Starting phenix.real_space_refine on Fri Jul 3 11:37:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2026/7jpq_22419.map" } resolution = 3.5 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= 0.000 sd= 0.004 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 P 6 5.49 5 Mg 2 5.21 5 S 65 5.16 5 C 8911 2.51 5 N 2339 2.21 5 O 2540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13863 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2436 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 7, 'TRANS': 289} Chain breaks: 2 Chain: "C" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4788 Classifications: {'peptide': 587} Link IDs: {'PTRANS': 24, 'TRANS': 562} Chain breaks: 9 Chain: "D" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3281 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 13, 'TRANS': 389} Chain breaks: 2 Chain: "E" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3294 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 19, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.58, per 1000 atoms: 0.19 Number of scatterers: 13863 At special positions: 0 Unit cell: (92.02, 113.42, 162.64, 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) S 65 16.00 P 6 15.00 Mg 2 11.99 O 2540 8.00 N 2339 7.00 C 8911 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: 0.87 Conformation dependent library (CDL) restraints added in 503.5 milliseconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3286 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 6 sheets defined 62.3% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 284 through 292 removed outlier: 3.903A pdb=" N LYS B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.643A pdb=" N HIS B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 330 Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 402 through 414 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.556A pdb=" N TRP B 433 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 473 through 484 removed outlier: 4.221A pdb=" N LEU B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 484 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 500 removed outlier: 3.816A pdb=" N LEU B 495 " --> pdb=" O ILE B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 522 Processing helix chain 'B' and resid 528 through 542 removed outlier: 3.602A pdb=" N LEU B 532 " --> pdb=" O SER B 528 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 539 " --> pdb=" O GLN B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 40 through 66 removed outlier: 3.555A pdb=" N TYR C 47 " --> pdb=" O ARG C 43 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 88 removed outlier: 3.776A pdb=" N ASN C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 removed outlier: 4.339A pdb=" N THR C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 126 " --> pdb=" O THR C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 removed outlier: 3.529A pdb=" N LEU C 148 " --> pdb=" O MET C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 192 removed outlier: 3.595A pdb=" N LEU C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.586A pdb=" N LEU C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS C 240 " --> pdb=" O ILE C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 263 removed outlier: 4.297A pdb=" N HIS C 260 " --> pdb=" O PRO C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.587A pdb=" N SER C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 293 removed outlier: 3.539A pdb=" N HIS C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'C' and resid 320 through 338 removed outlier: 3.624A pdb=" N PHE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 345 removed outlier: 3.707A pdb=" N VAL C 343 " --> pdb=" O PRO C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 removed outlier: 3.619A pdb=" N ARG C 353 " --> pdb=" O PRO C 349 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 356 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 369 Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.511A pdb=" N LYS C 378 " --> pdb=" O ARG C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 390 Processing helix chain 'C' and resid 390 through 426 removed outlier: 3.707A pdb=" N CYS C 418 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER C 425 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU C 426 " --> pdb=" O PHE C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 445 removed outlier: 3.527A pdb=" N LEU C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU C 444 " --> pdb=" O CYS C 440 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N LYS C 445 " --> pdb=" O THR C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 removed outlier: 4.047A pdb=" N ALA C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N MET C 462 " --> pdb=" O GLN C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 482 removed outlier: 4.248A pdb=" N THR