Starting phenix.real_space_refine on Fri Sep 11 15:29:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.map" model { file = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6nts_0510/09_2026/6nts_0510.cif" } resolution = 3.63 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 S 57 5.16 5 C 6378 2.51 5 N 1654 2.21 5 O 1862 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9956 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4543 Classifications: {'peptide': 583} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 556} Chain: "B" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2976 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain: "C" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2399 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'L2J': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.82, per 1000 atoms: 0.18 Number of scatterers: 9956 At special positions: 0 Unit cell: (96.824, 110.656, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 2 24.99 S 57 16.00 F 3 9.00 O 1862 8.00 N 1654 7.00 C 6378 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: 0.97 Conformation dependent library (CDL) restraints added in 348.2 milliseconds 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 3 sheets defined 74.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 11 through 17 Processing helix chain 'A' and resid 24 through 43 removed outlier: 3.506A pdb=" N ARG A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 41 " --> pdb=" O THR A 37 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 59 removed outlier: 5.099A pdb=" N LEU A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) Proline residue: A 53 - end of helix Processing helix chain 'A' and resid 62 through 76 Processing helix chain 'A' and resid 84 through 88 removed outlier: 4.149A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 98 removed outlier: 3.867A pdb=" N LEU A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.736A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.837A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.804A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 162 through 175 removed outlier: 3.692A pdb=" N GLN A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.529A pdb=" N ARG A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 214 removed outlier: 5.081A pdb=" N ILE A 206 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 217 through 233 removed outlier: 4.698A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.398A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 removed outlier: 3.666A pdb=" N GLU A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 266 through 275 removed outlier: 3.907A pdb=" N ALA A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 292 removed outlier: 4.743A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.567A pdb=" N LYS A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 4.821A pdb=" N LYS A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLU A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.565A pdb=" N VAL A 321 " --> pdb=" O CYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.767A pdb=" N LYS A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A 333 " --> pdb=" O CYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.935A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.806A pdb=" N ILE A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLU A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.680A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 removed outlier: 3.816A pdb=" N VAL A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 388 through 391' Processing helix chain 'A' and resid 396 through 412 removed outlier: 3.760A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.626A pdb=" N ARG A 420 " --> pdb=" O LYS A 416 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.956A pdb=" N PHE A 439 " --> pdb=" O GLY A 435 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP A 440 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.599A pdb=" N CYS A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 474 removed outlier: 3.556A pdb=" N ARG A 459 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 481 removed outlier: 3.957A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 removed outlier: 3.799A pdb=" N LYS A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 494 through 513 removed outlier: 3.734A pdb=" N THR A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 529 removed outlier: 3.611A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LEU A 522 " --> pdb=" O THR A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix removed outlier: 3.575A pdb=" N ALA A 529 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 548 removed outlier: 4.549A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 552 through 569 removed outlier: 3.538A pdb=" N LEU A 556 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N LYS A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) Proline residue: A 562 - end of helix removed outlier: 