Starting phenix.real_space_refine on Fri Jul 3 11:07:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cte_30462/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cte_30462/07_2026/7cte_30462.cif" } 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-6108/lib/python3.11/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: 2.34, per 1000 atoms: 0.17 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: 0.89 Conformation dependent library (CDL) restraints added in 390.9 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: 0.29 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: 1.63 Time building geometry restraints manager: 1.16 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: 6996 17.85 - 35.71: 1107 35.71 - 53.56: 272 53.56 - 71.41: 42 71.41 - 89.27: 15 Dihedral angle restraints: 8432 sinusoidal: 3465 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 8429 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 10.200 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 18.366 89.267 5176 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/Z covalent geometry : bond 0.01246 / 0.56 (13988) covalent geometry : angle 1.69239 / 0.94 (18936) hydrogen bonds : bond 0.17096 / 11.04 ( 637) hydrogen bonds : angle 8.45822 / 5.95 ( 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 : 0.495 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: 0.0940 time to fit residues: 41.8810 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 : 0.349 ------------------------------------------------------------------------------- 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... B 270 GLN B 291 ASN B 292 GLN B 306 HIS B 336 HIS B 372 GLN C 58 ASN C 62 GLN C 347 ASN ** C 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 555 ASN C 605 ASN C 613 ASN C 678 HIS D 98 HIS D 119 ASN D 175 ASN D 233 GLN D 271 ASN D 288 ASN E 27 HIS ** E 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS E 100 ASN E 168 ASN E 299 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.125192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102525 restraints weight = 34347.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.105279 restraints weight = 18816.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.107084 restraints weight = 12584.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.108280 restraints weight = 9692.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.108953 restraints weight = 8155.110| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3611 r_free = 0.3611 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 = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2217 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= 0.153 Angle : 0.779 10.446 18936 Z= 0.409 Chirality : 0.044 0.179 2165 Planarity : 0.006 0.077 2384 Dihedral : 8.172 78.469 1804 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.03 % Allowed : 23.23 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -2.81 (0.18), residues: 1633 helix: -1.24 (0.15), residues: 900 sheet: -2.67 (0.40), residues: 134 loop : -2.46 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 30 TYR 0.022 0.002 TYR C 453 PHE 0.037 0.002 PHE D 28 TRP 0.013 0.001 TRP D 249 HIS 0.008 0.001 HIS E 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (13988) covalent geometry : angle 0.77893 / 0.41 (18936) hydrogen bonds : bond 0.05268 / 3.42 ( 637) hydrogen bonds : angle 5.84776 / 4.16 ( 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 305 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 0.518 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 453 PRO cc_start: 0.7858 (Cg_endo) cc_final: 0.6983 (Cg_exo) REVERT: B 544 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.6098 (mm) REVERT: C 13 PHE cc_start: 0.7871 (OUTLIER) cc_final: 0.7389 (m-80) REVERT: C 52 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8093 (tm-30) REVERT: C 71 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7713 (t70) REVERT: C 139 LYS cc_start: 0.8263 (pttp) cc_final: 0.8063 (pttt) REVERT: C 222 MET cc_start: 0.7040 (tmm) cc_final: 0.6694 (tmm) REVERT: C 223 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 301 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8293 (mmmt) REVERT: C 318 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8633 (t0) REVERT: C 346 CYS cc_start: 0.8451 (m) cc_final: 0.7966 (m) REVERT: C 410 MET cc_start: 0.7802 (mtt) cc_final: 0.7507 (ttp) REVERT: C 426 LEU cc_start: 0.6721 (mt) cc_final: 