Starting phenix.real_space_refine on Wed Mar 4 13:27:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpq_22419/03_2026/7jpq_22419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpq_22419/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jpq_22419/03_2026/7jpq_22419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpq_22419/03_2026/7jpq_22419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jpq_22419/03_2026/7jpq_22419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpq_22419/03_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.09, per 1000 atoms: 0.22 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: 1.02 Conformation dependent library (CDL) restraints added in 648.2 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: 0.56 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: 2.15 Time building geometry restraints manager: 1.40 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: 7769 18.45 - 36.90: 678 36.90 - 55.35: 104 55.35 - 73.80: 25 73.80 - 92.24: 16 Dihedral angle restraints: 8592 sinusoidal: 3574 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 8589 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: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.220 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 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 : 14.611 92.245 5306 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 covalent geometry : bond 0.00772 (14155) covalent geometry : angle 1.13767 (19159) hydrogen bonds : bond 0.18174 ( 687) hydrogen bonds : angle 6.78891 ( 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 : 0.516 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: 0.1279 time to fit residues: 40.9552 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 : 0.559 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.132798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108964 restraints weight = 20272.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109856 restraints weight = 15187.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.110749 restraints weight = 14178.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111169 restraints weight = 11421.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111312 restraints weight = 10299.042| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14155 Z= 0.132 Angle : 0.559 5.602 19159 Z= 0.298 Chirality : 0.041 0.148 2188 Planarity : 0.004 0.065 2410 Dihedral : 7.607 76.809 1875 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.96 % Allowed : 5.87 % Favored : 93.17 % 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: -0.83 (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 0.015 0.001 TYR E 204 PHE 0.016 0.002 PHE C 548 TRP 0.010 0.001 TRP C 51 HIS 0.008 0.001 HIS C 576 Details of bonding type rmsd covalent geometry : bond 0.00291 (14155) covalent geometry : angle 0.55867 (19159) hydrogen bonds : bond 0.04817 ( 687) hydrogen bonds : angle 4.51639 ( 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 153 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.549 Fit side-chains REVERT: B 454 TYR cc_start: 0.8882 (m-80) cc_final: 0.8674 (m-80) REVERT: C 179 TYR cc_start: 0.6208 (m-80) cc_final: 0.5988 (m-80) REVERT: C 182 ASP cc_start: 0.7647 (t0) cc_final: 0.7414 (t0) REVERT: C 560 ASP cc_start: 0.7917 (t0) cc_final: 0.7473 (t0) REVERT: C 686 GLU cc_start: 0.6578 (mt-10) cc_final: 0.6349 (mt-10) REVERT: D 137 SER cc_start: 0.8663 (t) cc_final: 0.8445 (p) REVERT: E 6 ASN cc_start: 0.6704 (m-40) cc_final: 0.6482 (p0) REVERT: E 189 LYS cc_start: 0.8574 (ttmt) cc_final: 0.8211 (tttp) REVERT: E 248 ARG cc_start: 0.6833 (tpp-160) cc_final: 0.6111 (ttm-80) REVERT: E 263 LYS cc_start: 0.7182 (mmtm) cc_final: 0.6943 (ttmm) REVERT: E 398 HIS cc_start: 0.6243 (OUTLIER) cc_final: 0.5753 (t70) outliers start: 15 outliers final: 13 residues processed: 148 average time/residue: 0.1189 time to fit residues: 26.3735 Evaluate side-chains 131 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 8.9990 chunk 163 optimal weight: 0.0050 chunk 95 optimal weight: 1.9990 chunk 133 optimal weight: 0.0870 chunk 58 optimal weight: 0.0470 chunk 14 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 overall best weight: 0.8274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN D 212 HIS D 420 ASN E 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109346 restraints weight = 20326.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110487 restraints weight = 15357.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111242 restraints weight = 13233.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111850 restraints weight = 11193.