3.814A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 69 through 76 removed outlier: 4.037A pdb=" N GLN B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 81 Processing helix chain 'B' and resid 91 through 111 removed outlier: 3.930A pdb=" N GLU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 106 " --> pdb=" O ASN B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.668A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.230A pdb=" N LEU B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL B 162 " --> pdb=" O HIS B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 185 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 200 through 218 removed outlier: 3.565A pdb=" N ARG B 204 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 206 " --> pdb=" O ARG B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 245 through 257 removed outlier: 3.552A pdb=" N LEU B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 265 through 275 removed outlier: 3.713A pdb=" N LEU B 272 " --> pdb=" O HIS B 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 273 " --> pdb=" O LYS B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 removed outlier: 3.698A pdb=" N THR B 281 " --> pdb=" O PRO B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 301 removed outlier: 3.856A pdb=" N PHE B 299 " --> pdb=" O CYS B 295 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.698A pdb=" N VAL B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 removed outlier: 3.600A pdb=" N MET B 328 " --> pdb=" O GLN B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 362 removed outlier: 4.465A pdb=" N LYS B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE B 348 " --> pdb=" O GLN B 344 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) Proline residue: B 351 - end of helix removed outlier: 3.623A pdb=" N LYS B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 391 through 402 removed outlier: 4.139A pdb=" N PHE B 396 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 425 removed outlier: 3.540A pdb=" N VAL B 412 " --> pdb=" O ASN B 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.548A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 removed outlier: 3.601A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.154A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 6.108A pdb=" N THR C 53 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 3.503A pdb=" N PHE C 220 " --> pdb=" O ASP C 202 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1536 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: 1.19 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.57: 10076 1.57 - 1.92: 84 1.92 - 2.27: 0 2.27 - 2.62: 0 2.62 - 2.97: 1 Bond restraints: 10161 Sorted by residual: bond pdb=" C10 MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.427 2.965 -1.538 2.00e-02 2.50e+03 5.92e+03 bond pdb=" C02 L2J A 601 " pdb=" C03 L2J A 601 " ideal model delta sigma weight residual 1.396 1.293 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " ideal model delta sigma weight residual 1.388 1.488 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 1.327 1.231 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C07 L2J A 601 " pdb=" C08 L2J A 601 " ideal model delta sigma weight residual 1.402 1.320 0.082 2.00e-02 2.50e+03 1.70e+01 ... (remaining 10156 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 13721 3.18 - 6.35: 53 6.35 - 9.53: 1 9.53 - 12.70: 3 12.70 - 15.88: 2 Bond angle restraints: 13780 Sorted by residual: angle pdb=" O03 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" O04 L2J A 601 " ideal model delta sigma weight residual 116.82 100.94 15.88 3.00e+00 1.11e-01 2.80e+01 angle pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " pdb=" C10 MLL C 309 " ideal model delta sigma weight residual 117.67 133.31 -15.64 3.00e+00 1.11e-01 2.72e+01 angle pdb=" C19 L2J A 601 " pdb=" S01 L2J A 601 " pdb=" N02 L2J A 601 " ideal model delta sigma weight residual 100.55 111.98 -11.43 3.00e+00 1.11e-01 1.45e+01 angle pdb=" C01 L2J A 601 " pdb=" C06 L2J A 601 " pdb=" C05 L2J A 601 " ideal model delta sigma weight residual 119.28 108.25 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O9 MLL C 309 " ideal model delta sigma weight residual 110.79 121.00 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 13775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 5703 17.83 - 35.65: 387 35.65 - 53.48: 69 53.48 - 71.31: 16 71.31 - 89.14: 12 Dihedral angle restraints: 6187 sinusoidal: 2536 harmonic: 3651 Sorted by residual: dihedral pdb=" CA ARG A 537 " pdb=" C ARG A 537 " pdb=" N PHE A 538 " pdb=" CA PHE A 538 " ideal model delta harmonic sigma weight residual 180.00 158.37 21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA HIS B 364 " pdb=" C HIS B 364 " pdb=" N PHE B 365 " pdb=" CA PHE B 365 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CB GLU C 188 " pdb=" CG GLU C 188 " pdb=" CD GLU C 188 " pdb=" OE1 GLU C 188 " ideal model delta sinusoidal sigma weight residual 0.00 -89.14 89.14 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 