C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR C 482 " --> pdb=" O VAL C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 498 removed outlier: 3.721A pdb=" N GLU C 495 " --> pdb=" O ALA C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 567 removed outlier: 3.796A pdb=" N ASN C 554 " --> pdb=" O VAL C 550 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 555 " --> pdb=" O LEU C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 573 removed outlier: 3.621A pdb=" N GLN C 573 " --> pdb=" O PRO C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 579 removed outlier: 3.758A pdb=" N VAL C 578 " --> pdb=" O LEU C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 592 Processing helix chain 'C' and resid 599 through 604 removed outlier: 3.610A pdb=" N ASN C 604 " --> pdb=" O HIS C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 removed outlier: 3.641A pdb=" N TYR C 608 " --> pdb=" O ASN C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.979A pdb=" N GLU C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 644 through 657 removed outlier: 4.048A pdb=" N VAL C 655 " --> pdb=" O ALA C 651 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR C 657 " --> pdb=" O ALA C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 690 Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 40 through 57 Processing helix chain 'D' and resid 72 through 86 Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.525A pdb=" N SER D 91 " --> pdb=" O ILE D 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 87 through 92' Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 131 through 142 Processing helix chain 'D' and resid 160 through 165 removed outlier: 3.785A pdb=" N PHE D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA D 165 " --> pdb=" O PHE D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 165' Processing helix chain 'D' and resid 170 through 180 Processing helix chain 'D' and resid 197 through 201 Processing helix chain 'D' and resid 203 through 210 Processing helix chain 'D' and resid 222 through 234 removed outlier: 3.591A pdb=" N LEU D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 258 removed outlier: 3.783A pdb=" N ALA D 246 " --> pdb=" O ASP D 242 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 271 removed outlier: 3.520A pdb=" N ASN D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 288 removed outlier: 3.777A pdb=" N LEU D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 310 removed outlier: 3.628A pdb=" N LEU D 302 " --> pdb=" O THR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 321 removed outlier: 3.518A pdb=" N ASN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 340 removed outlier: 3.713A pdb=" N ILE D 338 " --> pdb=" O HIS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.527A pdb=" N VAL D 349 " --> pdb=" O ASN D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 382 removed outlier: 3.508A pdb=" N VAL D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS D 378 " --> pdb=" O LYS D 374 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 380 " --> pdb=" O PHE D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 417 Processing helix chain 'D' and resid 422 through 431 Processing helix chain 'E' and resid 11 through 23 Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.736A pdb=" N THR E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 82 Processing helix chain 'E' and resid 98 through 110 Processing helix chain 'E' and resid 127 through 133 removed outlier: 3.558A pdb=" N MET E 133 " --> pdb=" O LEU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 143 Processing helix chain 'E' and resid 143 through 149 Processing helix chain 'E' and resid 161 through 166 removed outlier: 4.074A pdb=" N PHE E 165 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 200 through 216 removed outlier: 3.777A pdb=" N VAL E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 232 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 237 through 242 removed outlier: 3.688A pdb=" N VAL E 241 " --> pdb=" O CYS E 237 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 242 " --> pdb=" O GLU E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 237 through 242' Processing helix chain 'E' and resid 249 through 267 removed outlier: 3.871A pdb=" N LEU E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Proline residue: E 259 - end of helix removed outlier: 3.786A pdb=" N GLN E 266 " --> pdb=" O LYS E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 320 through 322 No H-bonds generated for 'chain 'E' and resid 320 through 322' Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 359 through 370 Processing helix chain 'E' and resid 377 through 390 removed outlier: 3.770A pdb=" N PHE E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 423 removed outlier: 3.517A pdb=" N ILE E 416 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 431 removed