0.6489 (mt) REVERT: C 428 LYS cc_start: 0.7400 (tmtt) cc_final: 0.6454 (mttt) REVERT: C 476 PHE cc_start: 0.6522 (t80) cc_final: 0.6060 (t80) REVERT: D 86 GLU cc_start: 0.8295 (tt0) cc_final: 0.8082 (tt0) REVERT: D 108 LYS cc_start: 0.8269 (tttt) cc_final: 0.7873 (mmtt) REVERT: D 284 MET cc_start: 0.9201 (tpt) cc_final: 0.8981 (tpp) REVERT: E 101 ASP cc_start: 0.8380 (m-30) cc_final: 0.7941 (m-30) REVERT: E 171 CYS cc_start: 0.8059 (t) cc_final: 0.7257 (m) REVERT: E 236 TYR cc_start: 0.7599 (t80) cc_final: 0.7238 (t80) outliers start: 62 outliers final: 26 residues processed: 289 average time/residue: 0.0959 time to fit residues: 42.7561 Evaluate side-chains 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 0.8980 chunk 126 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 125 optimal weight: 0.0670 chunk 147 optimal weight: 0.0170 chunk 44 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 291 ASN B 362 HIS B 416 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN E 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.109331 restraints weight = 34781.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111495 restraints weight = 19177.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.112427 restraints weight = 13010.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.112835 restraints weight = 11373.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.113099 restraints weight = 10291.959| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2925 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 : 0.705 9.470 18936 Z= 0.364 Chirality : 0.042 0.169 2165 Planarity : 0.005 0.074 2384 Dihedral : 7.154 79.779 1792 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.42 % Allowed : 24.01 % Favored : 71.57 % 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: -2.00 (0.20), residues: 1633 helix: -0.51 (0.16), residues: 920 sheet: -2.41 (0.41), residues: 136 loop : -2.24 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 43 TYR 0.015 0.002 TYR D 255 PHE 0.042 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/Z covalent geometry : bond 0.00275 / 0.13 (13988) covalent geometry : angle 0.70476 / 0.36 (18936) hydrogen bonds : bond 0.04574 / 3.00 ( 637) hydrogen bonds : angle 5.31028 / 3.78 ( 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 302 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 234 time to evaluate : 0.575 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 357 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: B 544 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5971 (mm) REVERT: C 13 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.7294 (m-80) REVERT: C 71 ASP cc_start: 0.8101 (t0) cc_final: 0.7881 (t70) REVERT: C 139 LYS cc_start: 0.8219 (pttp) cc_final: 0.7977 (pttt) REVERT: C 144 MET cc_start: 0.8285 (tpt) cc_final: 0.8079 (tpt) REVERT: C 207 SER cc_start: 0.8717 (t) cc_final: 0.8448 (p) REVERT: C 222 MET cc_start: 0.6666 (tmm) cc_final: 0.6415 (tmm) REVERT: C 281 CYS cc_start: 0.7478 (m) cc_final: 0.7214 (m) REVERT: C 301 LYS cc_start: 0.8314 (mmmm) cc_final: 0.7981 (mmmt) REVERT: C 334 GLU cc_start: 0.7841 (tp30) cc_final: 0.7638 (tp30) REVERT: C 388 LEU cc_start: 0.8123 (tp) cc_final: 0.6997 (tp) REVERT: C 428 LYS cc_start: 0.7431 (tmtt) cc_final: 0.6520 (mttt) REVERT: C 486 HIS cc_start: 0.4612 (OUTLIER) cc_final: 0.3901 (t70) REVERT: C 663 MET cc_start: 0.6458 (ppp) cc_final: 0.6195 (ppp) REVERT: D 81 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8539 (tt) REVERT: D 108 LYS cc_start: 0.8182 (tttt) cc_final: 0.7871 (mmtt) REVERT: D 367 PHE cc_start: 0.7881 (m-80) cc_final: 0.7569 (m-10) REVERT: E 101 ASP cc_start: 0.8205 (m-30) cc_final: 0.7773 (m-30) REVERT: E 236 TYR cc_start: 0.7661 (t80) cc_final: 0.7256 (t80) outliers start: 68 outliers final: 31 residues processed: 282 average time/residue: 0.1010 time to fit residues: 44.1254 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 : 0.548 ------------------------------------------------------------------------------- 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 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 217 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 289 LEU Chi-restraints excluded: chain C residue 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 683 ARG 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 308 LEU 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 158 SER 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: 0.0970 chunk 21 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 399 GLN C 486 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 334 HIS D 380 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.104801 restraints weight = 35194.