6184 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1080 0.027 - 0.055: 309 0.055 - 0.082: 116 0.082 - 0.110: 54 0.110 - 0.137: 13 Chirality restraints: 1572 Sorted by residual: chirality pdb=" C18 L2J A 601 " pdb=" C13 L2J A 601 " pdb=" C17 L2J A 601 " pdb=" N01 L2J A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.45 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL C 52 " pdb=" N VAL C 52 " pdb=" C VAL C 52 " pdb=" CB VAL C 52 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA PHE A 538 " pdb=" N PHE A 538 " pdb=" C PHE A 538 " pdb=" CB PHE A 538 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.13 2.00e-01 2.50e+01 3.91e-01 ... (remaining 1569 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 90 " 0.015 5.00e-02 4.00e+02 2.25e-02 8.12e-01 pdb=" N PRO A 91 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 91 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 91 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 86 " 0.010 2.00e-02 2.50e+03 6.28e-03 7.89e-01 pdb=" CG TYR C 86 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR C 86 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 86 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 86 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 86 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 50 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.53e-01 pdb=" N PRO C 51 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.011 5.00e-02 4.00e+02 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 39 2.51 - 3.11: 7867 3.11 - 3.71: 15828 3.71 - 4.30: 21974 4.30 - 4.90: 35746 Nonbonded interactions: 81454 Sorted by model distance: nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 1.917 2.400 nonbonded pdb=" O GLY A 275 " pdb=" OG1 THR A 279 " model vdw 2.209 3.040 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.222 2.320 nonbonded pdb=" NE2 HIS C 59 " pdb="MN MN C 402 " model vdw 2.235 2.400 nonbonded pdb=" O GLY A 513 " pdb=" OG1 THR A 517 " model vdw 2.264 3.040 ... (remaining 81449 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=0.64 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.016 1.538 10161 Z= 0.780 Angle : 0.516 15.879 13780 Z= 0.247 Chirality : 0.034 0.137 1572 Planarity : 0.002 0.023 1764 Dihedral : 13.181 89.136 3809 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.22), residues: 1231 helix: -1.17 (0.17), residues: 793 sheet: -1.94 (0.87), residues: 35 loop : -1.41 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 185 TYR 0.013 0.001 TYR C 86 PHE 0.008 0.001 PHE A 538 TRP 0.010 0.000 TRP A 257 HIS 0.003 0.000 HIS B 364 Details of bonding type rmsd/Z covalent geometry : bond 0.01559 / 0.78 (10161) covalent geometry : angle 0.51645 / 0.25 (13780) hydrogen bonds : bond 0.12700 / 8.18 ( 528) hydrogen bonds : angle 5.16110 / 3.51 ( 1536) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 GLU cc_start: 0.8284 (pp20) cc_final: 0.8055 (pp20) REVERT: B 78 CYS cc_start: 0.8890 (m) cc_final: 0.8655 (m) REVERT: B 110 THR cc_start: 0.8511 (p) cc_final: 0.8239 (p) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.1045 time to fit residues: 17.3167 Evaluate side-chains 50 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 GLN B 111 ASN ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.047440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.040177 restraints weight = 67034.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.041304 restraints weight = 37530.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.042089 restraints weight = 24844.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.042638 restraints weight = 18377.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043015 restraints weight = 14652.237| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 10161 Z= 0.353 Angle : 0.913 10.489 13780 Z= 0.461 Chirality : 0.050 0.232 1572 Planarity : 0.006 0.078 1764 Dihedral : 5.206 29.064 1366 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.54 % Allowed : 8.51 % Favored : 89.95 % 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: -1.19 (0.24), residues: 1231 helix: -0.60 (0.17), residues: 815 sheet: -0.49 (1.02), residues: 31 loop : -0.86 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 168 TYR 0.023 0.003 TYR C 86 PHE 0.031 0.003 PHE A 538 TRP 0.041 0.003 TRP A 477 HIS 0.020 0.002 HIS C 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.35 (10161) covalent geometry : angle 0.91289 / 0.46 (13780) hydrogen bonds : bond 0.05395 / 3.47 ( 528) hydrogen bonds : angle 4.88658 / 3.45 ( 1536) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6566 (m-80) REVERT: B 81 LEU cc_start: 0.7931 (tp) cc_final: 0.7526 (mt) REVERT: B 85 MET cc_start: 0.7428 (tpp) cc_final: 0.7057 (tpp) REVERT: B 111 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7542 (p0) REVERT: B 328 MET cc_start: 0.8664 (mtm) cc_final: 0.8409 (mtm) outliers start: 17 outliers final: 8 residues processed: 61 average time/residue: 0.1006 time to fit residues: 8.8800 Evaluate side-chains 46 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 165 CYS Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 172 ASN A 339 GLN B 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041643 restraints weight = 65362.