outlier: 4.041A pdb=" N TYR E 430 " --> pdb=" O ASP E 426 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 443 through 447 removed outlier: 6.215A pdb=" N ASN B 310 " --> pdb=" O LEU B 444 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR B 446 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL B 312 " --> pdb=" O TYR B 446 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE B 311 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE B 424 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 313 " --> pdb=" O ILE B 424 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 133 through 136 removed outlier: 8.013A pdb=" N PHE C 250 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 103 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 252 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU C 105 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 95 through 100 removed outlier: 7.743A pdb=" N ILE D 215 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 64 " --> pdb=" O ILE D 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 385 through 387 Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 62 removed outlier: 7.411A pdb=" N SER E 32 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LEU E 177 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N PHE E 34 " --> pdb=" O LEU E 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 357 through 358 687 hydrogen bonds defined for protein. 2013 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: 1.70 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: 1.21 - 1.33: 3333 1.33 - 1.45: 2766 1.45 - 1.57: 7948 1.57 - 1.69: 11 1.69 - 1.81: 97 Bond restraints: 14155 Sorted by residual: bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.94e+01 bond pdb=" C5 ATP D 901 " pdb=" C6 ATP D 901 " ideal model delta sigma weight residual 1.409 1.473 -0.064 1.00e-02 1.00e+04 4.13e+01 bond pdb=" C5 ATP E 501 " pdb=" C6 ATP E 501 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.82e+01 bond pdb=" C4 ATP E 501 " pdb=" N9 ATP E 501 " ideal model delta sigma weight residual 1.374 1.325 0.049 1.00e-02 1.00e+04 2.44e+01 ... (remaining 14150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 18852 3.72 - 7.44: 273 7.44 - 11.16: 30 11.16 - 14.88: 1 14.88 - 18.60: 3 Bond angle restraints: 19159 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP E 501 " pdb=" O3A ATP E 501 " pdb=" PB ATP E 501 " ideal model delta sigma weight residual 136.83 119.61 17.22 1.00e+00 1.00e+00 2.97e+02 angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 123.07 16.80 1.00e+00 1.00e+00 2.82e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 122.14 14.69 1.00e+00 1.00e+00 2.16e+02 angle pdb=" C5 ATP E 501 " pdb=" C4 ATP E 501 " pdb=" N3 ATP E 501 " ideal model delta sigma weight residual 126.80 119.11 7.69 1.00e+00 1.00e+00 5.92e+01 ... (remaining 19154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.45: 7737 18.45 - 36.90: 663 36.90 - 55.35: 94 55.35 - 73.80: 24 73.80 - 92.24: 12 Dihedral angle restraints: 8530 sinusoidal: 3512 harmonic: 5018 Sorted by residual: dihedral pdb=" CA HIS D 34 " pdb=" C HIS D 34 " pdb=" N SER D 35 " pdb=" CA SER D 35 " ideal model delta harmonic sigma weight residual -180.00 -150.99 -29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN B 378 " pdb=" C ASN B 378 " pdb=" N LYS B 379 " pdb=" CA LYS B 379 " ideal model delta harmonic sigma weight residual 180.00 151.44 28.56 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA ARG D 397 " pdb=" C ARG D 397 " pdb=" N GLU D 398 " pdb=" CA GLU D 398 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1787 0.078 - 0.156: 339 0.156 - 0.234: 54 0.234 - 0.312: 7 0.312 - 0.389: 1 Chirality restraints: 2188 Sorted by residual: chirality pdb=" CB ILE B 421 " pdb=" CA ILE B 421 " pdb=" CG1 ILE B 421 " pdb=" CG2 ILE B 421 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CB THR B 449 " pdb=" CA THR B 449 " pdb=" OG1 THR B 449 " pdb=" CG2 THR B 449 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE C 447 " pdb=" CA ILE C 447 " pdb=" CG1 ILE C 447 " pdb=" CG2 ILE C 447 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2185 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 418 " -0.074 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO D 419 " 0.195 5.00e-02 4.00e+02 pdb=" CA PRO D 419 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO D 419 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 443 " 0.019 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B 443 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP B 443 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 443 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 443 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP B 443 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 443 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 443 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 