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112005 restraints weight = 10040.385| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14155 Z= 0.115 Angle : 0.499 5.467 19159 Z= 0.265 Chirality : 0.039 0.156 2188 Planarity : 0.004 0.051 2410 Dihedral : 7.064 72.621 1875 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.02 % Allowed : 7.73 % Favored : 91.25 % 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: -0.17 (0.20), residues: 1653 helix: 0.90 (0.17), residues: 952 sheet: -0.74 (0.41), residues: 140 loop : -1.67 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 564 TYR 0.015 0.001 TYR C 429 PHE 0.014 0.001 PHE C 548 TRP 0.008 0.001 TRP C 51 HIS 0.010 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00255 (14155) covalent geometry : angle 0.49940 (19159) hydrogen bonds : bond 0.04164 ( 687) hydrogen bonds : angle 4.19081 ( 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 144 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.536 Fit side-chains REVERT: C 179 TYR cc_start: 0.6210 (m-80) cc_final: 0.5943 (m-80) REVERT: C 182 ASP cc_start: 0.7659 (t0) cc_final: 0.7417 (t0) REVERT: C 686 GLU cc_start: 0.6696 (mt-10) cc_final: 0.6489 (mt-10) REVERT: D 111 LEU cc_start: 0.9072 (tp) cc_final: 0.8667 (tp) REVERT: D 137 SER cc_start: 0.8662 (t) cc_final: 0.8460 (p) REVERT: E 6 ASN cc_start: 0.6844 (m-40) cc_final: 0.6513 (p0) REVERT: E 189 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8160 (tttp) REVERT: E 248 ARG cc_start: 0.6844 (tpp-160) cc_final: 0.6118 (ttm-80) REVERT: E 263 LYS cc_start: 0.7090 (mmtm) cc_final: 0.6857 (ttmm) outliers start: 16 outliers final: 10 residues processed: 138 average time/residue: 0.0999 time to fit residues: 21.4480 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 449 THR Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR 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 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: 0.9990 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 156 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 123 optimal weight: 0.0040 chunk 92 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 310 ASN C 110 ASN C 636 HIS D 420 ASN E 232 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.111424 restraints weight = 20149.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.112092 restraints weight = 17929.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112478 restraints weight = 16012.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113410 restraints weight = 13630.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.113586 restraints weight = 11820.895| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14155 Z= 0.097 Angle : 0.458 5.377 19159 Z= 0.244 Chirality : 0.038 0.165 2188 Planarity : 0.003 0.045 2410 Dihedral : 6.647 70.940 1875 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.15 % Allowed : 8.62 % Favored : 90.23 % 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: 0.36 (0.20), residues: 1653 helix: 1.37 (0.17), residues: 953 sheet: -0.40 (0.42), residues: 125 loop : -1.54 (0.23), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 552 TYR 0.010 0.001 TYR E 204 PHE 0.015 0.001 PHE C 548 TRP 0.006 0.001 TRP C 51 HIS 0.005 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00205 (14155) covalent geometry : angle 0.45812 (19159) hydrogen bonds : bond 0.03449 ( 687) hydrogen bonds : angle 3.83654 ( 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 152 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.574 Fit side-chains REVERT: B 465 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7015 (tt) REVERT: C 182 ASP cc_start: 0.7701 (t0) cc_final: 0.7453 (t0) REVERT: C 422 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6461 (t80) REVERT: C 686 GLU cc_start: 0.6716 (mt-10) cc_final: 0.6512 (mt-10) REVERT: D 111 LEU cc_start: 0.9123 (tp) cc_final: 0.8678 (tp) REVERT: D 137 SER cc_start: 0.8654 (t) cc_final: 0.8446 (p) REVERT: E 6 ASN cc_start: 0.6870 (m-40) cc_final: 0.6624 (p0) REVERT: E 189 LYS cc_start: 0.8549 (ttmt) cc_final: 0.8154 (tttp) REVERT: E 248 ARG cc_start: 0.6893 (tpp-160) cc_final: 0.6135 (ttm-80) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.1113 time to fit residues: 24.9329 Evaluate side-chains 126 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 189 MET Chi-restraints excluded: chain C residue 407 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 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: 0.0770 chunk 2 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 153 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.4542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 110 ASN D 358 GLN D 420 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.108210 restraints weight = 20437.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109216 restraints weight = 15248.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109378 restraints weight = 14880.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.109849 restraints weight = 11985.