Starting phenix.real_space_refine on Thu Jul 31 20:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.map" model { file = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2025/7cte_30462.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 64 5.16 5 C 8810 2.51 5 N 2306 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 118 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13699 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2460 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 302, 2460 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4828 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 567} Chain breaks: 7 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3305 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 13, 'TRANS': 392} Chain breaks: 3 Chain: "E" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3044 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 18, 'TRANS': 354} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.61, per 1000 atoms: 0.56 Number of scatterers: 13699 At special positions: 0 Unit cell: (112.69, 121.804, 149.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 6 15.00 O 2513 8.00 N 2306 7.00 C 8810 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: 2.96 Conformation dependent library (CDL) restraints added in 1.6 seconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3256 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 11 sheets defined 61.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.782A pdb=" N TRP B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 331 Processing helix chain 'B' and resid 347 through 359 removed outlier: 3.851A pdb=" N VAL B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 383 removed outlier: 4.384A pdb=" N PHE B 380 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU B 382 " --> pdb=" O ASN B 378 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 414 removed outlier: 3.611A pdb=" N ILE B 409 " --> pdb=" O SER B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 removed outlier: 3.900A pdb=" N MET B 432 " --> pdb=" O ALA B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'B' and resid 473 through 483 removed outlier: 4.117A pdb=" N LEU B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 501 removed outlier: 3.562A pdb=" N LEU B 494 " --> pdb=" O GLY B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 566 through 573 removed outlier: 4.736A pdb=" N LEU B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 64 Processing helix chain 'C' and resid 66 through 83 removed outlier: 3.934A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 83 " --> pdb=" O LYS C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 removed outlier: 3.840A pdb=" N THR C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 163 removed outlier: 3.900A pdb=" N ILE C 162 " --> pdb=" O CYS C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 207 removed outlier: 4.112A pdb=" N LEU C 200 " --> pdb=" O ASP C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.684A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.085A pdb=" N HIS C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 270 Processing helix chain 'C' and resid 281 through 293 removed outlier: 4.401A pdb=" N THR C 287 " --> pdb=" O GLU C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 316 Processing helix chain 'C' and resid 321 through 339 removed outlier: 4.146A pdb=" N GLN C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 355 removed outlier: 4.299A pdb=" N ARG C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 380 through 388 removed outlier: 4.765A pdb=" N ALA C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 425 removed outlier: 4.130A pdb=" N GLU C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 400 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 414 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 415 " --> pdb=" O ASN C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 442 removed outlier: 3.623A pdb=" N LEU C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS C 440 " --> pdb=" O ARG C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 460 removed outlier: 3.522A pdb=" N ALA C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 482 Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.707A pdb=" N LEU C 487 " --> pdb=" O CYS C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'C' and resid 549 through 566 Processing helix chain 'C' and resid 569 through 574 removed outlier: 3.568A pdb=" N THR C 573 " --> pdb=" O LEU C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 584 through 593 removed outlier: 4.605A pdb=" N GLU C 590 " --> pdb=" O HIS C 586 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS C 591 " --> pdb=" O ALA C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 606 removed outlier: 3.861A pdb=" N HIS C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 Processing helix chain 'C' and resid 645 through 663 removed outlier: 3.605A pdb=" N TRP C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 691 removed outlier: 3.805A pdb=" N GLU C 687 " --> pdb=" O ARG C 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 30 removed outlier: 3.803A pdb=" N GLU D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG D 27 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 57 removed outlier: 4.054A pdb=" N GLU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 87 removed outlier: 3.505A pdb=" N LEU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 removed outlier: 3.596A pdb=" N LYS D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 removed outlier: 4.372A pdb=" N ASN D 122 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.628A pdb=" N PHE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 183 removed outlier: 