Starting phenix.real_space_refine on Wed Mar 4 13:05:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_30462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_30462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_30462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_30462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cte_30462/03_2026/7cte_30462.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU:plan': 2} 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: 2.76, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 623.2 milliseconds 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: 0.25 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: 1.74 Time building geometry restraints manager: 1.21 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.310 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.510 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.022 0.002 ARG B 493 TYR 0.073 0.007 TYR C 609 PHE 0.055 0.007 PHE D 28 TRP 0.032 0.006 TRP E 162 HIS 0.024 0.004 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.01246 (13988) covalent geometry : angle 1.69239 (18936) hydrogen bonds : bond 0.17096 ( 637) hydrogen bonds : angle 8.45822 ( 1896) *********************** 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 : 0.406 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: 0.7558 (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: 0.7446 (ttp80) REVERT: C 685 VAL cc_start: 0.7828 (p) cc_final: 0.7617 (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: 0.7797 (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: 0.1018 time to fit residues: 45.3217 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 B 563 ASN C 58 ASN 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 = 0.3841 r_free = 0.3841 target = 0.124850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102231 restraints weight = 34347.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104963 restraints weight = 18842.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.106782 restraints weight = 12624.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107947 restraints weight = 9692.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.108730 restraints weight = 8171.903| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3606 r_free = 0.3606 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2158 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 : 0.779 10.293 18936 Z= 0.410 Chirality : 0.043 0.181 2165 Planarity : 0.006 0.079 2384 Dihedral : 10.289 86.022 1866 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.90 % Allowed : 23.49 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.18), residues: 1633 helix: -1.24 (0.15), residues: 900 sheet: -2.70 (0.40), residues: 134 loop : -2.47 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 320 TYR 0.021 0.002 TYR E 207 PHE 0.036 0.002 PHE D 28 TRP 0.012 0.001 TRP D 249 HIS 0.009 0.001 HIS E 227 Details of bonding type rmsd covalent geometry : bond 0.00331 (13988) covalent geometry : angle 0.77900 (18936) hydrogen bonds : bond 0.05296 ( 637) hydrogen bonds : angle 5.85608 ( 1896) *********************** 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 302 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 242 time to evaluate : 0.534 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: 0.7838 (Cg_endo) cc_final: 0.6960 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.6103 (mm) REVERT: C 13 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7384 (m-80) REVERT: C 52 GLN cc_start: 0.8323 (tm-30) cc_final: 0.8092 (tm-30) REVERT: C 71 ASP cc_start: 0.8135 (OUTLIER) cc_final: 0.7735 (t70) REVERT: C 139 LYS cc_start: 0.8233 (pttp) cc_final: 0.8009 (pttt) REVERT: C 207 SER cc_start: 0.8862 (t) cc_final: 0.8505 (p) REVERT: C 222 MET cc_start: 0.7049 (tmm) cc_final: 0.6705 (tmm) REVERT: C 223 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7779 (mm-30) REVERT: C 301 LYS cc_start: 0.8646 (mmmm) cc_final: 0.8241 (mmmt) REVERT: C 318 ASP cc_start: 0.8934 (OUTLIER) cc_final: 0.8641 (t0) REVERT: C 334 GLU cc_start: 0.8068 (tp30) cc_final: 0.7807 (tp30) REVERT: C 346 CYS cc_start: 0.8459 (m) cc_final: 0.8011 (m) REVERT: C 410 MET cc_start: 0.7806 (mtt) cc_final: 0.7514 (ttp) REVERT: C 428 LYS cc_start: 0.7380 (tmtt) cc_final: 0.6430 (mttt) REVERT: C 476 PHE cc_start: 0.6554 (t80) cc_final: 0.6046 (t80) REVERT: D 86 GLU cc_start: 0.8295 (tt0) cc_final: 0.8083 (tt0) REVERT: D 108 LYS cc_start: 0.8273 (tttt) cc_final: 0.7875 (mmtt) REVERT: E 101 ASP cc_start: 0.8410 (m-30) cc_final: 0.7967 (m-30) REVERT: E 171 CYS cc_start: 0.8013 (t) cc_final: 0.7185 (m) REVERT: E 236 TYR cc_start: 0.7555 (t80) cc_final: 0.7174 (t80) outliers start: 60 outliers final: 26 residues processed: 288 average time/residue: 0.0925 time to fit residues: 41.1726 Evaluate side-chains 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 357 GLU 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 138 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 111 optimal weight: 0.0980 chunk 125 optimal weight: 2.9990 chunk 147 optimal weight: 0.0070 chunk 44 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.0980 chunk 24 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.3200 ------------------------------------------------------------------------------- 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 B 416 HIS C 62 GLN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN D 380 GLN E 62 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.131590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.109943 restraints weight = 34727.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.112286 restraints weight = 18793.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112993 restraints weight = 12443.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.113369 restraints weight = 11326.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.113493 restraints weight = 10082.351| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3701 r_free = 0.3701 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13988 Z= 0.131 Angle : 0.711 10.169 18936 Z= 0.367 Chirality : 0.042 0.174 2165 Planarity : 0.005 0.075 2384 Dihedral : 9.170 88.096 1854 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.49 % Allowed : 24.27 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.20), residues: 1633 helix: -0.51 (0.16), residues: 919 sheet: -2.39 (0.42), residues: 136 loop : -2.27 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 683 TYR 0.016 0.002 TYR D 255 PHE 0.044 0.002 PHE B 492 TRP 0.013 0.001 TRP D 428 HIS 0.010 0.001 HIS B 416 Details of bonding type rmsd covalent geometry : bond 0.00276 (13988) covalent geometry : angle 0.71086 (18936) hydrogen bonds : bond 0.04581 ( 637) hydrogen bonds : angle 5.30738 ( 1896) *********************** 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 308 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 239 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 357 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: B 544 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.6049 (mm) REVERT: C 13 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7268 (m-80) REVERT: C 71 ASP cc_start: 0.8103 (t0) cc_final: 0.7890 (t70) REVERT: C 139 LYS cc_start: 0.8194 (pttp) cc_final: 0.7951 (pttt) REVERT: C 207 SER cc_start: 0.8715 (t) cc_final: 0.8469 (p) REVERT: C 222 MET cc_start: 0.6644 (tmm) cc_final: 0.6389 (tmm) REVERT: C 281 CYS cc_start: 0.7502 (m) cc_final: 0.7215 (m) REVERT: C 301 LYS cc_start: 0.8294 (mmmm) cc_final: 0.7962 (mmmt) REVERT: C 334 GLU cc_start: 0.7852 (tp30) cc_final: 0.7649 (tp30) REVERT: C 388 LEU cc_start: 0.8115 (tp) cc_final: 0.6992 (tp) REVERT: C 428 LYS cc_start: 0.7435 (tmtt) cc_final: 0.6515 (mttt) REVERT: C 486 HIS cc_start: 0.4493 (OUTLIER) cc_final: 0.3803 (t70) REVERT: C 663 MET cc_start: 0.6398 (ppp) cc_final: 0.6123 (ppp) REVERT: D 81 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8493 (tt) REVERT: D 108 LYS cc_start: 0.8183 (tttt) cc_final: 0.7872 (mmtt) REVERT: D 367 PHE cc_start: 0.7898 (m-80) cc_final: 0.7591 (m-10) REVERT: E 101 ASP cc_start: 0.8191 (m-30) cc_final: 0.7754 (m-30) REVERT: E 236 TYR cc_start: 0.7668 (t80) cc_final: 0.7299 (t80) outliers start: 69 outliers final: 31 residues processed: 288 average time/residue: 0.0934 time to fit residues: 41.3820 Evaluate side-chains 236 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 TRP 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 63 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 363 CYS Chi-restraints excluded: chain C residue 483 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 D residue 28 PHE Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 319 HIS 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 215 PHE Chi-restraints excluded: chain E residue 240 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 431 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 486 HIS D 175 ASN D 334 HIS E 188 GLN E 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.126240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105175 restraints weight = 35107.