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.110489 restraints weight = 10909.033| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2355 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= 0.143 Angle : 0.498 5.235 19159 Z= 0.263 Chirality : 0.040 0.183 2188 Planarity : 0.004 0.045 2410 Dihedral : 6.739 71.069 1875 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.47 % Allowed : 9.77 % Favored : 88.76 % 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: 0.40 (0.21), residues: 1653 helix: 1.36 (0.17), residues: 961 sheet: -0.43 (0.41), residues: 132 loop : -1.48 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 705 TYR 0.012 0.001 TYR E 204 PHE 0.027 0.002 PHE B 569 TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00341 (14155) covalent geometry : angle 0.49759 (19159) hydrogen bonds : bond 0.04048 ( 687) hydrogen bonds : angle 3.94574 ( 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 136 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.530 Fit side-chains REVERT: B 330 MET cc_start: 0.8959 (mmm) cc_final: 0.8725 (mmm) REVERT: B 465 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7232 (tt) REVERT: B 522 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: C 182 ASP cc_start: 0.7844 (t0) cc_final: 0.7568 (t0) REVERT: C 422 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6380 (t80) REVERT: C 686 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6506 (mt-10) REVERT: D 111 LEU cc_start: 0.9145 (tp) cc_final: 0.8719 (tp) REVERT: D 137 SER cc_start: 0.8657 (t) cc_final: 0.8454 (p) REVERT: D 287 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8366 (tp) REVERT: E 189 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8182 (tttp) REVERT: E 248 ARG cc_start: 0.6917 (tpp-160) cc_final: 0.6178 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 130 average time/residue: 0.1096 time to fit residues: 22.1423 Evaluate side-chains 132 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 522 GLU 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 268 SER Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU 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 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 94 ILE 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: 0.9990 chunk 12 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 chunk 142 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 71 optimal weight: 0.0020 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3581 r_free = 0.3581 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110868 restraints weight = 20177.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111731 restraints weight = 16246.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112971 restraints weight = 13829.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113300 restraints weight = 10782.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113409 restraints weight = 9943.471| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14155 Z= 0.093 Angle : 0.444 5.357 19159 Z= 0.235 Chirality : 0.037 0.177 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.511 69.794 1875 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.34 % Allowed : 10.41 % 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: 0.67 (0.21), residues: 1653 helix: 1.58 (0.17), residues: 962 sheet: -0.37 (0.41), residues: 132 loop : -1.38 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 552 TYR 0.008 0.001 TYR C 429 PHE 0.021 0.001 PHE B 569 TRP 0.006 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00198 (14155) covalent geometry : angle 0.44377 (19159) hydrogen bonds : bond 0.03268 ( 687) hydrogen bonds : angle 3.72888 ( 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 136 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.551 Fit side-chains REVERT: B 330 MET cc_start: 0.8980 (mmm) cc_final: 0.8762 (mmm) REVERT: C 59 GLU cc_start: 0.7210 (pt0) cc_final: 0.6666 (mt-10) REVERT: C 182 ASP cc_start: 0.7831 (t0) cc_final: 0.7583 (t0) REVERT: C 422 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6538 (t80) REVERT: C 686 GLU cc_start: 0.6764 (mt-10) cc_final: 0.6563 (mt-10) REVERT: D 111 LEU cc_start: 0.9137 (tp) cc_final: 0.8691 (tp) REVERT: D 137 SER cc_start: 0.8652 (t) cc_final: 0.8447 (p) REVERT: D 287 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8324 (tp) REVERT: E 163 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7606 (mm-30) REVERT: E 189 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8200 (tttp) REVERT: E 248 ARG cc_start: 0.6925 (tpp-160) cc_final: 0.6193 (ttm-80) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.1067 time to fit residues: 21.5404 Evaluate side-chains 126 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 304 GLU Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 468 LEU 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 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: 6.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN C 110 ASN D 420 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 = 0.133602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109937 restraints weight = 20222.