4.962A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 202 Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 235 removed outlier: 3.985A pdb=" N LYS D 228 " --> pdb=" O PRO D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 259 Processing helix chain 'D' and resid 259 through 273 removed outlier: 3.567A pdb=" N ILE D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 289 removed outlier: 3.992A pdb=" N ALA D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 309 removed outlier: 3.849A pdb=" N CYS D 309 " --> pdb=" O ALA D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 320 removed outlier: 3.817A pdb=" N GLY D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.834A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 3.757A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET D 373 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS D 374 " --> pdb=" O PRO D 370 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 375 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE D 376 " --> pdb=" O VAL D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 415 removed outlier: 3.996A pdb=" N ILE D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'E' and resid 11 through 23 removed outlier: 4.105A pdb=" N GLY E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.917A pdb=" N THR E 53 " --> pdb=" O THR E 49 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.624A pdb=" N LEU E 72 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 110 removed outlier: 3.744A pdb=" N LYS E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN E 108 " --> pdb=" O ARG E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 removed outlier: 4.247A pdb=" N ASP E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 removed outlier: 3.948A pdb=" N ARG E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 removed outlier: 3.572A pdb=" N ALA E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 166 removed outlier: 3.701A pdb=" N PHE E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.767A pdb=" N GLY E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 244 Proline residue: E 234 - end of helix Proline residue: E 239 - end of helix Processing helix chain 'E' and resid 250 through 268 Proline residue: E 259 - end of helix removed outlier: 4.427A pdb=" N LYS E 263 " --> pdb=" O PRO E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 316 Processing helix chain 'E' and resid 323 through 328 removed outlier: 4.288A pdb=" N PHE E 327 " --> pdb=" O THR E 323 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE E 328 " --> pdb=" O ASP E 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 323 through 328' Processing helix chain 'E' and resid 358 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.678A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR E 389 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 422 Processing helix chain 'E' and resid 427 through 432 Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 314 removed outlier: 6.050A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.812A pdb=" N HIS B 336 " --> pdb=" O PHE C 13 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 13 " --> pdb=" O HIS B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 549 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 105 through 106 removed outlier: 5.977A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 133 through 136 Processing sheet with id=AA7, first strand: chain 'C' and resid 695 through 696 removed outlier: 3.823A pdb=" N LYS C 695 " --> pdb=" O ALA C 705 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA C 705 " --> pdb=" O LYS C 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 64 through 65 removed outlier: 8.273A pdb=" N ILE D 190 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE D 156 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N LEU D 192 " --> pdb=" O PHE D 156 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 158 " --> pdb=" O LEU D 192 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 155 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.551A pdb=" N ILE E 122 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 393 through 395 637 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3038 1.33 - 1.45: 3250 1.45 - 1.58: 7591 1.58 - 1.70: 15 1.70 - 1.82: 94 Bond restraints: 13988 Sorted by residual: bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.14e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.79e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.79e+01 bond pdb=" C5 ATP E 901 " pdb=" N7 ATP E 901 " ideal model delta sigma weight residual 1.387 1.328 0.059 1.00e-02 1.00e+04 3.51e+01 bond pdb=" CG1 ILE E 190 " pdb=" CD1 ILE E 190 " ideal model delta sigma weight residual 1.513 1.294 0.219 3.90e-02 6.57e+02 3.16e+01 ... (remaining 13983 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 18405 4.29 - 8.59: 442 8.59 - 12.88: 70 12.88 - 17.18: 13 17.18 - 21.47: 6 Bond angle restraints: 18936 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 118.40 21.47 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 120.53 19.34 1.00e+00 1.00e+00 3.74e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 118.51 18.32 1.00e+00 1.00e+00 3.36e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 120.57 16.26 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP E 901 " pdb=" C4 ATP E 901 " pdb=" N3 ATP E 901 " ideal model delta sigma weight residual 126.80 116.63 10.17 1.00e+00 1.00e+00 1.03e+02 ... (remaining 18931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 7013 17.85 - 35.71: 1123 35.71 - 53.56: 290 53.56 - 71.41: 52 71.41 - 89.27: 16 Dihedral angle restraints: 8494 sinusoidal: 3527 harmonic: 4967 Sorted by residual: dihedral pdb=" CA PRO C 628 " pdb=" C PRO C 628 " pdb=" N ASP C 629 " pdb=" CA