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106570 restraints weight = 20379.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.107618 restraints weight = 14312.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108361 restraints weight = 12509.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108507 restraints weight = 11378.089| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3627 r_free = 0.3627 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13988 Z= 0.218 Angle : 0.769 8.782 18936 Z= 0.397 Chirality : 0.045 0.185 2165 Planarity : 0.005 0.068 2384 Dihedral : 8.980 78.850 1854 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.27 % Allowed : 25.89 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.20), residues: 1633 helix: -0.35 (0.17), residues: 927 sheet: -2.30 (0.41), residues: 140 loop : -2.37 (0.24), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 43 TYR 0.026 0.002 TYR D 226 PHE 0.031 0.003 PHE C 479 TRP 0.017 0.002 TRP D 428 HIS 0.009 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00495 (13988) covalent geometry : angle 0.76944 (18936) hydrogen bonds : bond 0.04777 ( 637) hydrogen bonds : angle 5.34530 ( 1896) *********************** 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 287 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 206 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8615 (m-40) cc_final: 0.8344 (m-40) REVERT: B 443 TRP cc_start: 0.8889 (OUTLIER) cc_final: 0.8644 (m100) REVERT: B 492 PHE cc_start: 0.8507 (p90) cc_final: 0.8280 (p90) REVERT: B 544 LEU cc_start: 0.6384 (OUTLIER) cc_final: 0.6059 (mm) REVERT: C 13 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7590 (m-80) REVERT: C 139 LYS cc_start: 0.8287 (pttp) cc_final: 0.8067 (pttt) REVERT: C 207 SER cc_start: 0.8709 (t) cc_final: 0.8449 (p) REVERT: C 330 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9323 (tt) REVERT: C 388 LEU cc_start: 0.7287 (tp) cc_final: 0.6952 (tp) REVERT: C 428 LYS cc_start: 0.7516 (tmtt) cc_final: 0.6582 (mttt) REVERT: C 476 PHE cc_start: 0.6727 (t80) cc_final: 0.6514 (t80) REVERT: C 663 MET cc_start: 0.6688 (ppp) cc_final: 0.6369 (ppp) REVERT: D 81 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8607 (mm) REVERT: D 108 LYS cc_start: 0.8171 (tttt) cc_final: 0.7912 (mmtt) REVERT: D 420 ASN cc_start: 0.6931 (m-40) cc_final: 0.6702 (m-40) REVERT: E 69 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8013 (tt) REVERT: E 101 ASP cc_start: 0.8229 (m-30) cc_final: 0.7724 (m-30) REVERT: E 236 TYR cc_start: 0.7709 (t80) cc_final: 0.7395 (t80) outliers start: 81 outliers final: 53 residues processed: 266 average time/residue: 0.0865 time to fit residues: 36.1853 Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 186 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 426 HIS Chi-restraints excluded: chain B residue 443 TRP 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 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 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 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 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 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 290 VAL 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 326 ILE 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 69 LEU 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 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 323 THR Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU 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: 5.9990 chunk 98 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 HIS C 242 HIS C 399 GLN C 486 HIS D 275 ASN D 334 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107020 restraints weight = 35361.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.108490 restraints weight = 20195.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.109519 restraints weight = 14161.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110336 restraints weight = 12342.