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.111444 restraints weight = 15307.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.112247 restraints weight = 13569.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112576 restraints weight = 11339.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112950 restraints weight = 10138.610| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2622 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= 0.108 Angle : 0.451 5.284 19159 Z= 0.240 Chirality : 0.038 0.170 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.530 69.627 1875 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 10.60 % Favored : 87.93 % 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: 0.72 (0.21), residues: 1653 helix: 1.61 (0.17), residues: 963 sheet: -0.30 (0.41), residues: 132 loop : -1.37 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 397 TYR 0.017 0.001 TYR B 498 PHE 0.018 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 covalent geometry : bond 0.00247 (14155) covalent geometry : angle 0.45130 (19159) hydrogen bonds : bond 0.03442 ( 687) hydrogen bonds : angle 3.73274 ( 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 137 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.559 Fit side-chains REVERT: B 330 MET cc_start: 0.9006 (mmm) cc_final: 0.8776 (mmm) REVERT: C 59 GLU cc_start: 0.7266 (pt0) cc_final: 0.6697 (mt-10) REVERT: C 182 ASP cc_start: 0.7860 (t0) cc_final: 0.7620 (t0) REVERT: C 422 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6481 (t80) REVERT: C 686 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6580 (mt-10) REVERT: D 111 LEU cc_start: 0.9132 (tp) cc_final: 0.8688 (tp) REVERT: D 137 SER cc_start: 0.8654 (t) cc_final: 0.8444 (p) REVERT: D 287 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8308 (tp) REVERT: E 163 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7624 (mm-30) REVERT: E 189 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8151 (tttp) REVERT: E 248 ARG cc_start: 0.6915 (tpp-160) cc_final: 0.6206 (ttm-80) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 0.1192 time to fit residues: 23.8879 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 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 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 282 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 147 optimal weight: 0.0570 chunk 55 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 68 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN E 379 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111880 restraints weight = 20057.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113788 restraints weight = 17707.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114831 restraints weight = 14636.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115076 restraints weight = 11224.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.115430 restraints weight = 10269.064| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2701 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= 0.094 Angle : 0.442 5.475 19159 Z= 0.233 Chirality : 0.038 0.160 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.450 69.299 1875 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 11.17 % Favored : 87.48 % 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: 0.85 (0.21), residues: 1653 helix: 1.73 (0.17), residues: 958 sheet: -0.28 (0.41), residues: 132 loop : -1.29 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.015 0.001 TYR B 498 PHE 0.017 0.001 PHE B 569 TRP 0.006 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00206 (14155) covalent geometry : angle 0.44180 (19159) hydrogen bonds : bond 0.03240 ( 687) hydrogen bonds : angle 3.66847 ( 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 135 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.558 Fit side-chains REVERT: B 330 MET cc_start: 0.8943 (mmm) cc_final: 0.8730 (mmt) REVERT: C 59 GLU cc_start: 0.7222 (pt0) cc_final: 0.6625 (mt-10) REVERT: C 182 ASP cc_start: 0.7804 (t0) cc_final: 0.7602 (t0) REVERT: C 422 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.6594 (t80) REVERT: C 686 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6606 (mt-10) REVERT: D 111 LEU cc_start: 0.9183 (tp) cc_final: 0.8747 (tp) REVERT: D 287 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8406 (tp) REVERT: D 373 MET cc_start: 0.8566 (tpp) cc_final: 0.8232 (tpp) REVERT: E 163 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: E 189 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8233 (tttp) REVERT: E 248 ARG cc_start: 0.6849 (tpp-160) cc_final: 0.6284 (ttm-80) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.1002 time to fit residues: 20.6146 Evaluate side-chains 130 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 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 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 157 optimal weight: 0.7980 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: 8.9990 chunk 40 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 420 ASN E 195 HIS E 383 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107807 restraints weight = 20411.