 ARG 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 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.0470 chunk 154 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 155 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 162 optimal weight: 9.9990 overall best weight: 0.6682 ------------------------------------------------------------------------------- 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** C 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.226062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.175211 restraints weight = 15178.720| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.77 r_work: 0.3401 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.3542 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= 0.116 Angle : 0.561 11.543 20559 Z= 0.295 Chirality : 0.040 0.160 2309 Planarity : 0.004 0.043 2562 Dihedral : 8.730 87.479 2125 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.70 % Allowed : 28.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.20), residues: 1788 helix: 0.41 (0.16), residues: 1075 sheet: -1.76 (0.44), residues: 113 loop : -1.11 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 246 HIS 0.003 0.001 HIS C 294 PHE 0.030 0.001 PHE A 409 TYR 0.022 0.001 TYR A 157 ARG 0.010 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03641 ( 752) hydrogen bonds : angle 3.85496 ( 2130) covalent geometry : bond 0.00258 (15169) covalent geometry : angle 0.56135 (20559) *********************** 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 261 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7595 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 56 LYS cc_start: 0.7285 (mmtm) cc_final: 0.6663 (mtmt) REVERT: A 93 ASP cc_start: 0.7342 (t0) cc_final: 0.7064 (m-30) REVERT: A 119 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7358 (pt) REVERT: A 123 ASP cc_start: 0.6378 (t70) cc_final: 0.6026 (t0) REVERT: A 137 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7906 (tm) REVERT: A 238 MET cc_start: 0.8382 (tpp) cc_final: 0.7887 (tmm) REVERT: A 284 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8683 (mp) REVERT: A 298 ARG cc_start: 0.7646 (ptm160) cc_final: 0.6655 (ttp80) REVERT: A 367 MET cc_start: 0.7825 (mmm) cc_final: 0.7418 (tpp) REVERT: A 401 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7523 (tp) REVERT: A 414 ASN cc_start: 0.7371 (t0) cc_final: 0.7084 (t0) REVERT: A 448 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7454 (mtp85) REVERT: A 485 MET cc_start: 0.7887 (tmm) cc_final: 0.7145 (mmp) REVERT: B 122 ASP cc_start: 0.7656 (p0) cc_final: 0.7319 (p0) REVERT: B 177 GLN cc_start: 0.7453 (mt0) cc_final: 0.6736 (mm-40) REVERT: B 180 TYR cc_start: 0.5593 (OUTLIER) cc_final: 0.5298 (t80) REVERT: B 221 ASN cc_start: 0.8046 (t0) cc_final: 0.7537 (t0) REVERT: B 280 MET cc_start: 0.9159 (mmp) cc_final: 0.8883 (mmp) REVERT: B 310 MET cc_start: 0.8904 (ptt) cc_final: 0.8251 (ptt) REVERT: B 334 ARG cc_start: 0.7364 (ppt-90) cc_final: 0.6201 (mmp-170) REVERT: B 417 GLN cc_start: 0.7243 (mm110) cc_final: 0.6871 (tt0) REVERT: B 432 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5899 (mt-10) REVERT: B 491 ARG cc_start: 0.6760 (ptt-90) cc_final: 0.6126 (ptm-80) REVERT: B 498 ARG cc_start: 0.7565 (ttm170) cc_final: 0.6979 (ttm170) REVERT: C 83 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7989 (mmm-85) REVERT: C 84 LYS cc_start: 0.8472 (ptpp) cc_final: 0.8084 (pttm) REVERT: C 160 PHE cc_start: 0.8593 (t80) cc_final: 0.8366 (t80) REVERT: C 177 ARG cc_start: 0.7479 (mtm110) cc_final: 0.7184 (ttm-80) REVERT: C 215 ARG cc_start: 0.7800 (mtm180) cc_final: 0.7096 (mmp80) REVERT: C 244 MET cc_start: 0.8975 (tpp) cc_final: 0.8598 (mmm) REVERT: C 326 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7766 (ttt) REVERT: C 352 LYS cc_start: 0.6737 (tppp) cc_final: 0.6400 (ttpt) REVERT: C 381 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6139 (mp) REVERT: C 383 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7441 (tm-30) REVERT: C 451 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7340 (tp) REVERT: D 84 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7779 (pttm) REVERT: D 177 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7406 (ttm-80) REVERT: D 215 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7484 (mmp80) REVERT: D 232 LEU cc_start: 0.8620 (mt) cc_final: 0.8359 (mt) REVERT: D 326 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5624 (ptt) REVERT: D 