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.106317 restraints weight = 20281.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107434 restraints weight = 14125.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.108186 restraints weight = 12011.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.108248 restraints weight = 10880.789| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3625 r_free = 0.3625 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13988 Z= 0.223 Angle : 0.773 8.855 18936 Z= 0.398 Chirality : 0.046 0.188 2165 Planarity : 0.005 0.067 2384 Dihedral : 7.009 81.753 1791 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.86 % Allowed : 24.85 % Favored : 69.29 % 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: -1.82 (0.20), residues: 1633 helix: -0.30 (0.17), residues: 919 sheet: -2.31 (0.41), residues: 140 loop : -2.30 (0.24), residues: 574 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 0.018 0.002 TRP D 428 HIS 0.008 0.001 HIS C 486 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (13988) covalent geometry : angle 0.77322 / 0.40 (18936) hydrogen bonds : bond 0.04816 / 3.18 ( 637) hydrogen bonds : angle 5.33792 / 3.82 ( 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 296 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 206 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8627 (m-40) cc_final: 0.8361 (m-40) REVERT: B 492 PHE cc_start: 0.8520 (p90) cc_final: 0.8317 (p90) REVERT: B 544 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6060 (mm) REVERT: C 13 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7631 (m-80) REVERT: C 71 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7990 (t70) REVERT: C 139 LYS cc_start: 0.8307 (pttp) cc_final: 0.8083 (pttt) REVERT: C 207 SER cc_start: 0.8690 (t) cc_final: 0.8437 (p) REVERT: C 330 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9307 (tt) REVERT: C 388 LEU cc_start: 0.7241 (tp) cc_final: 0.6896 (tp) REVERT: C 426 LEU cc_start: 0.6875 (mt) cc_final: 0.6664 (mt) REVERT: C 428 LYS cc_start: 0.7511 (tmtt) cc_final: 0.6557 (mttt) REVERT: C 476 PHE cc_start: 0.6669 (t80) cc_final: 0.6411 (t80) REVERT: C 663 MET cc_start: 0.6836 (ppp) cc_final: 0.6518 (ppp) REVERT: D 81 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 108 LYS cc_start: 0.8176 (tttt) cc_final: 0.7910 (mmtt) REVERT: D 381 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: D 420 ASN cc_start: 0.6970 (m-40) cc_final: 0.6759 (m-40) REVERT: E 69 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8086 (tt) REVERT: E 101 ASP cc_start: 0.8224 (m-30) cc_final: 0.7702 (m-30) REVERT: E 171 CYS cc_start: 0.7844 (t) cc_final: 0.7235 (m) REVERT: E 236 TYR cc_start: 0.7719 (t80) cc_final: 0.7243 (t80) outliers start: 90 outliers final: 56 residues processed: 268 average time/residue: 0.0981 time to fit residues: 41.0190 Evaluate side-chains 254 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 359 VAL 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 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 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 366 ILE Chi-restraints excluded: chain C residue 486 HIS Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 VAL 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 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 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 184 ILE Chi-restraints excluded: chain E residue 209 ASN 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 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: 6.9990 chunk 111 optimal weight: 0.2980 chunk 163 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 147 optimal weight: 0.0020 chunk 149 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 HIS C 242 HIS C 399 GLN C 486 HIS ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 ASN D 334 HIS E 297 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.126810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.105860 restraints weight = 35505.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.107344 restraints weight = 20306.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.108457 restraints weight = 14168.