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110445 restraints weight = 11160.801| |-----------------------------------------------------------------------------| r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 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 = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13988 Z= 0.148 Angle : 0.698 9.692 18936 Z= 0.360 Chirality : 0.043 0.235 2165 Planarity : 0.005 0.068 2384 Dihedral : 8.647 76.613 1854 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.01 % Allowed : 27.39 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.20), residues: 1633 helix: -0.11 (0.17), residues: 929 sheet: -2.21 (0.41), residues: 136 loop : -2.28 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 43 TYR 0.021 0.002 TYR D 226 PHE 0.026 0.002 PHE C 479 TRP 0.013 0.001 TRP C 649 HIS 0.012 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00332 (13988) covalent geometry : angle 0.69788 (18936) hydrogen bonds : bond 0.04354 ( 637) hydrogen bonds : angle 5.14888 ( 1896) *********************** 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 280 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 203 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8598 (m-40) cc_final: 0.7952 (m-40) REVERT: B 404 LYS cc_start: 0.7596 (tttt) cc_final: 0.7390 (tmmt) REVERT: B 492 PHE cc_start: 0.8521 (p90) cc_final: 0.8274 (p90) REVERT: B 544 LEU cc_start: 0.6266 (OUTLIER) cc_final: 0.5989 (mm) REVERT: C 13 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7547 (m-80) REVERT: C 139 LYS cc_start: 0.8220 (pttp) cc_final: 0.7996 (pttt) REVERT: C 207 SER cc_start: 0.8708 (t) cc_final: 0.8478 (p) REVERT: C 222 MET cc_start: 0.6844 (tmm) cc_final: 0.6518 (tmm) REVERT: C 330 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9163 (tt) REVERT: C 388 LEU cc_start: 0.7326 (tp) cc_final: 0.6950 (tp) REVERT: C 428 LYS cc_start: 0.7456 (tmtt) cc_final: 0.6517 (mttt) REVERT: C 476 PHE cc_start: 0.6533 (t80) cc_final: 0.6165 (t80) REVERT: C 487 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5597 (mt) REVERT: D 81 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8572 (tt) REVERT: D 108 LYS cc_start: 0.8202 (tttt) cc_final: 0.7911 (mmtt) REVERT: D 297 MET cc_start: 0.7502 (pmm) cc_final: 0.7247 (mpp) REVERT: D 381 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: D 420 ASN cc_start: 0.6867 (m-40) cc_final: 0.6625 (m-40) REVERT: E 10 CYS cc_start: 0.6867 (m) cc_final: 0.6169 (t) REVERT: E 101 ASP cc_start: 0.8204 (m-30) cc_final: 0.7730 (m-30) REVERT: E 171 CYS cc_start: 0.7827 (t) cc_final: 0.7169 (m) REVERT: E 236 TYR cc_start: 0.7634 (t80) cc_final: 0.7361 (t80) outliers start: 77 outliers final: 45 residues processed: 263 average time/residue: 0.0873 time to fit residues: 36.0690 Evaluate side-chains 239 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 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 275 LEU Chi-restraints excluded: chain C residue 289 LEU 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 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 95 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 291 THR 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 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 388 VAL Chi-restraints excluded: chain E residue 402 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 42 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 6 optimal weight: 0.0870 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 486 HIS D 334 HIS D 362 HIS E 118 GLN ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.130320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109496 restraints weight = 35046.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111354 restraints weight = 19631.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.112334 restraints weight = 13295.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112922 restraints weight = 11470.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.113520 restraints weight = 10338.831| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3677 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= 0.131 Angle : 0.681 14.927 18936 Z= 0.345 Chirality : 0.043 0.339 2165 Planarity : 0.004 0.066 2384 Dihedral : 8.353 77.688 1854 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.68 % Allowed : 27.20 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.21), residues: 1633 helix: 0.11 (0.17), residues: 933 sheet: -2.08 (0.41), residues: 137 loop : -2.16 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 43 TYR 0.024 0.001 TYR D 226 PHE 0.031 0.002 PHE C 244 TRP 0.013 0.001 TRP C 649 HIS 0.025 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00283 (13988) covalent geometry : angle 0.68094 (18936) hydrogen bonds : bond 0.04063 ( 637) hydrogen bonds : angle 4.96388 ( 1896) *********************** 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 293 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 221 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8517 (m-40) cc_final: 0.7877 (m110) REVERT: B 404 LYS cc_start: 0.7583 (tttt) cc_final: 0.7366 (tmmt) REVERT: B 492 PHE cc_start: 0.8499 (p90) cc_final: 0.8094 (p90) REVERT: B 544 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6042 (mm) REVERT: C 13 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: C 139 LYS cc_start: 0.8163 (pttp) cc_final: 0.7936 (pttt) REVERT: C 207 SER cc_start: 0.8613 (t) cc_final: 0.8405 (p) REVERT: C 222 MET cc_start: 0.6938 (tmm) cc_final: 0.6545 (tmm) REVERT: C 301 LYS cc_start: 0.8107 (mmmm) cc_final: 0.7648 (mmmt) REVERT: C 388 LEU cc_start: 0.7328 (tp) cc_final: 0.6924 (tp) REVERT: C 428 LYS cc_start: 0.7532 (tmtt) cc_final: 0.6563 (mttt) REVERT: C 476 PHE cc_start: 0.6479 (t80) cc_final: 0.6076 (t80) REVERT: C 487 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5633 (mm) REVERT: D 81 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8551 (tt) REVERT: D 108 LYS cc_start: 0.8194 (tttt) cc_final: 0.7918 (mmtt) REVERT: D 218 MET cc_start: 0.7049 (tpp) cc_final: 0.6722 (mmt) REVERT: D 381 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8164 (mp10) REVERT: D 420 ASN cc_start: 0.6930 (m-40) cc_final: 0.6672 (m-40) REVERT: E 10 CYS cc_start: 0.6888 (m) cc_final: 0.6367 (t) REVERT: E 101 ASP cc_start: 0.8215 (m-30) cc_final: 0.7788 (m-30) REVERT: E 171 CYS cc_start: 0.7766 (t) cc_final: 0.7103 (m) outliers start: 72 outliers final: 48 residues processed: 279 average time/residue: 0.0888 time to fit residues: 39.0091 Evaluate side-chains 247 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 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 74 ILE 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 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 431 LEU Chi-restraints excluded: chain C residue 486 HIS 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 166 HIS Chi-restraints excluded: chain D residue 172 LEU 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 254 TRP 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 413 LEU Chi-restraints excluded: chain E residue 428 ILE 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 29 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 131 optimal weight: 0.0870 chunk 81 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 HIS C 146 HIS ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS E 209 ASN E 297 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.127107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.106153 restraints weight = 35289.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.108172 restraints weight = 19953.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.109782 restraints weight = 13193.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.109909 restraints weight = 10940.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110135 restraints weight = 10218.280| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3637 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3637 r_free = 0.3637 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 13988 Z= 0.190 Angle : 0.743 12.826 18936 Z= 0.376 Chirality : 0.045 0.308 2165 Planarity : 0.005 0.062 2384 Dihedral : 8.402 76.192 1854 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 5.20 % Allowed : 27.07 % Favored : 67.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.21), residues: 1633 helix: 0.15 (0.17), residues: 929 sheet: -2.20 (0.39), residues: 146 loop : -2.15 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.027 0.002 TYR D 226 PHE 0.025 0.002 PHE C 479 TRP 0.016 0.001 TRP D 428 HIS 0.009 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00433 (13988) covalent geometry : angle 0.74274 (18936) hydrogen bonds : bond 0.04346 ( 637) hydrogen bonds : angle 5.09927 ( 1896) *********************** 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 271 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8597 (m-40) cc_final: 0.7982 (m-40) REVERT: B 404 LYS cc_start: 0.7774 (tttt) cc_final: 0.7551 (tmmt) REVERT: B 443 TRP cc_start: 0.8897 (OUTLIER) cc_final: 0.8637 (m100) REVERT: B 492 PHE cc_start: 0.8512 (p90) cc_final: 0.8040 (p90) REVERT: B 544 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6085 (mm) REVERT: C 13 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: C 207 SER cc_start: 0.8654 (t) cc_final: 0.8437 (p) REVERT: C 222 MET cc_start: 0.7070 (tmm) cc_final: 0.6702 (tmm) REVERT: C 262 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8853 (tt) REVERT: C 297 GLN cc_start: 0.7420 (tm-30) cc_final: 0.7218 (tm-30) REVERT: C 301 LYS cc_start: 0.8202 (mmmm) cc_final: 0.7580 (mmtt) REVERT: C 428 LYS cc_start: 0.7559 (tmtt) cc_final: 0.6562 (mttt) REVERT: C 476 PHE cc_start: 0.6589 (t80) cc_final: 0.6120 (t80) REVERT: C 487 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6119 (mm) REVERT: D 31 GLN cc_start: 0.8275 (pp30) cc_final: 0.7949 (pp30) REVERT: D 81 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8531 (tt) REVERT: D 108 LYS cc_start: 0.8219 (tttt) cc_final: 0.7897 (mmtt) REVERT: D 218 MET cc_start: 0.7081 (tpp) cc_final: 0.6830 (mmt) REVERT: D 381 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8175 (mp10) REVERT: E 10 CYS cc_start: 0.7177 (m) cc_final: 0.6703 (t) REVERT: E 101 ASP cc_start: 0.8349 (m-30) cc_final: 0.7822 (m-30) REVERT: E 171 CYS cc_start: 0.8001 (t) cc_final: 0.7307 (m) outliers start: 80 outliers final: 57 residues processed: 255 average time/residue: 0.0869 time to fit residues: 35.3329 Evaluate side-chains 243 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 426 HIS Chi-restraints excluded: chain B residue 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 478 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 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 262 LEU 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 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 431 LEU Chi-restraints excluded: chain C residue 481 SER 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 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 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 319 HIS Chi-restraints excluded: chain D residue 326 ILE 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 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 413 LEU 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 155 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 380 GLN ** E 209 ASN ** 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 = 0.3939 r_free = 0.3939 target = 0.129585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.108739 restraints weight = 34927.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.110678 restraints weight = 19242.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.111416 restraints weight = 13131.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.111884 restraints weight = 11874.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.112078 restraints weight = 10479.070| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13988 Z= 0.135 Angle : 0.692 12.447 18936 Z= 0.351 Chirality : 0.043 0.266 2165 Planarity : 0.005 0.066 2384 Dihedral : 8.153 75.825 1854 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.75 % Allowed : 28.17 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.21), residues: 1633 helix: 0.25 (0.17), residues: 928 sheet: -2.15 (0.41), residues: 136 loop : -2.09 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.023 0.001 TYR D 226 PHE 0.049 0.002 PHE C 244 TRP 0.012 0.001 TRP C 649 HIS 0.009 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00304 (13988) covalent geometry : angle 0.69179 (18936) hydrogen bonds : bond 0.04074 ( 637) hydrogen bonds : angle 4.95223 ( 1896) *********************** 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 277 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 204 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8548 (m-40) cc_final: 0.7926 (m110) REVERT: B 492 PHE cc_start: 0.8501 (p90) cc_final: 0.8043 (p90) REVERT: B 544 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5932 (mm) REVERT: C 13 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: C 222 MET cc_start: 0.7096 (tmm) cc_final: 0.6711 (tmm) REVERT: C 301 LYS cc_start: 0.8028 (mmmm) cc_final: 0.7457 (mmtt) REVERT: C 428 LYS cc_start: 0.7542 (tmtt) cc_final: 0.6589 (mttt) REVERT: C 476 PHE cc_start: 0.6607 (t80) cc_final: 0.6107 (t80) REVERT: D 81 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8559 (tt) REVERT: D 108 LYS cc_start: 0.8153 (tttt) cc_final: 0.7890 (mmtt) REVERT: D 218 MET cc_start: 0.7008 (tpp) cc_final: 0.6795 (mmt) REVERT: D 236 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7034 (tt) REVERT: D 381 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8174 (mp10) REVERT: E 10 CYS cc_start: 0.7001 (m) cc_final: 0.6601 (t) REVERT: E 101 ASP cc_start: 0.8263 (m-30) cc_final: 0.7788 (m-30) REVERT: E 171 CYS cc_start: 0.7929 (t) cc_final: 0.7256 (m) outliers start: 73 outliers final: 55 residues processed: 259 average time/residue: 0.0854 time to fit residues: 35.4488 Evaluate side-chains 