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.042786 restraints weight = 36549.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.043592 restraints weight = 24185.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.044168 restraints weight = 17826.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.044515 restraints weight = 14186.306| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10161 Z= 0.118 Angle : 0.593 7.985 13780 Z= 0.295 Chirality : 0.040 0.179 1572 Planarity : 0.003 0.035 1764 Dihedral : 4.719 23.931 1366 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.27 % Allowed : 9.32 % Favored : 89.41 % 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: -0.30 (0.25), residues: 1231 helix: 0.10 (0.19), residues: 820 sheet: -0.03 (1.08), residues: 31 loop : -0.58 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 249 TYR 0.017 0.001 TYR B 107 PHE 0.025 0.001 PHE A 538 TRP 0.020 0.001 TRP A 477 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10161) covalent geometry : angle 0.59331 / 0.29 (13780) hydrogen bonds : bond 0.03397 / 2.20 ( 528) hydrogen bonds : angle 4.21649 / 2.95 ( 1536) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6732 (m-80) outliers start: 14 outliers final: 6 residues processed: 54 average time/residue: 0.0898 time to fit residues: 7.1829 Evaluate side-chains 43 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 86 TYR Chi-restraints excluded: chain C residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 268 HIS ** 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 = 0.3307 r_free = 0.3307 target = 0.047260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.039931 restraints weight = 66351.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.041078 restraints weight = 37121.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041878 restraints weight = 24505.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.042443 restraints weight = 18061.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.042837 restraints weight = 14394.352| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10161 Z= 0.156 Angle : 0.612 6.621 13780 Z= 0.305 Chirality : 0.041 0.136 1572 Planarity : 0.004 0.036 1764 Dihedral : 4.532 21.296 1366 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.72 % Allowed : 10.32 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1231 helix: 0.41 (0.19), residues: 822 sheet: 1.09 (1.43), residues: 21 loop : -0.46 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.011 0.001 TYR B 107 PHE 0.018 0.002 PHE A 538 TRP 0.028 0.002 TRP B 156 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (10161) covalent geometry : angle 0.61219 / 0.30 (13780) hydrogen bonds : bond 0.03585 / 2.31 ( 528) hydrogen bonds : angle 4.16749 / 2.93 ( 1536) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6729 (m-80) outliers start: 19 outliers final: 8 residues processed: 59 average time/residue: 0.0805 time to fit residues: 7.0943 Evaluate side-chains 44 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.047325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.040064 restraints weight = 65673.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.041220 restraints weight = 36757.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.042001 restraints weight = 24185.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.042546 restraints weight = 17821.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.042931 restraints weight = 14173.775| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10161 Z= 0.129 Angle : 0.583 9.299 13780 Z= 0.287 Chirality : 0.040 0.134 1572 Planarity : 0.003 0.037 1764 Dihedral : 4.458 21.703 1366 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.63 % Allowed : 11.13 % Favored : 87.24 % 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: 0.41 (0.25), residues: 1231 helix: 0.66 (0.19), residues: 815 sheet: -0.25 (1.03), residues: 31 loop : -0.29 (0.35), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.012 0.001 TYR B 107 PHE 0.017 0.001 PHE A 538 TRP 0.019 0.001 TRP A 477 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10161) covalent geometry : angle 0.58325 / 0.29 (13780) hydrogen bonds : bond 0.03178 / 2.06 ( 528) hydrogen bonds : angle 4.08405 / 2.87 ( 1536) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 36 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: A 521 MET cc_start: 0.8141 (mpp) cc_final: 0.7342 (mtm) REVERT: B 75 LEU cc_start: 0.9363 (tp) cc_final: 0.9151 (mt) outliers start: 18 outliers final: 11 residues processed: 50 average time/residue: 0.0664 time to fit residues: 5.6765 Evaluate side-chains 48 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 42 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 ASN ** 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 = 0.3332 r_free = 0.3332 target = 0.047766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040509 restraints weight = 64779.