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.109044 restraints weight = 12292.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109180 restraints weight = 11353.238| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- 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 = 0.85 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 = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3637 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13988 Z= 0.168 Angle : 0.722 13.443 18936 Z= 0.370 Chirality : 0.044 0.238 2165 Planarity : 0.005 0.066 2384 Dihedral : 6.766 73.944 1791 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 5.27 % Allowed : 26.48 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.55 (0.20), residues: 1633 helix: -0.07 (0.17), residues: 922 sheet: -2.27 (0.41), residues: 135 loop : -2.19 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 43 TYR 0.023 0.002 TYR D 226 PHE 0.027 0.002 PHE C 479 TRP 0.013 0.001 TRP D 428 HIS 0.010 0.001 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (13988) covalent geometry : angle 0.72158 / 0.37 (18936) hydrogen bonds : bond 0.04466 / 2.95 ( 637) hydrogen bonds : angle 5.19160 / 3.71 ( 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 290 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 209 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 291 ASN cc_start: 0.8618 (m-40) cc_final: 0.7939 (m-40) REVERT: B 492 PHE cc_start: 0.8522 (p90) cc_final: 0.8283 (p90) REVERT: B 544 LEU cc_start: 0.6294 (OUTLIER) cc_final: 0.5985 (mm) REVERT: C 13 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 71 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7912 (t70) REVERT: C 139 LYS cc_start: 0.8268 (pttp) cc_final: 0.8034 (pttt) REVERT: C 144 MET cc_start: 0.8364 (tpt) cc_final: 0.8162 (tpt) REVERT: C 207 SER cc_start: 0.8733 (t) cc_final: 0.8519 (p) REVERT: C 330 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 388 LEU cc_start: 0.7322 (tp) cc_final: 0.6912 (tp) REVERT: C 428 LYS cc_start: 0.7499 (tmtt) cc_final: 0.6536 (mttt) REVERT: C 476 PHE cc_start: 0.6562 (t80) cc_final: 0.6243 (t80) REVERT: D 81 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8576 (tt) REVERT: D 108 LYS cc_start: 0.8179 (tttt) cc_final: 0.7911 (mmtt) REVERT: D 420 ASN cc_start: 0.7056 (m-40) cc_final: 0.6839 (m-40) REVERT: E 10 CYS cc_start: 0.6988 (m) cc_final: 0.6398 (t) REVERT: E 101 ASP cc_start: 0.8165 (m-30) cc_final: 0.7728 (m-30) REVERT: E 171 CYS cc_start: 0.7879 (t) cc_final: 0.7234 (m) REVERT: E 236 TYR cc_start: 0.7632 (t80) cc_final: 0.7218 (t80) outliers start: 81 outliers final: 49 residues processed: 272 average time/residue: 0.1010 time to fit residues: 42.5155 Evaluate side-chains 245 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 191 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 71 ASP 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 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 399 GLN Chi-restraints excluded: chain C residue 557 VAL 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 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 27 HIS Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 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: 1.9990 chunk 13 optimal weight: 0.0050 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.0050 chunk 14 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 362 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.130845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.110097 restraints weight = 35009.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111670 restraints weight = 19701.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.112683 restraints weight = 13801.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.113357 restraints weight = 12023.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.113460 restraints weight = 11008.075| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- 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 = 0.86 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 = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13988 Z= 0.125 Angle : 0.683 12.442 18936 Z= 0.345 Chirality : 0.042 0.366 2165 Planarity : 0.005 0.066 2384 Dihedral : 6.354 71.624 1791 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 4.23 % Allowed : 27.46 % Favored : 68.31 % 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: 0.11 (0.17), residues: 931 sheet: -2.04 (0.41), residues: 137 loop : -2.14 