339 GLU cc_start: 0.6660 (tm-30) cc_final: 0.6024 (mp0) REVERT: D 434 LYS cc_start: 0.3783 (OUTLIER) cc_final: 0.3267 (ttpt) REVERT: D 450 GLN cc_start: 0.6615 (tp40) cc_final: 0.6246 (mm-40) REVERT: D 485 MET cc_start: 0.5059 (mpp) cc_final: 0.4365 (ptm) outliers start: 59 outliers final: 37 residues processed: 249 average time/residue: 1.2067 time to fit residues: 331.9120 Evaluate side-chains 254 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 203 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 284 LEU 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 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 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 339 ARG 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 C residue 58 ARG 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 326 MET Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 399 VAL 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 326 MET Chi-restraints excluded: chain D residue 356 SER 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 Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 48 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 119 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 B 495 GLN 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 = 0.229170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188850 restraints weight = 14979.736| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.45 r_work: 0.3479 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15169 Z= 0.123 Angle : 0.564 10.338 20559 Z= 0.296 Chirality : 0.041 0.175 2309 Planarity : 0.004 0.043 2562 Dihedral : 8.664 89.925 2125 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.20 % Allowed : 27.65 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1788 helix: 0.43 (0.16), residues: 1081 sheet: -1.66 (0.45), residues: 113 loop : -1.16 (0.27), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 246 HIS 0.004 0.001 HIS C 294 PHE 0.031 0.001 PHE A 409 TYR 0.011 0.001 TYR D 210 ARG 0.011 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03754 ( 752) hydrogen bonds : angle 3.83810 ( 2130) covalent geometry : bond 0.00282 (15169) covalent geometry : angle 0.56445 (20559) *********************** 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 270 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 203 time to evaluate : 1.495 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7562 (OUTLIER) cc_final: 0.6595 (t80) REVERT: A 56 LYS cc_start: 0.7159 (mmtm) cc_final: 0.6586 (mtmt) REVERT: A 93 ASP cc_start: 0.7293 (t0) cc_final: 0.7037 (m-30) REVERT: A 119 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7406 (pt) REVERT: A 123 ASP cc_start: 0.6383 (t70) cc_final: 0.6060 (t0) REVERT: A 137 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7932 (tm) REVERT: A 238 MET cc_start: 0.8323 (tpp) cc_final: 0.7941 (tmm) REVERT: A 284 LEU cc_start: 0.9088 (mp) cc_final: 0.8755 (mt) REVERT: A 298 ARG cc_start: 0.7560 (ptm160) cc_final: 0.6550 (ttp80) REVERT: A 326 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8096 (ptt) REVERT: A 401 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7539 (tp) REVERT: A 414 ASN cc_start: 0.7356 (t0) cc_final: 0.7087 (t0) REVERT: A 485 MET cc_start: 0.7780 (tmm) cc_final: 0.7055 (mmp) REVERT: A 488 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6448 (mm) REVERT: B 122 ASP cc_start: 0.7627 (p0) cc_final: 0.7287 (p0) REVERT: B 177 GLN cc_start: 0.7335 (mt0) cc_final: 0.6738 (mm-40) REVERT: B 180 TYR cc_start: 0.5644 (OUTLIER) cc_final: 0.5378 (t80) REVERT: B 307 MET cc_start: 0.8817 (ptt) cc_final: 0.8601 (ptt) REVERT: B 310 MET cc_start: 0.8932 (ptt) cc_final: 0.8214 (ptt) REVERT: B 334 ARG cc_start: 0.7468 (ppt-90) cc_final: 0.6261 (mmp-170) REVERT: B 394 GLN cc_start: 0.7251 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 417 GLN cc_start: 0.7206 (mm110) cc_final: 0.6869 (tt0) REVERT: B 432 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: B 444 TYR cc_start: 0.7882 (m-80) cc_final: 0.7075 (m-80) REVERT: B 491 ARG cc_start: 0.6795 (ptt-90) cc_final: 0.6169 (ptm-80) REVERT: B 498 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7362 (ttm170) REVERT: C 83 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8011 (mmm-85) REVERT: C 84 LYS cc_start: 0.8304 (ptpp) cc_final: 0.7950 (pttm) REVERT: C 177 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7151 (ttm-80) REVERT: C 215 ARG cc_start: 0.7738 (mtm180) cc_final: 0.7207 (mmp80) REVERT: C 244 MET cc_start: 0.8938 (tpp) cc_final: 0.8552 (mmm) REVERT: C 326 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7773 (ttt) REVERT: C 352 LYS cc_start: 0.6842 (tppp) cc_final: 0.6466 (ttpt) REVERT: C 381 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6225 (mp) REVERT: C 383 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7401 (tm-30) REVERT: C 412 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7403 (mp) REVERT: C 451 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7298 (tp) REVERT: D 84 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7805 (pttm) REVERT: D 177 ARG cc_start: 0.7983 (ttp80) cc_final: 0.7456 (ttm-80) REVERT: D 232 LEU cc_start: 0.8594 (mt) cc_final: 0.8364 (mt) REVERT: D 326 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.5739 (ptt) REVERT: D 339 GLU cc_start: 0.6716 (tm-30) cc_final: 0.6128 (mp0) REVERT: D 434 LYS cc_start: 0.3931 (OUTLIER) cc_final: 0.3411 (ttpt) REVERT: D 450 GLN cc_start: 0.6602 (tp40) cc_final: 0.6261 (mm-40) REVERT: D 485 MET cc_start: 0.4787 (mpp) cc_final: 0.4235 (ptm) outliers start: 67 outliers final: 41 residues processed: 257 average time/residue: 1.1879 time to fit residues: 337.9728 Evaluate side-chains 252 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 372 LEU 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 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 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 339 ARG 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 C residue 58 ARG Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 322 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 381 LEU 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 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 249 THR Chi-restraints excluded: chain D residue 297 SER Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain D residue 356 SER 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 Chi-restraints excluded: chain D residue 488 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 179 random chunks: chunk 169 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 50 optimal weight: 0.0570 chunk 127 optimal weight: 0.7980 chunk 121 optimal weight: 0.0070 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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** C 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.230101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.190084 restraints weight = 15087.067| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.39 r_work: 0.3522 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15169 Z= 0.110 Angle : 0.555 9.885 20559 Z= 0.291 Chirality : 0.040 0.168 2309 Planarity : 0.004 0.044 2562 Dihedral : 8.412 86.623 2123 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.51 % Allowed : 28.40 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.20), residues: 1788 helix: 0.57 (0.16), residues: 1082 sheet: -1.44 (0.44), residues: 118 loop : -1.15 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 246 HIS 0.003 0.001 HIS C 294 PHE 0.032 0.001 PHE A 409 TYR 0.023 0.001 TYR A 157 ARG 0.012 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 752) hydrogen bonds : angle 3.78668 ( 2130) covalent geometry : bond 0.00245 (15169) covalent geometry : angle 0.55477 (20559) ********************** 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 253 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 53 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.6584 (t80) REVERT: A 56 LYS cc_start: 0.7252 (mmtm) cc_final: 0.6663 (mtmt) REVERT: A 93 ASP cc_start: 0.7183 (t0) cc_final: 0.6924 (m-30) REVERT: A 119 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7411 (pt) REVERT: A 123 ASP cc_start: 0.6411 (t70) cc_final: 0.6110 (t0) REVERT: A 137 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7924 (tm) REVERT: A 215 ARG cc_start: 0.7708 (mtp85) cc_final: 0.6762 (ptt90) REVERT: A 238 MET cc_start: 0.8263 (tpp) cc_final: 0.7968 (tmm) REVERT: A 284 LEU cc_start: 0.9081 (mp) cc_final: 0.8731 (mt) REVERT: A 298 ARG cc_start: 0.7563 (ptm160) cc_final: 0.6538 (ttp80) REVERT: A 326 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8147 (ptt) REVERT: A 401 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7700 (tp) REVERT: A 414 ASN cc_start: 0.7357 (t0) cc_final: 0.7122 (t0) REVERT: A 485 MET cc_start: 0.7690 (tmm) cc_final: 0.7053 (mmp) REVERT: B 122 ASP cc_start: 0.7516 (p0) cc_final: 0.7166 (p0) REVERT: B 177 GLN cc_start: 