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041661 restraints weight = 36147.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.042462 restraints weight = 23732.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042955 restraints weight = 17321.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.043380 restraints weight = 13858.421| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 10161 Z= 0.105 Angle : 0.557 6.982 13780 Z= 0.273 Chirality : 0.040 0.226 1572 Planarity : 0.003 0.037 1764 Dihedral : 4.300 21.161 1366 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.72 % Allowed : 11.67 % Favored : 86.61 % 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: 0.58 (0.25), residues: 1231 helix: 0.81 (0.19), residues: 822 sheet: -0.29 (1.01), residues: 31 loop : -0.28 (0.35), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 221 TYR 0.012 0.001 TYR B 107 PHE 0.015 0.001 PHE A 538 TRP 0.017 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (10161) covalent geometry : angle 0.55665 / 0.27 (13780) hydrogen bonds : bond 0.02894 / 1.89 ( 528) hydrogen bonds : angle 3.99717 / 2.79 ( 1536) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 39 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8554 (m-80) cc_final: 0.8186 (m-10) REVERT: B 75 LEU cc_start: 0.9318 (tp) cc_final: 0.9107 (mt) outliers start: 19 outliers final: 15 residues processed: 52 average time/residue: 0.0724 time to fit residues: 5.9237 Evaluate side-chains 51 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Chi-restraints excluded: chain C residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040280 restraints weight = 64776.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041444 restraints weight = 36275.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.042224 restraints weight = 23830.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.042708 restraints weight = 17526.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.043134 restraints weight = 14075.745| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.5764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10161 Z= 0.111 Angle : 0.569 7.683 13780 Z= 0.277 Chirality : 0.039 0.142 1572 Planarity : 0.003 0.038 1764 Dihedral : 4.187 20.432 1366 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.27 % Allowed : 12.22 % Favored : 86.52 % 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: 0.70 (0.25), residues: 1231 helix: 0.90 (0.19), residues: 816 sheet: -0.34 (1.00), residues: 31 loop : -0.20 (0.34), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 221 TYR 0.026 0.001 TYR A 60 PHE 0.014 0.001 PHE A 538 TRP 0.018 0.001 TRP A 477 HIS 0.003 0.001 HIS A 340 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (10161) covalent geometry : angle 0.56892 / 0.28 (13780) hydrogen bonds : bond 0.02934 / 1.91 ( 528) hydrogen bonds : angle 3.98862 / 2.79 ( 1536) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8566 (m-80) cc_final: 0.8203 (m-10) REVERT: A 521 MET cc_start: 0.8118 (mpp) cc_final: 0.7635 (mtm) outliers start: 14 outliers final: 12 residues processed: 48 average time/residue: 0.0759 time to fit residues: 5.9717 Evaluate side-chains 46 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 25 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.040278 restraints weight = 64348.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041410 restraints weight = 36012.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042201 restraints weight = 23734.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.042684 restraints weight = 17429.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.043101 restraints weight = 14034.620| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10161 Z= 0.105 Angle : 0.563 7.924 13780 Z= 0.272 Chirality : 0.039 0.264 1572 Planarity : 0.003 0.038 1764 Dihedral : 4.146 20.211 1366 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.27 % Allowed : 12.58 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1231 helix: 0.97 (0.19), residues: 814 sheet: -0.40 (0.99), residues: 31 loop : -0.20 (0.34), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.024 0.001 TYR B 400 PHE 0.014 0.001 PHE A 538 TRP 0.016 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (10161) covalent geometry : angle 0.56258 / 0.27 (13780) hydrogen bonds : bond 0.02838 / 1.85 ( 528) hydrogen bonds : angle 3.97289 / 2.77 ( 1536) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8545 (m-80) cc_final: 0.8187 (m-10) REVERT: A 521 MET cc_start: 0.8139 (mpp) cc_final: 0.7667 (mtm) REVERT: B 328 MET cc_start: 0.8683 (mtt) cc_final: 0.8177 (mtm) outliers start: 14 outliers final: 11 residues processed: 46 average time/residue: 0.0700 time to fit residues: 5.4306 Evaluate side-chains 46 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 92 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.040095 restraints weight = 64159.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.041207 restraints weight = 35738.