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.018 0.001 TYR D 226 PHE 0.029 0.002 PHE C 244 TRP 0.011 0.001 TRP C 649 HIS 0.008 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13988) covalent geometry : angle 0.68342 / 0.35 (18936) hydrogen bonds : bond 0.04071 / 2.69 ( 637) hydrogen bonds : angle 4.94696 / 3.53 ( 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 294 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8557 (m-40) cc_final: 0.7876 (m110) REVERT: B 492 PHE cc_start: 0.8528 (p90) cc_final: 0.8171 (p90) REVERT: B 544 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.6021 (mm) REVERT: C 13 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7488 (m-80) REVERT: C 139 LYS cc_start: 0.8124 (pttp) cc_final: 0.7889 (pttt) REVERT: C 301 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7627 (mmmt) REVERT: C 388 LEU cc_start: 0.7366 (tp) cc_final: 0.6943 (tp) REVERT: C 428 LYS cc_start: 0.7506 (tmtt) cc_final: 0.6569 (mptt) REVERT: C 476 PHE cc_start: 0.6586 (t80) cc_final: 0.6065 (t80) REVERT: C 683 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7783 (ptm160) REVERT: D 31 GLN cc_start: 0.8316 (pp30) cc_final: 0.8081 (pt0) REVERT: D 81 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8552 (tt) REVERT: D 108 LYS cc_start: 0.8187 (tttt) cc_final: 0.7921 (mmtt) REVERT: D 218 MET cc_start: 0.7027 (tpp) cc_final: 0.6738 (mmt) REVERT: D 233 GLN cc_start: 0.8437 (tp40) cc_final: 0.8108 (tp-100) REVERT: D 297 MET cc_start: 0.7373 (pmm) cc_final: 0.7129 (mpp) REVERT: D 381 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: E 10 CYS cc_start: 0.6937 (m) cc_final: 0.6415 (t) REVERT: E 101 ASP cc_start: 0.8230 (m-30) cc_final: 0.7795 (m-30) REVERT: E 171 CYS cc_start: 0.7781 (t) cc_final: 0.7057 (m) REVERT: E 236 TYR cc_start: 0.7684 (t80) cc_final: 0.7250 (t80) outliers start: 65 outliers final: 43 residues processed: 278 average time/residue: 0.0937 time to fit residues: 40.4593 Evaluate side-chains 251 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 63 GLU 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 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 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 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 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: 10.0000 chunk 6 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 131 optimal weight: 0.0970 chunk 81 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 542 HIS C 146 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS D 380 GLN ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106933 restraints weight = 35189.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.109126 restraints weight = 19576.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.109732 restraints weight = 13263.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.110176 restraints weight = 11713.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.110276 restraints weight = 10477.112| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13988 Z= 0.166 Angle : 0.716 11.465 18936 Z= 0.363 Chirality : 0.044 0.322 2165 Planarity : 0.005 0.062 2384 Dihedral : 6.247 59.258 1791 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.68 % Allowed : 27.78 % Favored : 67.53 % 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: -1.24 (0.21), residues: 1633 helix: 0.17 (0.17), residues: 934 sheet: -2.15 (0.39), residues: 146 loop : -2.08 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 43 TYR 0.026 0.002 TYR D 226 PHE 0.040 0.002 PHE C 582 TRP 0.015 0.001 TRP D 428 HIS 0.011 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (13988) covalent geometry : angle 0.71609 / 0.36 (18936) hydrogen bonds : bond 0.04187 / 2.77 ( 637) hydrogen bonds : angle 4.96933 / 3.55 ( 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 278 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 206 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8574 (m-40) cc_final: 0.7934 (m110) REVERT: B 492 PHE cc_start: 0.8529 (p90) cc_final: 0.8080 (p90) REVERT: B 544 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.6010 (mm) REVERT: C 13 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7574 (m-80) REVERT: C 301 LYS cc_start: 0.8110 (mmmm) cc_final: 0.7505 (mmtt) REVERT: C 428 LYS cc_start: 0.7568 (tmtt) cc_final: 0.6605 (mptt) REVERT: C 476 PHE cc_start: 0.6660 (t80) cc_final: 0.6123 (t80) REVERT: D 81 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8564 (tt) REVERT: D 108 LYS