443 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 240 " -0.010 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE D 240 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE D 240 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE D 240 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE D 240 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 240 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D 240 " -0.001 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 97 2.65 - 3.21: 12192 3.21 - 3.78: 20358 3.78 - 4.34: 27399 4.34 - 4.90: 45478 Nonbonded interactions: 105524 Sorted by model distance: nonbonded pdb=" OG1 THR D 74 " pdb="MG MG D 902 " model vdw 2.088 2.170 nonbonded pdb=" O3B ATP D 901 " pdb="MG MG D 902 " model vdw 2.097 2.170 nonbonded pdb=" OD1 ASN C 644 " pdb=" N THR C 700 " model vdw 2.319 3.120 nonbonded pdb=" O PHE B 380 " pdb=" ND2 ASN B 417 " model vdw 2.355 3.120 nonbonded pdb=" O THR B 448 " pdb=" OG1 THR B 448 " model vdw 2.356 3.040 ... (remaining 105519 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.160 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 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 : 0.008 0.077 14155 Z= 0.379 Angle : 1.138 18.604 19159 Z= 0.665 Chirality : 0.063 0.389 2188 Planarity : 0.007 0.113 2410 Dihedral : 14.269 92.245 5244 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -2.05 (0.18), residues: 1653 helix: -1.00 (0.15), residues: 928 sheet: -1.07 (0.41), residues: 146 loop : -1.80 (0.22), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG E 131 TYR 0.044 0.003 TYR E 204 PHE 0.052 0.004 PHE D 138 TRP 0.061 0.004 TRP B 443 HIS 0.013 0.003 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00772 / 0.38 (14155) covalent geometry : angle 1.13767 / 0.67 (19159) hydrogen bonds : bond 0.18174 / 12.41 ( 687) hydrogen bonds : angle 6.78891 / 4.84 ( 2013) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.506 Fit side-chains REVERT: B 454 TYR cc_start: 0.8961 (m-80) cc_final: 0.8625 (m-80) REVERT: B 474 LEU cc_start: 0.4687 (mm) cc_final: 0.3908 (pt) REVERT: B 475 SER cc_start: 0.8036 (p) cc_final: 0.7819 (p) REVERT: B 497 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7831 (mtmm) REVERT: C 189 MET cc_start: 0.7405 (mtp) cc_final: 0.7086 (ttp) REVERT: C 281 CYS cc_start: 0.7745 (m) cc_final: 0.7370 (m) REVERT: C 304 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7471 (pm20) REVERT: C 686 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6433 (mt-10) REVERT: D 137 SER cc_start: 0.8633 (t) cc_final: 0.8279 (p) REVERT: D 184 GLN cc_start: 0.6493 (tp-100) cc_final: 0.5854 (pp30) REVERT: E 6 ASN cc_start: 0.6643 (m-40) cc_final: 0.6378 (p0) REVERT: E 119 THR cc_start: 0.8286 (m) cc_final: 0.8038 (p) REVERT: E 189 LYS cc_start: 0.8373 (ttmt) cc_final: 0.7963 (tttp) REVERT: E 248 ARG cc_start: 0.6810 (tpp-160) cc_final: 0.5731 (ttt-90) REVERT: E 263 LYS cc_start: 0.7064 (mmtm) cc_final: 0.6713 (ttmm) REVERT: E 280 LYS cc_start: 0.6695 (tmtt) cc_final: 0.6441 (mptt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1107 time to fit residues: 35.4409 Evaluate side-chains 124 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 62 GLN C 110 ASN C 500 GLN C 576 HIS C 677 HIS D 19 GLN D 36 ASN D 61 ASN D 212 HIS D 288 ASN D 420 ASN E 195 HIS E 260 HIS E 398 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.132733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108955 restraints weight = 20273.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110732 restraints weight = 15836.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111527 restraints weight = 12787.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111919 restraints weight = 10694.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112017 restraints weight = 9503.480| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14155 Z= 0.133 Angle : 0.561 5.706 19159 Z= 0.298 Chirality : 0.041 0.152 2188 Planarity : 0.004 0.066 2410 Dihedral : 5.401 74.605 1813 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.96 % Allowed : 5.75 % Favored : 93.30 % 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: -0.75 (0.19), residues: 1653 helix: 0.34 (0.16), residues: 952 sheet: -0.82 (0.42), residues: 131 loop : -1.78 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 205 TYR 0.016 0.001 TYR E 204 PHE 0.023 0.002 PHE C 548 TRP 0.011 0.001 TRP B 443 HIS 0.007 0.001 HIS C 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14155) covalent geometry : angle 0.56077 / 0.30 (19159) hydrogen bonds : bond 0.04831 / 3.19 ( 687) hydrogen bonds : angle 4.53138 / 3.21 ( 2013) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.466 Fit side-chains REVERT: B 454 TYR cc_start: 0.8882 (m-80) cc_final: 0.8672 (m-80) REVERT: C 179 TYR cc_start: 0.6229 (m-80) cc_final: 0.6007 (m-80) REVERT: C 560 ASP cc_start: 0.7916 (t0) cc_final: 0.7494 (t0) REVERT: C 686 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6357 (mt-10) REVERT: E 6 ASN cc_start: 0.6697 (m-40) cc_final: 0.6475 (p0) REVERT: E 189 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8199 (tttp) REVERT: E 248 ARG cc_start: 0.6831 (tpp-160) cc_final: 0.6132 (ttm-80) REVERT: E 263 LYS cc_start: 0.7205 (mmtm) cc_final: 0.6965 (ttmm) REVERT: E 398 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5749 (t70) outliers start: 15 outliers final: 13 residues processed: 147 average time/residue: 0.1051 time to fit residues: 23.2479 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 212 HIS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 195 HIS Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 398 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 144 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 58 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 212 HIS D 420 ASN E 195 HIS E 232 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.105639 restraints weight = 20577.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107236 restraints weight = 15592.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.108306 restraints weight = 12771.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108558 restraints weight = 10412.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108842 restraints weight = 9546.391| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14155 Z= 0.181 Angle : 0.563 5.413 19159 Z= 0.297 Chirality : 0.042 0.164 2188 Planarity : 0.004 0.063 2410 Dihedral : 5.219 74.586 1813 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.21 % Allowed : 7.73 % Favored : 91.06 % 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: -0.39 (0.20), residues: 1653 helix: 0.67 (0.17), residues: 957 sheet: -0.85 (0.39), residues: 147 loop : -1.69 (0.24), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 564 TYR 0.018 0.002 TYR E 204 PHE 0.020 0.002 PHE C 319 TRP 0.011 0.001 TRP C 51 HIS 0.012 0.002 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (14155) covalent geometry : angle 0.56317 / 0.30 (19159) hydrogen bonds : bond 0.04993 / 3.31 ( 687) hydrogen bonds : angle 4.39698 / 3.11 ( 2013) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.325 Fit side-chains REVERT: C 686 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6533 (mt-10) REVERT: D 332 MET cc_start: 0.9086 (mtm) cc_final: 0.8860 (mtt) REVERT: E 6 ASN cc_start: 0.6923 (m-40) cc_final: 0.6649 (p0) REVERT: E 189 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8176 (tttp) REVERT: E 248 ARG cc_start: 0.6842 (tpp-160) cc_final: 0.6117 (ttm-80) REVERT: E 263 LYS cc_start: 0.7175 (mmtm) cc_final: 0.6939 (ttmm) outliers start: 19 outliers final: 13 residues processed: 134 average time/residue: 0.1003 time to fit residues: 20.1973 Evaluate side-chains 125 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 156 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 310 ASN C 110 ASN D 36 ASN D 358 GLN D 420 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109949 restraints weight = 20233.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111034 restraints weight = 15400.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111480 restraints weight = 13448.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111971 restraints weight = 11547.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.112303 restraints weight = 10482.025| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14155 Z= 0.103 Angle : 0.470 5.320 19159 Z= 0.250 Chirality : 0.038 0.171 2188 Planarity : 0.003 0.045 2410 Dihedral : 4.888 72.611 1813 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.21 % Allowed : 8.49 % Favored : 90.29 % 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: 0.15 (0.20), residues: 1653 helix: 1.16 (0.17), residues: 958 sheet: -0.57 (0.41), residues: 132 loop : -1.59 (0.24), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 397 TYR 0.016 0.001 TYR B 498 PHE 0.016 0.001 PHE C 548 TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14155) covalent geometry : angle 0.47033 / 0.25 (19159) hydrogen bonds : bond 0.03717 / 2.44 ( 687) hydrogen bonds : angle 3.97071 / 2.80 ( 2013) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.416 Fit side-chains REVERT: B 465 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7136 (tt) REVERT: C 422 PHE cc_start: 0.7096 (OUTLIER) cc_final: 0.6214 (t80) REVERT: D 111 LEU cc_start: 0.9136 (tp) cc_final: 0.8700 (tp) REVERT: E 6 ASN cc_start: 0.7035 (m-40) cc_final: 0.6650 (p0) REVERT: E 163 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: E 189 LYS cc_start: 0.8576 (ttmt) cc_final: 0.8169 (tttp) REVERT: E 248 ARG cc_start: 0.6864 (tpp-160) cc_final: 0.6136 (ttm-80) REVERT: E 263 LYS cc_start: 0.7078 (mmtm) cc_final: 0.6867 (ttmm) outliers start: 19 outliers final: 11 residues processed: 140 average time/residue: 0.0997 time to fit residues: 21.1859 Evaluate side-chains 122 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 108 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 76 optimal weight: 0.0060 chunk 153 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 110 ASN C 636 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.111085 restraints weight = 20274.