ASP C 629 " ideal model delta harmonic sigma weight residual 180.00 135.48 44.52 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA ASP E 400 " pdb=" C ASP E 400 " pdb=" N GLN E 401 " pdb=" CA GLN E 401 " ideal model delta harmonic sigma weight residual 180.00 135.82 44.18 0 5.00e+00 4.00e-02 7.81e+01 dihedral pdb=" CA SER C 280 " pdb=" C SER C 280 " pdb=" N CYS C 281 " pdb=" CA CYS C 281 " ideal model delta harmonic sigma weight residual -180.00 -136.32 -43.68 0 5.00e+00 4.00e-02 7.63e+01 ... (remaining 8491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1886 0.112 - 0.224: 242 0.224 - 0.335: 27 0.335 - 0.447: 8 0.447 - 0.559: 2 Chirality restraints: 2165 Sorted by residual: chirality pdb=" CG LEU C 414 " pdb=" CB LEU C 414 " pdb=" CD1 LEU C 414 " pdb=" CD2 LEU C 414 " both_signs ideal model delta sigma weight residual False -2.59 -2.03 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CG LEU B 570 " pdb=" CB LEU B 570 " pdb=" CD1 LEU B 570 " pdb=" CD2 LEU B 570 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.38e+00 ... (remaining 2162 not shown) Planarity restraints: 2384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 609 " 0.062 2.00e-02 2.50e+03 3.51e-02 2.47e+01 pdb=" CG TYR C 609 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR C 609 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR C 609 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR C 609 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 609 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR C 609 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 609 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 627 " -0.068 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 628 " 0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 628 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 628 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 28 " -0.042 2.00e-02 2.50e+03 2.95e-02 1.53e+01 pdb=" CG PHE D 28 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE D 28 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 28 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE D 28 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE D 28 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE D 28 " -0.031 2.00e-02 2.50e+03 ... (remaining 2381 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3006 2.78 - 3.31: 12473 3.31 - 3.84: 22510 3.84 - 4.37: 24542 4.37 - 4.90: 41935 Nonbonded interactions: 104466 Sorted by model distance: nonbonded pdb=" O ALA C 654 " pdb=" OG1 THR C 658 " model vdw 2.246 3.040 nonbonded pdb=" O TRP B 433 " pdb=" OG SER E 382 " model vdw 2.274 3.040 nonbonded pdb=" O SER B 385 " pdb=" OG SER B 385 " model vdw 2.288 3.040 nonbonded pdb=" O SER D 91 " pdb=" OG SER D 91 " model vdw 2.296 3.040 nonbonded pdb=" O LYS C 202 " pdb=" OG1 THR C 206 " model vdw 2.317 3.040 ... (remaining 104461 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 29.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.012 0.219 13988 Z= 0.559 Angle : 1.692 21.469 18936 Z= 0.944 Chirality : 0.080 0.559 2165 Planarity : 0.011 0.100 2384 Dihedral : 18.732 89.267 5238 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.80 % Favored : 93.02 % Rotamer: Outliers : 2.93 % Allowed : 19.32 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.94 % 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: -4.71 (0.16), residues: 1633 helix: -3.09 (0.12), residues: 878 sheet: -2.98 (0.38), residues: 139 loop : -2.92 (0.21), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.006 TRP E 162 HIS 0.024 0.004 HIS C 486 PHE 0.055 0.007 PHE D 28 TYR 0.073 0.007 TYR C 609 ARG 0.022 0.002 ARG B 493 Details of bonding type rmsd hydrogen bonds : bond 0.17096 ( 637) hydrogen bonds : angle 8.45822 ( 1896) covalent geometry : bond 0.01246 (13988) covalent geometry : angle 1.69239 (18936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 337 VAL cc_start: 0.8948 (t) cc_final: 0.8746 (t) REVERT: C 52 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 139 LYS cc_start: 0.8128 (pttp) cc_final: 0.7854 (pttm) REVERT: C 222 MET cc_start: 0.7180 (tmm) cc_final: 0.6806 (tmm) REVERT: C 252 ILE cc_start: 0.9070 (mt) cc_final: 0.8689 (tt) REVERT: C 410 MET cc_start: 0.7804 (mtt) cc_final: 0.7561 (ttt) REVERT: C 426 LEU cc_start: 0.6801 (mt) cc_final: 0.6504 (mt) REVERT: C 428 LYS cc_start: 0.7166 (tmtt) cc_final: 0.5961 (mptt) REVERT: C 477 LYS cc_start: 0.8000 (mttt) cc_final: 0.7491 (pttt) REVERT: C 683 ARG cc_start: 0.8191 (ttp-170) cc_final: 0.7444 (ttp80) REVERT: C 685 VAL cc_start: 0.7828 (p) cc_final: 0.7620 (p) REVERT: D 81 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8821 (mm) REVERT: D 108 LYS cc_start: 0.8351 (tttt) cc_final: 0.7850 (mmtt) REVERT: D 257 SER cc_start: 0.8942 (OUTLIER) cc_final: 0.8572 (p) REVERT: D 335 LEU cc_start: 0.8512 (tt) cc_final: 0.8304 (tt) REVERT: D 367 PHE cc_start: 0.7957 (m-80) cc_final: 0.7446 (m-80) REVERT: D 381 GLN cc_start: 0.8980 (mm-40) cc_final: 0.8523 (mp10) REVERT: E 101 ASP cc_start: 0.8463 (m-30) cc_final: 0.7793 (m-30) REVERT: E 145 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7719 (tp-100) REVERT: E 152 VAL cc_start: 0.8363 (OUTLIER) cc_final: 0.7779 (t) REVERT: E 171 CYS cc_start: 0.8694 (t) cc_final: 0.8458 (t) outliers start: 45 outliers final: 7 residues processed: 295 average time/residue: 0.2459 time to fit residues: 107.1781 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 194 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 369 ILE Chi-restraints excluded: chain B residue 426 HIS Chi-restraints excluded: chain B residue 434 ASP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 402 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 96 optimal weight: 0.0980 chunk 150 optimal weight: 4.