cc_start: 0.8158 (tttt) cc_final: 0.7926 (mmtt) REVERT: D 218 MET cc_start: 0.6976 (tpp) cc_final: 0.6723 (mmt) REVERT: D 233 GLN cc_start: 0.8440 (tp40) cc_final: 0.8128 (tp-100) REVERT: D 297 MET cc_start: 0.7409 (pmm) cc_final: 0.7148 (mpp) REVERT: D 381 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: E 10 CYS cc_start: 0.7051 (m) cc_final: 0.6656 (t) REVERT: E 101 ASP cc_start: 0.8234 (m-30) cc_final: 0.7750 (m-30) REVERT: E 171 CYS cc_start: 0.7877 (t) cc_final: 0.7155 (m) REVERT: E 236 TYR cc_start: 0.7760 (t80) cc_final: 0.7376 (t80) outliers start: 72 outliers final: 55 residues processed: 260 average time/residue: 0.0903 time to fit residues: 37.1115 Evaluate side-chains 252 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 193 time to evaluate : 0.530 ------------------------------------------------------------------------------- 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 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 275 LEU Chi-restraints excluded: chain C residue 289 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 387 LEU 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 580 VAL Chi-restraints excluded: chain C residue 593 ASN 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 155 optimal weight: 0.5980 chunk 50 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.131089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.110316 restraints weight = 34979.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.111756 restraints weight = 19908.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112948 restraints weight = 13953.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.113528 restraints weight = 12105.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.113680 restraints weight = 11031.719| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4195 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= 0.129 Angle : 0.680 11.865 18936 Z= 0.343 Chirality : 0.042 0.268 2165 Planarity : 0.004 0.067 2384 Dihedral : 5.963 57.455 1791 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 4.29 % Allowed : 28.43 % Favored : 67.27 % 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: -1.08 (0.21), residues: 1633 helix: 0.31 (0.17), residues: 932 sheet: -2.10 (0.41), residues: 136 loop : -2.03 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.024 0.001 TYR D 226 PHE 0.034 0.002 PHE C 582 TRP 0.014 0.001 TRP C 649 HIS 0.008 0.001 HIS E 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (13988) covalent geometry : angle 0.68011 / 0.34 (18936) hydrogen bonds : bond 0.03934 / 2.59 ( 637) hydrogen bonds : angle 4.81152 / 3.44 ( 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 285 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 219 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8570 (m-40) cc_final: 0.7943 (m110) REVERT: B 492 PHE cc_start: 0.8519 (p90) cc_final: 0.8079 (p90) REVERT: C 13 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: C 144 MET cc_start: 0.8335 (tpt) cc_final: 0.8104 (tpt) REVERT: C 428 LYS cc_start: 0.7524 (tmtt) cc_final: 0.6575 (mptt) REVERT: C 437 GLU cc_start: 0.7381 (mp0) cc_final: 0.7025 (mm-30) REVERT: C 476 PHE cc_start: 0.6616 (t80) cc_final: 0.6059 (t80) REVERT: D 81 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8555 (tt) REVERT: D 108 LYS cc_start: 0.8139 (tttt) cc_final: 0.7866 (mmtt) REVERT: D 218 MET cc_start: 0.6959 (tpp) cc_final: 0.6747 (mmt) REVERT: D 233 GLN cc_start: 0.8386 (tp40) cc_final: 0.8106 (tp-100) REVERT: D 236 LEU cc_start: 0.7307 (mt) cc_final: 0.7056 (tt) REVERT: D 381 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: E 10 CYS cc_start: 0.6866 (m) cc_final: 0.6461 (t) REVERT: E 101 ASP cc_start: 0.8220 (m-30) cc_final: 0.7784 (m-30) REVERT: E 171 CYS cc_start: 0.7783 (t) cc_final: 0.7086 (m) REVERT: E 236 TYR cc_start: 0.7719 (t80) cc_final: 0.7275 (t80) outliers start: 66 outliers final: 51 residues processed: 264 average time/residue: 0.0975 time to fit residues: 40.5635 Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 195 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 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 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 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 593 ASN 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 308 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 381 GLN Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 61 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 HIS ** E 118 GLN ** 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 = 0.3881 r_free = 0.3881 target = 0.124887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.103932 restraints weight = 35664.