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 426 HIS Chi-restraints excluded: chain B residue 443 TRP 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 42 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 102 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 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 431 LEU 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 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 236 LEU Chi-restraints excluded: chain D residue 291 THR 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 305 TYR 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 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 61 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 160 optimal weight: 0.0670 chunk 4 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 123 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 380 GLN ** E 209 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 = 0.3956 r_free = 0.3956 target = 0.130736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.109907 restraints weight = 35169.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111998 restraints weight = 19011.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112824 restraints weight = 12856.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.113144 restraints weight = 11364.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113454 restraints weight = 10333.946| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4222 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= 0.128 Angle : 0.701 12.339 18936 Z= 0.350 Chirality : 0.043 0.233 2165 Planarity : 0.005 0.071 2384 Dihedral : 7.939 76.976 1854 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.90 % Allowed : 29.60 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1633 helix: 0.33 (0.17), residues: 924 sheet: -2.05 (0.41), residues: 136 loop : -2.00 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.025 0.001 TYR E 204 PHE 0.051 0.002 PHE C 244 TRP 0.015 0.001 TRP C 649 HIS 0.010 0.001 HIS C 486 Details of bonding type rmsd covalent geometry : bond 0.00286 (13988) covalent geometry : angle 0.70053 (18936) hydrogen bonds : bond 0.03954 ( 637) hydrogen bonds : angle 4.89101 ( 1896) *********************** 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 268 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 208 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8565 (m-40) cc_final: 0.7963 (m110) REVERT: B 492 PHE cc_start: 0.8513 (p90) cc_final: 0.8041 (p90) REVERT: C 13 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7508 (m-80) REVERT: C 222 MET cc_start: 0.7175 (tmm) cc_final: 0.6717 (tmm) REVERT: C 428 LYS cc_start: 0.7603 (tmtt) cc_final: 0.6660 (mttt) REVERT: C 476 PHE cc_start: 0.6610 (t80) cc_final: 0.6125 (t80) REVERT: D 81 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8599 (tt) REVERT: D 108 LYS cc_start: 0.8149 (tttt) cc_final: 0.7864 (mmtt) REVERT: D 218 MET cc_start: 0.6902 (tpp) cc_final: 0.6680 (mmt) REVERT: D 236 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.7029 (tt) REVERT: D 381 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8211 (mp10) REVERT: E 10 CYS cc_start: 0.6898 (m) cc_final: 0.6492 (t) REVERT: E 101 ASP cc_start: 0.8303 (m-30) cc_final: 0.7795 (m-30) REVERT: E 171 CYS cc_start: 0.7914 (t) cc_final: 0.7189 (m) outliers start: 60 outliers final: 51 residues processed: 250 average time/residue: 0.0884 time to fit residues: 34.9702 Evaluate side-chains 250 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 443 TRP Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE 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 321 VAL 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 431 LEU 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 236 LEU 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 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 215 PHE Chi-restraints excluded: chain E residue 237 CYS 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 305 TYR 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 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: 0.0570 chunk 116 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 162 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.2304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 380 GLN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3929 r_free = 0.3929 target = 0.128855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.107941 restraints weight = 35287.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.109761 restraints weight = 19720.