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 GLN B 292 GLN B 306 HIS B 336 HIS B 372 GLN C 58 ASN C 62 GLN C 347 ASN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 605 ASN C 613 ASN C 678 HIS D 98 HIS D 119 ASN D 175 ASN D 233 GLN D 271 ASN D 288 ASN E 27 HIS ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 100 ASN E 168 ASN E 299 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102432 restraints weight = 34467.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105164 restraints weight = 18927.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106941 restraints weight = 12754.908| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13988 Z= 0.159 Angle : 0.794 10.915 18936 Z= 0.415 Chirality : 0.044 0.193 2165 Planarity : 0.006 0.078 2384 Dihedral : 10.306 85.152 1866 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.03 % Allowed : 23.03 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.19 % 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: -2.84 (0.18), residues: 1633 helix: -1.27 (0.15), residues: 899 sheet: -2.69 (0.40), residues: 134 loop : -2.46 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 249 HIS 0.008 0.001 HIS E 227 PHE 0.035 0.002 PHE D 28 TYR 0.021 0.002 TYR C 453 ARG 0.005 0.001 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.05431 ( 637) hydrogen bonds : angle 5.88961 ( 1896) covalent geometry : bond 0.00338 (13988) covalent geometry : angle 0.79353 (18936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 453 PRO cc_start: 0.7889 (Cg_endo) cc_final: 0.6979 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6092 (mm) REVERT: C 13 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: C 52 GLN cc_start: 0.8330 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 71 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7742 (t70) REVERT: C 139 LYS cc_start: 0.8239 (pttp) cc_final: 0.8035 (pttt) REVERT: C 222 MET cc_start: 0.7037 (tmm) cc_final: 0.6686 (tmm) REVERT: C 223 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7784 (mm-30) REVERT: C 301 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8214 (mmmt) REVERT: C 318 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8629 (t0) REVERT: C 334 GLU cc_start: 0.8020 (tp30) cc_final: 0.7770 (tp30) REVERT: C 346 CYS cc_start: 0.8519 (m) cc_final: 0.8065 (m) REVERT: C 410 MET cc_start: 0.7785 (mtt) cc_final: 0.7500 (ttp) REVERT: C 426 LEU cc_start: 0.6700 (mt) cc_final: 0.6466 (mt) REVERT: C 428 LYS cc_start: 0.7386 (tmtt) cc_final: 0.6443 (mttt) REVERT: C 476 PHE cc_start: 0.6521 (t80) cc_final: 0.6028 (t80) REVERT: D 86 GLU cc_start: 0.8322 (tt0) cc_final: 0.8097 (tt0) REVERT: D 108 LYS cc_start: 0.8268 (tttt) cc_final: 0.7878 (mmtt) REVERT: D 284 MET cc_start: 0.9222 (tpt) cc_final: 0.8995 (tpp) REVERT: E 101 ASP cc_start: 0.8408 (m-30) cc_final: 0.7979 (m-30) REVERT: E 171 CYS cc_start: 0.8060 (t) cc_final: 0.7212 (m) REVERT: E 236 TYR cc_start: 0.7543 (t80) cc_final: 0.7162 (t80) outliers start: 62 outliers final: 25 residues processed: 289 average time/residue: 0.2140 time to fit residues: 95.8130 Evaluate side-chains 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 555 ASN Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 163 optimal weight: 0.0000 chunk 110 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 416 HIS ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.124809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.103632 restraints weight = 35258.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105139 restraints weight = 19839.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106197 restraints weight = 13928.252| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3591 r_free = 0.3591 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13988 Z= 0.239 Angle : 0.811 9.105 18936 Z= 0.421 Chirality : 0.046 0.180 2165 Planarity : 0.005 0.072 2384 Dihedral : 9.528 78.746 1854 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.40 % Allowed : 24.46 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.06 % 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: -2.21 (0.20), residues: 1633 helix: -0.63 (0.16), residues: 921 sheet: -2.59 (0.39), residues: 146 loop : -2.40 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 428 HIS 0.011 0.002 HIS D 334 PHE 0.043 0.003 PHE B 492 TYR 0.020 0.002 TYR D 226 ARG 0.014 0.001 ARG C 683 Details of bonding type rmsd hydrogen bonds : bond 0.05241 ( 637) hydrogen bonds : angle 5.65400 ( 1896) covalent geometry : bond 0.00541 (13988) covalent geometry : angle 0.81139 (18936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 207 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: B 357 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: B 453 PRO cc_start: 0.7529 (Cg_endo) cc_final: 0.6778 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6051 (mm) REVERT: C 13 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7603 (m-80) REVERT: C 71 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7930 (t70) REVERT: C 139 LYS cc_start: 0.8311 (pttp) cc_final: 0.8075 (pttt) REVERT: C 207 SER cc_start: 0.8830 (t) cc_final: 0.8509 (p) REVERT: C 222 MET cc_start: 0.6946 (tmm) cc_final: 0.6374 (tmm) REVERT: C 318 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8544 (t0) REVERT: C 330 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9325 (tt) REVERT: C 388 LEU cc_start: 0.8071 (tp) cc_final: 0.6940 (tp) REVERT: C 428 LYS cc_start: 0.7484 (tmtt) cc_final: 0.6513 (mttt) REVERT: C 663 MET cc_start: 0.6474 (ppp) cc_final: 0.6232 (ppp) REVERT: D 81 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8615 (mm) REVERT: D 108 LYS cc_start: 0.8194 (tttt) cc_final: 0.7916 (mmtt) REVERT: D 269 HIS cc_start: 0.7620 (m170) cc_final: 0.7408 (m170) REVERT: D 367 PHE cc_start: 0.8008 (m-80) cc_final: 0.7695 (m-10) REVERT: E 101 ASP cc_start: 0.8250 (m-30) cc_final: 0.7792 (m-30) REVERT: E 171 CYS cc_start: 0.8252 (t) cc_final: 0.8048 (t) REVERT: E 172 PHE cc_start: 0.8357 (t80) cc_final: 0.8110 (t80) REVERT: E 236 TYR cc_start: 0.7723 (t80) cc_final: 0.7274 (t80) outliers start: 83 outliers final: 46 residues processed: 270 average time/residue: 0.2229 time to fit residues: 92.1525 Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 188 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 108 optimal weight: 9.