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.105379 restraints weight = 20362.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.106497 restraints weight = 13994.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.107659 restraints weight = 11909.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.107796 restraints weight = 10601.532| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.93 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3618 r_free = 0.3618 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13988 Z= 0.253 Angle : 0.825 12.599 18936 Z= 0.415 Chirality : 0.047 0.304 2165 Planarity : 0.005 0.069 2384 Dihedral : 6.372 64.786 1791 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.62 % Allowed : 28.95 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.28 (0.21), residues: 1633 helix: 0.16 (0.17), residues: 924 sheet: -2.23 (0.38), residues: 150 loop : -2.08 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 43 TYR 0.031 0.002 TYR D 226 PHE 0.050 0.003 PHE C 244 TRP 0.019 0.002 TRP C 649 HIS 0.010 0.002 HIS D 334 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.25 (13988) covalent geometry : angle 0.82515 / 0.42 (18936) hydrogen bonds : bond 0.04722 / 3.11 ( 637) hydrogen bonds : angle 5.23212 / 3.73 ( 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 255 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 184 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8627 (m-40) cc_final: 0.8022 (m-40) REVERT: B 443 TRP cc_start: 0.8985 (OUTLIER) cc_final: 0.8734 (m100) REVERT: B 492 PHE cc_start: 0.8521 (p90) cc_final: 0.8049 (p90) REVERT: C 13 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: C 144 MET cc_start: 0.8416 (tpt) cc_final: 0.8136 (tpt) REVERT: C 428 LYS cc_start: 0.7580 (tmtt) cc_final: 0.6558 (mptt) REVERT: C 476 PHE cc_start: 0.6690 (t80) cc_final: 0.6191 (t80) REVERT: D 81 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8312 (mm) REVERT: D 108 LYS cc_start: 0.8242 (tttt) cc_final: 0.7961 (mmtt) REVERT: D 218 MET cc_start: 0.7077 (tpp) cc_final: 0.6870 (mmt) REVERT: D 233 GLN cc_start: 0.8429 (tp40) cc_final: 0.8147 (tp-100) REVERT: D 236 LEU cc_start: 0.7398 (mt) cc_final: 0.7139 (tt) REVERT: D 381 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8093 (mp10) REVERT: E 10 CYS cc_start: 0.7015 (m) cc_final: 0.6587 (t) REVERT: E 101 ASP cc_start: 0.8361 (m-30) cc_final: 0.7778 (m-30) REVERT: E 171 CYS cc_start: 0.8053 (t) cc_final: 0.7331 (m) REVERT: E 236 TYR cc_start: 0.7794 (t80) cc_final: 0.7188 (t80) outliers start: 71 outliers final: 58 residues processed: 239 average time/residue: 0.0873 time to fit residues: 33.3061 Evaluate side-chains 235 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 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 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 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 366 ILE 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 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 676 ILE Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 695 LYS Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 291 THR 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 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 191 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 265 MET Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 374 VAL Chi-restraints excluded: chain E residue 388 VAL Chi-restraints excluded: chain E residue 402 LEU Chi-restraints excluded: chain E residue 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: 0.7980 chunk 116 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 91 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.127270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.106486 restraints weight = 35402.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.107912 restraints weight = 20358.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.109298 restraints weight = 14031.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.110036 restraints weight = 11667.