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110919 restraints weight = 13527.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.111564 restraints weight = 11395.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.111663 restraints weight = 10425.414| |-----------------------------------------------------------------------------| r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13988 Z= 0.173 Angle : 0.738 12.520 18936 Z= 0.370 Chirality : 0.044 0.233 2165 Planarity : 0.005 0.074 2384 Dihedral : 7.988 75.159 1854 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.90 % Allowed : 29.54 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.21), residues: 1633 helix: 0.32 (0.17), residues: 928 sheet: -2.13 (0.39), residues: 146 loop : -2.10 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 43 TYR 0.028 0.002 TYR D 226 PHE 0.049 0.002 PHE C 244 TRP 0.018 0.002 TRP D 428 HIS 0.009 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00400 (13988) covalent geometry : angle 0.73783 (18936) hydrogen bonds : bond 0.04156 ( 637) hydrogen bonds : angle 5.01438 ( 1896) ********************** 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 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8571 (m-40) cc_final: 0.7956 (m110) REVERT: B 492 PHE cc_start: 0.8540 (p90) cc_final: 0.8067 (p90) REVERT: C 13 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: C 428 LYS cc_start: 0.7639 (tmtt) cc_final: 0.6680 (mttt) REVERT: C 476 PHE cc_start: 0.6626 (t80) cc_final: 0.6103 (t80) REVERT: D 81 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8619 (tt) REVERT: D 108 LYS cc_start: 0.8192 (tttt) cc_final: 0.7975 (mmtt) REVERT: D 218 MET cc_start: 0.6922 (tpp) cc_final: 0.6692 (mmt) REVERT: D 236 LEU cc_start: 0.7313 (OUTLIER) cc_final: 0.7087 (tt) REVERT: D 381 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8176 (mp10) REVERT: E 10 CYS cc_start: 0.6901 (m) cc_final: 0.6585 (t) REVERT: E 101 ASP cc_start: 0.8268 (m-30) cc_final: 0.7757 (m-30) REVERT: E 171 CYS cc_start: 0.7963 (t) cc_final: 0.7281 (m) REVERT: E 237 CYS cc_start: 0.8506 (m) cc_final: 0.8182 (m) outliers start: 60 outliers final: 51 residues processed: 239 average time/residue: 0.0887 time to fit residues: 33.4017 Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 190 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 426 HIS Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain C residue 13 PHE Chi-restraints excluded: chain C residue 74 ILE 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 321 VAL 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 431 LEU 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 95 LEU 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 236 LEU 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 305 TYR 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 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 68 optimal weight: 8.9990 chunk 144 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 308 GLN C 312 ASN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3944 r_free = 0.3944 target = 0.129910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.109129 restraints weight = 35288.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.111229 restraints weight = 19510.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111969 restraints weight = 13269.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112541 restraints weight = 11310.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.112593 restraints weight = 10082.016| |-----------------------------------------------------------------------------| r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 13988 Z= 0.142 Angle : 0.707 13.013 18936 Z= 0.354 Chirality : 0.043 0.208 2165 Planarity : 0.005 0.056 2384 Dihedral : 7.850 73.602 1854 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.90 % Allowed : 29.86 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.21), residues: 1633 helix: 0.39 (0.17), residues: 926 sheet: -2.12 (0.39), residues: 146 loop : -2.06 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 43 TYR 0.019 0.001 TYR D 226 PHE 0.047 0.002 PHE C 244 TRP 0.018 0.001 TRP C 649 HIS 0.008 0.001 HIS E 193 Details of bonding type rmsd covalent geometry : bond 0.00326 (13988) covalent geometry : angle 0.70683 (18936) hydrogen bonds : bond 0.03960 ( 637) hydrogen bonds : angle 4.92422 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.01 seconds wall clock time: 38 minutes 52.65 seconds (2332.65 seconds total)