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112349 restraints weight = 16762.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113537 restraints weight = 13659.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.113820 restraints weight = 10470.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113944 restraints weight = 9732.145| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14155 Z= 0.097 Angle : 0.454 5.347 19159 Z= 0.240 Chirality : 0.038 0.177 2188 Planarity : 0.003 0.043 2410 Dihedral : 4.719 72.239 1813 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.09 % Allowed : 9.83 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.21), residues: 1653 helix: 1.41 (0.17), residues: 961 sheet: -0.47 (0.41), residues: 132 loop : -1.46 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 705 TYR 0.014 0.001 TYR B 498 PHE 0.028 0.001 PHE B 569 TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (14155) covalent geometry : angle 0.45429 / 0.24 (19159) hydrogen bonds : bond 0.03462 / 2.27 ( 687) hydrogen bonds : angle 3.82323 / 2.69 ( 2013) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.447 Fit side-chains REVERT: B 330 MET cc_start: 0.8894 (mmm) cc_final: 0.8676 (mmm) REVERT: B 465 LEU cc_start: 0.7470 (OUTLIER) cc_final: 0.7184 (tt) REVERT: C 422 PHE cc_start: 0.7061 (OUTLIER) cc_final: 0.6393 (t80) REVERT: D 111 LEU cc_start: 0.9134 (tp) cc_final: 0.8709 (tp) REVERT: D 287 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 338 ILE cc_start: 0.8593 (tp) cc_final: 0.8042 (tt) REVERT: E 189 LYS cc_start: 0.8577 (ttmt) cc_final: 0.8156 (tttp) REVERT: E 248 ARG cc_start: 0.6907 (tpp-160) cc_final: 0.6215 (ttm-80) outliers start: 17 outliers final: 11 residues processed: 138 average time/residue: 0.0920 time to fit residues: 19.4102 Evaluate side-chains 124 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 122 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 139 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109370 restraints weight = 20284.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110436 restraints weight = 15041.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111055 restraints weight = 14126.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111587 restraints weight = 11486.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111705 restraints weight = 10057.296| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14155 Z= 0.101 Angle : 0.453 5.181 19159 Z= 0.239 Chirality : 0.038 0.182 2188 Planarity : 0.003 0.043 2410 Dihedral : 4.629 71.846 1813 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.40 % Allowed : 10.34 % Favored : 88.25 % 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: 0.60 (0.21), residues: 1653 helix: 1.52 (0.17), residues: 962 sheet: -0.36 (0.41), residues: 132 loop : -1.40 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 397 TYR 0.015 0.001 TYR C 429 PHE 0.028 0.001 PHE B 569 TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14155) covalent geometry : angle 0.45276 / 0.24 (19159) hydrogen bonds : bond 0.03439 / 2.26 ( 687) hydrogen bonds : angle 3.77808 / 2.66 ( 2013) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.527 Fit side-chains REVERT: B 330 MET cc_start: 0.8976 (mmm) cc_final: 0.8775 (mmm) REVERT: B 465 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7267 (tp) REVERT: C 422 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6504 (t80) REVERT: D 111 LEU cc_start: 0.9138 (tp) cc_final: 0.8711 (tp) REVERT: D 287 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8360 (tp) REVERT: D 338 ILE cc_start: 0.8635 (tp) cc_final: 0.8104 (tt) REVERT: E 163 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7635 (mm-30) REVERT: E 189 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8153 (tttp) REVERT: E 248 ARG cc_start: 0.6921 (tpp-160) cc_final: 0.6210 (ttm-80) outliers start: 22 outliers final: 13 residues processed: 132 average time/residue: 0.1028 time to fit residues: 20.5577 Evaluate side-chains 128 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 269 GLN D 420 ASN E 379 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.133671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.109855 restraints weight = 20233.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112288 restraints weight = 16113.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.113177 restraints weight = 12282.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113320 restraints weight = 10153.