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.110158 restraints weight = 10625.524| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13988 Z= 0.183 Angle : 0.777 12.523 18936 Z= 0.388 Chirality : 0.045 0.284 2165 Planarity : 0.005 0.071 2384 Dihedral : 6.292 67.147 1791 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.97 % Allowed : 29.54 % 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: -1.27 (0.21), residues: 1633 helix: 0.21 (0.17), residues: 923 sheet: -2.32 (0.38), residues: 146 loop : -2.13 (0.26), residues: 564 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 0.051 0.002 PHE C 244 TRP 0.020 0.001 TRP C 649 HIS 0.009 0.001 HIS E 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13988) covalent geometry : angle 0.77668 / 0.39 (18936) hydrogen bonds : bond 0.04422 / 2.92 ( 637) hydrogen bonds : angle 5.11639 / 3.66 ( 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 248 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 291 ASN cc_start: 0.8586 (m-40) cc_final: 0.7947 (m110) REVERT: B 443 TRP cc_start: 0.8961 (OUTLIER) cc_final: 0.8658 (m100) REVERT: B 480 VAL cc_start: 0.7421 (t) cc_final: 0.7159 (p) REVERT: B 492 PHE cc_start: 0.8533 (p90) cc_final: 0.8077 (p90) REVERT: C 13 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7719 (m-80) REVERT: C 144 MET cc_start: 0.8444 (tpt) cc_final: 0.8215 (tpt) REVERT: C 428 LYS cc_start: 0.7573 (tmtt) cc_final: 0.6564 (mptt) REVERT: C 476 PHE cc_start: 0.6561 (t80) cc_final: 0.5967 (t80) REVERT: D 108 LYS cc_start: 0.8216 (tttt) cc_final: 0.7955 (mmtt) REVERT: D 233 GLN cc_start: 0.8431 (tp40) cc_final: 0.8224 (tp-100) REVERT: D 236 LEU cc_start: 0.7354 (mt) cc_final: 0.7074 (tt) REVERT: D 381 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8064 (mp10) REVERT: E 10 CYS cc_start: 0.6991 (m) cc_final: 0.6517 (t) REVERT: E 101 ASP cc_start: 0.8345 (m-30) cc_final: 0.7794 (m-30) REVERT: E 171 CYS cc_start: 0.8065 (t) cc_final: 0.7309 (m) REVERT: E 236 TYR cc_start: 0.7675 (t80) cc_final: 0.7279 (t80) outliers start: 61 outliers final: 56 residues processed: 236 average time/residue: 0.0937 time to fit residues: 35.6496 Evaluate side-chains 240 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 181 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 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 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 481 SER Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 631 CYS Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 93 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 166 HIS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 326 ILE 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 191 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 215 PHE Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 241 VAL Chi-restraints excluded: chain E residue 254 TRP Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 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: 0.0970 chunk 144 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 28 optimal weight: 8.9990 chunk 97 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 416 HIS C 58 ASN ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 HIS ** 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 = 0.3968 r_free = 0.3968 target = 0.131653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.110597 restraints weight = 35133.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112631 restraints weight = 19377.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.113760 restraints weight = 12971.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.114304 restraints weight = 11354.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.114508 restraints weight = 10436.664| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13988 Z= 0.130 Angle : 0.726 12.658 18936 Z= 0.360 Chirality : 0.043 0.217 2165 Planarity : 0.005 0.071 2384 Dihedral : 5.890 63.406 1791 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.32 % Allowed : 30.32 % Favored : 66.36 % 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: 0.38 (0.17), residues: 932 sheet: -1.93 (0.43), residues: 124 loop : -2.13 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 43 TYR 0.021 0.001 TYR D 226 PHE 0.048 0.002 PHE C 244 TRP 0.018 0.001 TRP C 649 HIS 0.011 0.001 HIS B 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13988) covalent geometry : angle 0.72642 / 0.36 (18936) hydrogen bonds : bond 0.03930 / 2.59 ( 637) hydrogen bonds : angle 4.88370 / 3.49 ( 1896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2298.61 seconds wall clock time: 40 minutes 37.47 seconds (2437.47 seconds total)