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041991 restraints weight = 23642.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042525 restraints weight = 17376.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042908 restraints weight = 13831.678| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10161 Z= 0.110 Angle : 0.567 8.482 13780 Z= 0.275 Chirality : 0.039 0.225 1572 Planarity : 0.003 0.042 1764 Dihedral : 4.094 20.140 1366 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.36 % Allowed : 12.67 % Favored : 85.97 % 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: 0.88 (0.25), residues: 1231 helix: 1.06 (0.19), residues: 806 sheet: -0.37 (0.99), residues: 31 loop : -0.16 (0.34), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.024 0.001 TYR B 400 PHE 0.014 0.001 PHE A 538 TRP 0.017 0.001 TRP A 477 HIS 0.002 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (10161) covalent geometry : angle 0.56734 / 0.27 (13780) hydrogen bonds : bond 0.02861 / 1.86 ( 528) hydrogen bonds : angle 3.97344 / 2.77 ( 1536) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 36 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8578 (m-80) cc_final: 0.8214 (m-10) REVERT: A 521 MET cc_start: 0.8181 (mpp) cc_final: 0.7726 (mtm) REVERT: B 81 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8079 (mm) outliers start: 15 outliers final: 12 residues processed: 48 average time/residue: 0.0729 time to fit residues: 5.9506 Evaluate side-chains 49 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 268 HIS ** 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 = 0.3287 r_free = 0.3287 target = 0.046263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039179 restraints weight = 63996.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.040298 restraints weight = 35696.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.041066 restraints weight = 23570.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041599 restraints weight = 17395.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041973 restraints weight = 13881.365| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10161 Z= 0.132 Angle : 0.601 8.815 13780 Z= 0.291 Chirality : 0.041 0.277 1572 Planarity : 0.004 0.040 1764 Dihedral : 4.205 21.451 1366 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.36 % Allowed : 12.76 % Favored : 85.88 % 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: 0.81 (0.25), residues: 1231 helix: 1.04 (0.19), residues: 809 sheet: -0.48 (0.95), residues: 31 loop : -0.26 (0.34), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 21 TYR 0.020 0.001 TYR B 400 PHE 0.016 0.001 PHE A 538 TRP 0.019 0.001 TRP A 477 HIS 0.003 0.001 HIS A 127 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (10161) covalent geometry : angle 0.60084 / 0.29 (13780) hydrogen bonds : bond 0.03228 / 2.10 ( 528) hydrogen bonds : angle 4.09984 / 2.86 ( 1536) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2462 Ramachandran restraints generated. 1231 Oldfield, 0 Emsley, 1231 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 35 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 85 TYR cc_start: 0.8530 (m-80) cc_final: 0.8180 (m-10) REVERT: B 81 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8092 (mm) outliers start: 15 outliers final: 12 residues processed: 47 average time/residue: 0.0709 time to fit residues: 5.7206 Evaluate side-chains 47 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 439 PHE Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 333 ILE Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 425 MET Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 230 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.046892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.039730 restraints weight = 64917.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040863 restraints weight = 36115.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041650 restraints weight = 23862.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.042197 restraints weight = 17509.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.042575 restraints weight = 13913.860| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10161 Z= 0.106 Angle : 0.583 8.891 13780 Z= 0.280 Chirality : 0.040 0.267 1572 Planarity : 0.003 0.039 1764 Dihedral : 4.135 20.554 1366 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.09 % Allowed : 13.12 % Favored : 85.79 % 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: 0.83 (0.25), residues: 1231 helix: 1.07 (0.19), residues: 815 sheet: -0.38 (0.96), residues: 31 loop : -0.32 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 21 TYR 0.023 0.001 TYR B 400 PHE 0.015 0.001 PHE B 353 TRP 0.018 0.001 TRP A 477 HIS 0.002 0.000 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10161) covalent geometry : angle 0.58272 / 0.28 (13780) hydrogen bonds : bond 0.02897 / 1.90 ( 528) hydrogen bonds : angle 4.02452 / 2.81 ( 1536) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1393.36 seconds wall clock time: 24 minutes 50.23 seconds (1490.23 seconds total)