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113792 restraints weight = 9306.901| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14155 Z= 0.097 Angle : 0.444 5.351 19159 Z= 0.235 Chirality : 0.038 0.186 2188 Planarity : 0.003 0.042 2410 Dihedral : 4.517 70.982 1813 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.79 % Allowed : 10.60 % Favored : 87.61 % 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: 0.76 (0.21), residues: 1653 helix: 1.65 (0.17), residues: 964 sheet: -0.29 (0.41), residues: 132 loop : -1.34 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.014 0.001 TYR D 174 PHE 0.024 0.001 PHE B 569 TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS E 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (14155) covalent geometry : angle 0.44441 / 0.24 (19159) hydrogen bonds : bond 0.03264 / 2.15 ( 687) hydrogen bonds : angle 3.67488 / 2.59 ( 2013) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.377 Fit side-chains REVERT: B 330 MET cc_start: 0.8980 (mmm) cc_final: 0.8763 (mmm) REVERT: C 59 GLU cc_start: 0.7243 (pt0) cc_final: 0.6632 (mt-10) REVERT: C 422 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6483 (t80) REVERT: D 111 LEU cc_start: 0.9154 (tp) cc_final: 0.8718 (tp) REVERT: D 287 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8350 (tp) REVERT: D 338 ILE cc_start: 0.8609 (tp) cc_final: 0.8045 (tt) REVERT: D 373 MET cc_start: 0.8571 (tpp) cc_final: 0.8197 (tpp) REVERT: E 163 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: E 189 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8201 (tttp) REVERT: E 248 ARG cc_start: 0.6898 (tpp-160) cc_final: 0.6281 (ttm-80) outliers start: 28 outliers final: 19 residues processed: 134 average time/residue: 0.0921 time to fit residues: 19.0130 Evaluate side-chains 132 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 282 GLN Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 chunk 123 optimal weight: 0.0570 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112479 restraints weight = 20066.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.114216 restraints weight = 16926.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115051 restraints weight = 13779.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.115364 restraints weight = 11509.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.115533 restraints weight = 10191.254| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14155 Z= 0.088 Angle : 0.433 5.761 19159 Z= 0.228 Chirality : 0.037 0.177 2188 Planarity : 0.003 0.042 2410 Dihedral : 4.402 70.281 1813 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 11.43 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.21), residues: 1653 helix: 1.76 (0.17), residues: 964 sheet: -0.09 (0.42), residues: 125 loop : -1.33 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.012 0.001 TYR C 429 PHE 0.023 0.001 PHE B 569 TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (14155) covalent geometry : angle 0.43324 / 0.23 (19159) hydrogen bonds : bond 0.03023 / 1.98 ( 687) hydrogen bonds : angle 3.57884 / 2.52 ( 2013) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.411 Fit side-chains REVERT: C 422 PHE cc_start: 0.6945 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 111 LEU cc_start: 0.9150 (tp) cc_final: 0.8721 (tp) REVERT: D 287 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8332 (tp) REVERT: D 338 ILE cc_start: 0.8603 (tp) cc_final: 0.8040 (tt) REVERT: D 373 MET cc_start: 0.8567 (tpp) cc_final: 0.8156 (tpp) REVERT: E 163 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: E 189 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8197 (tttp) REVERT: E 248 ARG cc_start: 0.6944 (tpp-160) cc_final: 0.6316 (ttm-80) outliers start: 21 outliers final: 16 residues processed: 133 average time/residue: 0.0961 time to fit residues: 19.7676 Evaluate side-chains 130 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 157 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 393 HIS D 420 ASN E 195 HIS E 379 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104309 restraints weight = 20717.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.105150 restraints weight = 18800.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.106285 restraints weight = 14503.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107071 restraints weight = 11760.