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 486 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 275 ASN E 297 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.125996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.104808 restraints weight = 34928.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.106470 restraints weight = 19431.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108039 restraints weight = 13476.751| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3624 r_free = 0.3624 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 13988 Z= 0.188 Angle : 0.739 8.739 18936 Z= 0.384 Chirality : 0.044 0.187 2165 Planarity : 0.005 0.068 2384 Dihedral : 9.008 71.752 1854 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 5.92 % Allowed : 26.15 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.06 % 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: -1.83 (0.20), residues: 1633 helix: -0.30 (0.17), residues: 924 sheet: -2.50 (0.41), residues: 135 loop : -2.29 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 249 HIS 0.006 0.001 HIS C 486 PHE 0.030 0.002 PHE C 479 TYR 0.019 0.002 TYR C 453 ARG 0.016 0.001 ARG C 683 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 637) hydrogen bonds : angle 5.38412 ( 1896) covalent geometry : bond 0.00429 (13988) covalent geometry : angle 0.73934 (18936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 202 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8602 (m110) cc_final: 0.8040 (m-40) REVERT: B 357 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7915 (mp0) REVERT: B 492 PHE cc_start: 0.8563 (p90) cc_final: 0.8314 (p90) REVERT: B 544 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6041 (mm) REVERT: C 13 PHE cc_start: 0.8215 (OUTLIER) cc_final: 0.7700 (m-80) REVERT: C 71 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7952 (t70) REVERT: C 139 LYS cc_start: 0.8289 (pttp) cc_final: 0.8044 (pttt) REVERT: C 207 SER cc_start: 0.8681 (t) cc_final: 0.8422 (p) REVERT: C 222 MET cc_start: 0.7032 (tmm) cc_final: 0.6832 (tmm) REVERT: C 281 CYS cc_start: 0.7712 (m) cc_final: 0.7477 (m) REVERT: C 318 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8547 (t0) REVERT: C 330 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9164 (tt) REVERT: C 388 LEU cc_start: 0.7392 (tp) cc_final: 0.6983 (tp) REVERT: C 428 LYS cc_start: 0.7476 (tmtt) cc_final: 0.6524 (mttt) REVERT: C 663 MET cc_start: 0.6665 (ppp) cc_final: 0.6318 (ppp) REVERT: D 81 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8589 (mm) REVERT: D 108 LYS cc_start: 0.8223 (tttt) cc_final: 0.7893 (mmtt) REVERT: D 367 PHE cc_start: 0.8004 (m-80) cc_final: 0.7755 (m-10) REVERT: D 381 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8090 (mp10) REVERT: E 101 ASP cc_start: 0.8403 (m-30) cc_final: 0.7838 (m-30) REVERT: E 171 CYS cc_start: 0.8212 (t) cc_final: 0.7978 (t) REVERT: E 179 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8585 (m-80) REVERT: E 236 TYR cc_start: 0.7694 (t80) cc_final: 0.7225 (t80) outliers start: 91 outliers final: 47 residues processed: 270 average time/residue: 0.2111 time to fit residues: 88.7523 Evaluate side-chains 242 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 186 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 541 ASP Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 179 PHE Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 119 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 16 optimal weight: 0.0070 chunk 153 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 HIS C 486 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107222 restraints weight = 34917.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108735 restraints weight = 19837.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.110307 restraints weight = 13999.804| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13988 Z= 0.140 Angle : 0.684 10.892 18936 Z= 0.354 Chirality : 0.044 0.488 2165 Planarity : 0.005 0.067 2384 Dihedral : 8.566 69.162 1854 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 4.29 % Allowed : 28.89 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.06 % 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: -1.49 (0.21), residues: 1633 helix: -0.00 (0.17), residues: 921 sheet: -2.42 (0.40), residues: 135 loop : -2.14 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 649 HIS 0.022 0.001 HIS C 486 PHE 0.037 0.002 PHE C 244 TYR 0.014 0.002 TYR D 226 ARG 0.012 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04303 ( 637) hydrogen bonds : angle 5.12079 ( 1896) covalent geometry : bond 0.00311 (13988) covalent geometry : angle 0.68397 (18936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 210 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8494 (m110) cc_final: 0.8040 (m-40) REVERT: B 357 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8017 (mp0) REVERT: B 443 TRP cc_start: 0.8915 (OUTLIER) cc_final: 0.8710 (m100) REVERT: B 492 PHE cc_start: 0.8520 (p90) cc_final: 0.8207 (p90) REVERT: B 544 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5991 (mm) REVERT: C 13 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: C 71 ASP cc_start: 0.8138 (t0) cc_final: 0.7903 (t70) REVERT: C 207 SER cc_start: 0.8679 (t) cc_final: 0.8462 (p) REVERT: C 301 LYS