0.7371 (mt0) cc_final: 0.6784 (mm-40) REVERT: B 180 TYR cc_start: 0.5628 (OUTLIER) cc_final: 0.5391 (t80) REVERT: B 280 MET cc_start: 0.9101 (mmp) cc_final: 0.8799 (mmp) REVERT: B 307 MET cc_start: 0.8778 (ptt) cc_final: 0.8567 (ptt) REVERT: B 310 MET cc_start: 0.8868 (ptt) cc_final: 0.8038 (ptt) REVERT: B 334 ARG cc_start: 0.7452 (ppt-90) cc_final: 0.6237 (mmp-170) REVERT: B 417 GLN cc_start: 0.7150 (mm110) cc_final: 0.6839 (tt0) REVERT: B 432 GLU cc_start: 0.6363 (OUTLIER) cc_final: 0.5928 (mt-10) REVERT: B 491 ARG cc_start: 0.6807 (ptt-90) cc_final: 0.6198 (ptm-80) REVERT: B 498 ARG cc_start: 0.7682 (ttm170) cc_final: 0.7254 (ttp-110) REVERT: C 83 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8060 (mmm-85) REVERT: C 84 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7863 (pttm) REVERT: C 177 ARG cc_start: 0.7489 (mtm110) cc_final: 0.7141 (ttm-80) REVERT: C 215 ARG cc_start: 0.7845 (mtm180) cc_final: 0.7232 (mmp80) REVERT: C 244 MET cc_start: 0.8911 (tpp) cc_final: 0.8510 (mmm) REVERT: C 326 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7809 (ttt) REVERT: C 335 ARG cc_start: 0.6844 (mtt-85) cc_final: 0.6605 (mtt180) REVERT: C 352 LYS cc_start: 0.6854 (tppp) cc_final: 0.6523 (ttpt) REVERT: C 381 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6272 (mp) REVERT: C 383 GLN cc_start: 0.7785 (tm-30) cc_final: 0.7361 (tm-30) REVERT: C 412 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7458 (mp) REVERT: C 451 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7292 (tp) REVERT: D 84 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7772 (pttm) REVERT: D 177 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7476 (ttm-80) REVERT: D 232 LEU cc_start: 0.8609 (mt) cc_final: 0.8366 (mt) REVERT: D 326 MET cc_start: 0.6636 (OUTLIER) cc_final: 0.5784 (ptt) REVERT: D 339 GLU cc_start: 0.6701 (tm-30) cc_final: 0.6162 (mp0) REVERT: D 434 LYS cc_start: 0.4129 (OUTLIER) cc_final: 0.3558 (ttpt) REVERT: D 485 MET cc_start: 0.4928 (mpp) cc_final: 0.4404 (ptm) outliers start: 56 outliers final: 38 residues processed: 242 average time/residue: 1.1914 time to fit residues: 319.2970 Evaluate side-chains 250 residues out of total 1595 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 197 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 119 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 153 SER Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 326 MET Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 THR 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 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 339 ARG Chi-restraints excluded: chain B residue 375 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 514 VAL Chi-restraints excluded: chain C residue 83 ARG Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 326 MET Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 381 LEU 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 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 326 MET Chi-restraints excluded: chain D residue 356 SER 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 99 optimal weight: 0.5980 chunk 169 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 chunk 108 optimal weight: 0.0030 chunk 140 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 360 HIS ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.230346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.190498 restraints weight = 15118.540| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.47 r_work: 0.3512 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3337 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15169 Z= 0.111 Angle : 0.552 9.454 20559 Z= 0.289 Chirality : 0.040 0.165 2309 Planarity : 0.004 0.044 2562 Dihedral : 8.265 89.499 2123 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.89 % Allowed : 27.84 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.20), residues: 1788 helix: 0.66 (0.16), residues: 1082 sheet: -1.21 (0.47), residues: 108 loop : -1.19 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 246 HIS 0.004 0.001 HIS C 294 PHE 0.031 0.001 PHE A 409 TYR 0.010 0.001 TYR D 283 ARG 0.011 0.000 ARG C 467 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 752) hydrogen bonds : angle 3.75126 ( 2130) covalent geometry : bond 0.00248 (15169) covalent geometry : angle 0.55157 (20559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14562.95 seconds wall clock time: 255 minutes 25.13 seconds (15325.13 seconds total)