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.107330 restraints weight = 10727.075| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14155 Z= 0.250 Angle : 0.593 5.275 19159 Z= 0.311 Chirality : 0.044 0.185 2188 Planarity : 0.004 0.042 2410 Dihedral : 4.834 72.992 1813 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.66 % Allowed : 11.69 % Favored : 86.65 % 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: 0.32 (0.21), residues: 1653 helix: 1.26 (0.17), residues: 959 sheet: -0.20 (0.43), residues: 132 loop : -1.53 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 397 TYR 0.020 0.002 TYR B 498 PHE 0.025 0.002 PHE C 147 TRP 0.010 0.002 TRP B 433 HIS 0.008 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.25 (14155) covalent geometry : angle 0.59319 / 0.31 (19159) hydrogen bonds : bond 0.04942 / 3.30 ( 687) hydrogen bonds : angle 4.14405 / 2.93 ( 2013) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.391 Fit side-chains REVERT: C 422 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.6642 (t80) REVERT: C 636 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7099 (t70) REVERT: D 287 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8344 (tp) REVERT: D 338 ILE cc_start: 0.8680 (tp) cc_final: 0.8208 (tt) REVERT: D 373 MET cc_start: 0.8582 (tpp) cc_final: 0.8144 (tpp) REVERT: E 163 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: E 189 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8197 (tttp) REVERT: E 248 ARG cc_start: 0.7053 (tpp-160) cc_final: 0.6273 (ttm-80) outliers start: 26 outliers final: 17 residues processed: 134 average time/residue: 0.0988 time to fit residues: 20.2840 Evaluate side-chains 125 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 HIS Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 163 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 420 ASN E 383 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108087 restraints weight = 20180.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109541 restraints weight = 17461.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.110620 restraints weight = 13264.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111104 restraints weight = 10637.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.111373 restraints weight = 9795.251| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14155 Z= 0.112 Angle : 0.480 5.735 19159 Z= 0.253 Chirality : 0.038 0.176 2188 Planarity : 0.003 0.041 2410 Dihedral : 4.648 73.134 1813 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.40 % Allowed : 12.01 % Favored : 86.59 % 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: 0.65 (0.21), residues: 1653 helix: 1.56 (0.17), residues: 962 sheet: -0.18 (0.43), residues: 132 loop : -1.44 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 143 TYR 0.019 0.001 TYR B 498 PHE 0.019 0.001 PHE B 569 TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14155) covalent geometry : angle 0.48005 / 0.25 (19159) hydrogen bonds : bond 0.03626 / 2.39 ( 687) hydrogen bonds : angle 3.82408 / 2.70 ( 2013) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.498 Fit side-chains REVERT: C 422 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6631 (t80) REVERT: D 287 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8374 (tp) REVERT: D 338 ILE cc_start: 0.8620 (tp) cc_final: 0.8111 (tt) REVERT: D 373 MET cc_start: 0.8582 (tpp) cc_final: 0.8177 (tpp) REVERT: E 163 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: E 189 LYS cc_start: 0.8676 (ttmt) cc_final: 0.8259 (tttp) REVERT: E 248 ARG cc_start: 0.7017 (tpp-160) cc_final: 0.6295 (ttm-80) outliers start: 22 outliers final: 18 residues processed: 128 average time/residue: 0.1001 time to fit residues: 19.7178 Evaluate side-chains 129 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 439 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 376 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 62 optimal weight: 0.9990 chunk 75 optimal weight: 0.0170 chunk 32 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 82 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 overall best weight: 0.6622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 379 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109355 restraints weight = 20276.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110607 restraints weight = 17003.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.111789 restraints weight = 13586.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112089 restraints weight = 10631.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.112314 restraints weight = 9772.117| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14155 Z= 0.102 Angle : 0.467 5.640 19159 Z= 0.245 Chirality : 0.038 0.164 2188 Planarity : 0.003 0.042 2410 Dihedral : 4.504 71.903 1813 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.28 % Allowed : 12.39 % Favored : 86.33 % 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: 0.82 (0.21), residues: 1653 helix: 1.69 (0.17), residues: 963 sheet: -0.13 (0.43), residues: 132 loop : -1.36 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.019 0.001 TYR B 498 PHE 0.024 0.001 PHE C 372 TRP 0.007 0.001 TRP B 433 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (14155) covalent geometry : angle 0.46660 / 0.24 (19159) hydrogen bonds : bond 0.03315 / 2.18 ( 687) hydrogen bonds : angle 3.68835 / 2.61 ( 2013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1688.86 seconds wall clock time: 30 minutes 6.83 seconds (1806.83 seconds total)