cc_start: 0.8313 (mmmm) cc_final: 0.7808 (mmmt) REVERT: C 318 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8541 (t0) REVERT: C 330 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9132 (tt) REVERT: C 388 LEU cc_start: 0.7365 (tp) cc_final: 0.6921 (tp) REVERT: C 428 LYS cc_start: 0.7575 (tmtt) cc_final: 0.6560 (mttt) REVERT: D 81 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8511 (tt) REVERT: D 108 LYS cc_start: 0.8181 (tttt) cc_final: 0.7922 (mmtt) REVERT: D 218 MET cc_start: 0.7013 (tpp) cc_final: 0.6756 (mmt) REVERT: D 233 GLN cc_start: 0.8485 (tp40) cc_final: 0.8268 (tp40) REVERT: D 381 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8118 (mp10) REVERT: E 10 CYS cc_start: 0.6886 (m) cc_final: 0.6291 (t) REVERT: E 101 ASP cc_start: 0.8202 (m-30) cc_final: 0.7737 (m-30) REVERT: E 171 CYS cc_start: 0.8094 (t) cc_final: 0.7833 (t) REVERT: E 236 TYR cc_start: 0.7731 (t80) cc_final: 0.7401 (t80) outliers start: 66 outliers final: 40 residues processed: 257 average time/residue: 0.2214 time to fit residues: 87.8148 Evaluate side-chains 238 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 330 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 80 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 HIS ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.130483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109427 restraints weight = 35129.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.111494 restraints weight = 19228.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.112139 restraints weight = 13041.473| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13988 Z= 0.124 Angle : 0.659 13.864 18936 Z= 0.337 Chirality : 0.042 0.310 2165 Planarity : 0.004 0.064 2384 Dihedral : 8.165 67.076 1854 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.20 % Allowed : 27.72 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.21 (0.21), residues: 1633 helix: 0.21 (0.17), residues: 930 sheet: -2.16 (0.41), residues: 141 loop : -2.07 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 443 HIS 0.009 0.001 HIS E 193 PHE 0.024 0.002 PHE C 479 TYR 0.015 0.001 TYR D 350 ARG 0.008 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.03929 ( 637) hydrogen bonds : angle 4.89219 ( 1896) covalent geometry : bond 0.00273 (13988) covalent geometry : angle 0.65923 (18936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8543 (m110) cc_final: 0.8100 (m110) REVERT: B 357 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: B 492 PHE cc_start: 0.8524 (p90) cc_final: 0.8196 (p90) REVERT: B 544 LEU cc_start: 0.6252 (OUTLIER) cc_final: 0.6012 (mm) REVERT: C 13 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: C 301 LYS cc_start: 0.8251 (mmmm) cc_final: 0.7864 (mmmt) REVERT: C 318 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8552 (t0) REVERT: C 396 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7581 (tm-30) REVERT: C 428 LYS cc_start: 0.7531 (tmtt) cc_final: 0.6509 (mttt) REVERT: C 487 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5100 (mm) REVERT: D 81 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8517 (tt) REVERT: D 108 LYS cc_start: 0.8127 (tttt) cc_final: 0.7876 (mmtt) REVERT: D 218 MET cc_start: 0.6944 (tpp) cc_final: 0.6696 (mmt) REVERT: D 233 GLN cc_start: 0.8467 (tp40) cc_final: 0.8098 (tp-100) REVERT: D 367 PHE cc_start: 0.7877 (m-80) cc_final: 0.7644 (m-10) REVERT: D 381 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: E 10 CYS cc_start: 0.6739 (m) cc_final: 0.6368 (t) REVERT: E 101 ASP cc_start: 0.8272 (m-30) cc_final: 0.7772 (m-30) REVERT: E 171 CYS cc_start: 0.8035 (t) cc_final: 0.7766 (t) REVERT: E 236 TYR cc_start: 0.7711 (t80) cc_final: 0.7290 (t80) outliers start: 80 outliers final: 51 residues processed: 281 average time/residue: 0.2108 time to fit residues: 91.8335 Evaluate side-chains 252 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 194 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 63 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 31 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 HIS C 58 ASN C 399 GLN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 380 GLN ** E 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 = 0.3882 r_free = 0.3882 target = 0.125392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104571 restraints weight = 35507.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.105881 restraints weight = 20459.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.107067 restraints weight = 14428.463| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3590 r_free = 0.3590 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13988 Z= 0.248 Angle : 0.788 12.460 18936 Z= 0.402 Chirality : 0.047 0.247 2165 Planarity : 0.005 0.062 2384 Dihedral : 8.458 62.421 1854 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 6.05 % Allowed : 27.85 % Favored : 66.10 % 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: -1.36 (0.21), residues: 1633 helix: 0.10 (0.17), residues: 925 sheet: -2.11 (0.41), residues: 144 loop : -2.16 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 443 HIS 0.009 0.001 HIS E 193 PHE 0.047 0.003 PHE C 244 TYR 0.023 0.002 TYR B 460 ARG 0.007 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 637) hydrogen bonds : angle 5.21982 ( 1896) covalent geometry : bond 0.00564 (13988) covalent geometry : angle 0.78798 (18936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 188 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8561 (m110) cc_final: 0.8071 (m-40) REVERT: B 492 PHE cc_start: 0.8517 (p90) cc_final: 0.8007 (p90) REVERT: B 544 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6099 (mm) REVERT: C 13 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7702 (m-80) REVERT: C 301 LYS cc_start: 0.8305 (mmmm) cc_final: 0.7812 (mmmt) REVERT: C 318 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8481 (t0) REVERT: C 428 LYS cc_start: 0.7630 (tmtt) cc_final: 0.6618 (mptt) REVERT: C 486 HIS cc_start: 0.2858 (t-170) cc_final: 0.2606 (t-170) REVERT: D 81 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8675 (mm) REVERT: D 108 LYS cc_start: 0.8178 (tttt) cc_final: 0.7904 (mmtt) REVERT: D 167 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.6442 (m90) REVERT: D 218 MET cc_start: 0.7027 (tpp) cc_final: 0.6805 (mmt) REVERT: D 233 GLN cc_start: 0.8477 (tp40) cc_final: 0.8160 (tp-100) REVERT: D 236 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7299 (tt) REVERT: D 367 PHE cc_start: 0.7913 (m-80) cc_final: 0.7677 (m-10) REVERT: D 381 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: E 10 CYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6679 (t) REVERT: E 101 ASP cc_start: 0.8253 (m-30) cc_final: 0.7756 (m-30) REVERT: E 171 CYS cc_start: 0.8289 (t) cc_final: 0.7975 (t) REVERT: E 172 PHE cc_start: 0.8464 (t80) cc_final: 0.8222 (t80) REVERT: E 236 TYR cc_start: 0.7758 (t80) cc_final: 0.7247 (t80) outliers start: 93 outliers final: 64 residues processed: 259 average time/residue: 0.2316 time to fit residues: 94.4550 Evaluate side-chains 250 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 178 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 399 GLN Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 93 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 163 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.126877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106131 restraints weight = 35350.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108098 restraints weight = 19714.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.108805 restraints weight = 13582.314| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13988 Z= 0.180 Angle : 0.743 12.319 18936 Z= 0.377 Chirality : 0.045 0.301 2165 Planarity : 0.005 0.067 2384 Dihedral : 8.297 63.666 1854 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 5.20 % Allowed : 28.95 % Favored : 65.84 % 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: -1.34 (0.21), residues: 1633 helix: 0.14 (0.17), residues: 923 sheet: -2.23 (0.40), residues: 143 loop : -2.17 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 649 HIS 0.012 0.001 HIS D 334 PHE 0.043 0.002 PHE C 244 TYR 0.022 0.002 TYR D 350 ARG 0.004 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 637) hydrogen bonds : angle 5.12185 ( 1896) covalent geometry : bond 0.00417 (13988) covalent geometry : angle 0.74342 (18936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 190 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8543 (m110) cc_final: 0.8093 (m-40) REVERT: B 357 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: B 492 PHE cc_start: 0.8517 (p90) cc_final: 0.7978 (p90) REVERT: B 544 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5954 (mm) REVERT: C 13 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7672 (m-80) REVERT: C 297 GLN cc_start: 0.7368 (tm-30) cc_final: 0.7147 (tm-30) REVERT: C 318 ASP cc_start: 0.8833 (OUTLIER) cc_final: 0.8512 (t0) REVERT: C 428 LYS cc_start: 0.7634 (tmtt) cc_final: 0.6617 (mptt) REVERT: C 487 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5258 (mm) REVERT: D 81 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8682 (mm) REVERT: D 108 LYS cc_start: 0.8168 (tttt) cc_final: 0.7900 (mmtt) REVERT: D 218 MET cc_start: 0.6995 (tpp) cc_final: 0.6786 (mmt) REVERT: D 233 GLN cc_start: 0.8395 (tp40) cc_final: 0.8121 (tp-100) REVERT: D 236 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7158 (tt) REVERT: D 367 PHE cc_start: 0.7862 (m-80) cc_final: 0.7602 (m-10) REVERT: D 381 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8084 (mp10) REVERT: E 10 CYS cc_start: 0.6791 (m) cc_final: 0.6352 (t) REVERT: E 101 ASP cc_start: 0.8283 (m-30) cc_final: 0.7793 (m-30) REVERT: E 171 CYS cc_start: 0.8267 (t) cc_final: 0.7884 (t) REVERT: E 236 TYR cc_start: 0.7556 (t80) cc_final: 0.7268 (t80) outliers start: 80 outliers final: 62 residues processed: 247 average time/residue: 0.2416 time to fit residues: 94.3140 Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 359 VAL Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 544 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 413 LEU Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 72 optimal weight: 0.0070 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 362 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.130784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109905 restraints weight = 34866.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111805 restraints weight = 19036.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.112927 restraints weight = 13152.183| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13988 Z= 0.127 Angle : 0.689 11.930 18936 Z= 0.346 Chirality : 0.042 0.179 2165 Planarity : 0.004 0.070 2384 Dihedral : 7.987 64.092 1854 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.23 % Allowed : 29.67 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.21), residues: 1633 helix: 0.35 (0.17), residues: 927 sheet: -2.10 (0.40), residues: 145 loop : -2.16 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 443 HIS 0.007 0.001 HIS E 193 PHE 0.039 0.002 PHE C 244 TYR 0.019 0.001 TYR B 498 ARG 0.003 0.000 ARG C 683 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 637) hydrogen bonds : angle 4.88573 ( 1896) covalent geometry : bond 0.00285 (13988) covalent geometry : angle 0.68871 (18936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 205 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8504 (m110) cc_final: 0.8053 (m110) REVERT: B 357 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8127 (mp0) REVERT: B 492 PHE cc_start: 0.8483 (p90) cc_final: 0.7967 (p90) REVERT: C 13 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: C 318 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8559 (t0) REVERT: C 428 LYS cc_start: 0.7619 (tmtt) cc_final: 0.6613 (mttt) REVERT: C 487 LEU cc_start: 0.5634 (OUTLIER) cc_final: 0.4992 (mm) REVERT: D 81 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8592 (tt) REVERT: D 108 LYS cc_start: 0.8139 (tttt) cc_final: 0.7856 (mmtt) REVERT: D 233 GLN cc_start: 0.8394 (tp40) cc_final: 0.8146 (tp-100) REVERT: D 236 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6976 (tt) REVERT: D 367 PHE cc_start: 0.7769 (m-80) cc_final: 0.7526 (m-10) REVERT: D 381 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: E 10 CYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6214 (t) REVERT: E 101 ASP cc_start: 0.8268 (m-30) cc_final: 0.7787 (m-30) REVERT: E 171 CYS cc_start: 0.8118 (t) cc_final: 0.7045 (m) REVERT: E 236 TYR cc_start: 0.7600 (t80) cc_final: 0.7372 (t80) outliers start: 65 outliers final: 46 residues processed: 249 average time/residue: 0.3058 time to fit residues: 119.9573 Evaluate side-chains 244 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 190 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 591 HIS Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 10 CYS Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 14 optimal weight: 0.0980 chunk 9 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.128929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.108350 restraints weight = 34974.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110264 restraints weight = 19349.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111186 restraints weight = 13362.489| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13988 Z= 0.159 Angle : 0.724 13.169 18936 Z= 0.362 Chirality : 0.044 0.188 2165 Planarity : 0.004 0.054 2384 Dihedral : 7.959 67.185 1854 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 3.64 % Allowed : 30.45 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.10 (0.21), residues: 1633 helix: 0.36 (0.17), residues: 925 sheet: -2.13 (0.41), residues: 143 loop : -2.12 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 443 HIS 0.008 0.001 HIS E 193 PHE 0.038 0.002 PHE C 244 TYR 0.017 0.002 TYR E 207 ARG 0.003 0.000 ARG B 320 Details of bonding type rmsd hydrogen bonds : bond 0.04130 ( 637) hydrogen bonds : angle 4.95244 ( 1896) covalent geometry : bond 0.00365 (13988) covalent geometry : angle 0.72415 (18936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8515 (m110) cc_final: 0.8066 (m-40) REVERT: B 357 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8113 (mp0) REVERT: B 480 VAL cc_start: 0.7383 (t) cc_final: 0.7118 (p) REVERT: B 492 PHE cc_start: 0.8486 (p90) cc_final: 0.7995 (p90) REVERT: C 13 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7572 (m-80) REVERT: C 318 ASP cc_start: 0.8797 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 428 LYS cc_start: 0.7640 (tmtt) cc_final: 0.6602 (mttt) REVERT: C 487 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5100 (mm) REVERT: D 81 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8583 (tt) REVERT: D 108 LYS cc_start: 0.8149 (tttt) cc_final: 0.7929 (mmtt) REVERT: D 167 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.6339 (m90) REVERT: D 233 GLN cc_start: 0.8437 (tp40) cc_final: 0.8152 (tp-100) REVERT: D 236 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7080 (tt) REVERT: D 367 PHE cc_start: 0.7855 (m-80) cc_final: 0.7610 (m-10) REVERT: D 381 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: E 10 CYS cc_start: 0.6712 (m) cc_final: 0.6334 (t) REVERT: E 101 ASP cc_start: 0.8349 (m-30) cc_final: 0.7814 (m-30) REVERT: E 171 CYS cc_start: 0.8203 (t) cc_final: 0.7106 (m) outliers start: 56 outliers final: 46 residues processed: 235 average time/residue: 0.2306 time to fit residues: 84.9565 Evaluate side-chains 241 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 363 MET Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 419 TYR Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 250 PHE Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 429 TYR Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 167 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 184 ILE Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 409 CYS Chi-restraints excluded: chain E residue 419 ILE Chi-restraints excluded: chain E residue 428 ILE Chi-restraints excluded: chain E residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 11 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 80 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.108922 restraints weight = 35326.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110488 restraints weight = 19837.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.111427 restraints weight = 13891.281| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13988 Z= 0.144 Angle : 0.716 13.248 18936 Z= 0.358 Chirality : 0.043 0.183 2165 Planarity : 0.004 0.054 2384 Dihedral : 7.936 67.986 1854 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.97 % Allowed : 30.64 % Favored : 65.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.07 (0.21), residues: 1633 helix: 0.38 (0.17), residues: 928 sheet: -2.07 (0.41), residues: 145 loop : -2.12 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 443 HIS 0.011 0.001 HIS D 334 PHE 0.038 0.002 PHE C 244 TYR 0.046 0.002 TYR B 498 ARG 0.003 0.000 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 637) hydrogen bonds : angle 4.91596 ( 1896) covalent geometry : bond 0.00330 (13988) covalent geometry : angle 0.71602 (18936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5358.21 seconds wall clock time: 97 minutes 14.69 seconds (5834.69 seconds total)