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.109113 restraints weight = 17713.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.110423 restraints weight = 13539.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110486 restraints weight = 10945.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111412 restraints weight = 9965.116| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2678 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= 0.149 Angle : 0.500 5.429 19159 Z= 0.264 Chirality : 0.040 0.161 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.681 71.006 1875 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.72 % Allowed : 11.17 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 964 sheet: -0.23 (0.42), residues: 132 loop : -1.45 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 397 TYR 0.016 0.001 TYR B 498 PHE 0.017 0.002 PHE C 147 TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00361 (14155) covalent geometry : angle 0.50002 (19159) hydrogen bonds : bond 0.04097 ( 687) hydrogen bonds : angle 3.90376 ( 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: 27 poor density : 115 time to evaluate : 0.528 Fit side-chains REVERT: B 330 MET cc_start: 0.9032 (mmm) cc_final: 0.8805 (mmm) REVERT: C 59 GLU cc_start: 0.7305 (pt0) cc_final: 0.6730 (mt-10) REVERT: C 422 PHE cc_start: 0.7131 (OUTLIER) cc_final: 0.6701 (t80) REVERT: C 686 GLU cc_start: 0.6791 (mt-10) cc_final: 0.6567 (mt-10) REVERT: D 287 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8384 (tp) REVERT: D 373 MET cc_start: 0.8555 (tpp) cc_final: 0.8178 (tpp) REVERT: E 163 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: E 189 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8204 (tttp) REVERT: E 248 ARG cc_start: 0.6908 (tpp-160) cc_final: 0.6205 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 134 average time/residue: 0.1084 time to fit residues: 22.4336 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 : 0.531 ------------------------------------------------------------------------------- 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 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 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 SER 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 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 82 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 161 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110536 restraints weight = 20066.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111234 restraints weight = 17720.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.112577 restraints weight = 15056.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.112947 restraints weight = 12228.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113227 restraints weight = 11483.152| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14155 Z= 0.109 Angle : 0.469 5.658 19159 Z= 0.247 Chirality : 0.038 0.153 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.548 70.730 1875 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.40 % Allowed : 11.69 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 958 sheet: -0.19 (0.42), residues: 132 loop : -1.36 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 397 TYR 0.013 0.001 TYR B 498 PHE 0.015 0.001 PHE B 569 TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 Details of bonding type rmsd covalent geometry : bond 0.00252 (14155) covalent geometry : angle 0.46872 (19159) hydrogen bonds : bond 0.03513 ( 687) hydrogen bonds : angle 3.76518 ( 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 : 0.615 Fit side-chains REVERT: C 59 GLU cc_start: 0.7318 (pt0) cc_final: 0.6666 (mt-10) REVERT: C 422 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6797 (t80) REVERT: C 686 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6642 (mt-10) REVERT: D 111 LEU cc_start: 0.9196 (tp) cc_final: 0.8787 (tp) REVERT: D 287 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8397 (tp) REVERT: D 373 MET cc_start: 0.8578 (tpp) cc_final: 0.8225 (tpp) REVERT: E 163 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7551 (mm-30) REVERT: E 189 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8291 (tttp) REVERT: E 248 ARG cc_start: 0.6963 (tpp-160) cc_final: 0.6348 (ttm-80) outliers start: 22 outliers final: 17 residues processed: 128 average time/residue: 0.1072 time to fit residues: 21.4493 Evaluate side-chains 129 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 SER 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 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: 1.9990 chunk 75 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 82 optimal weight: 0.0980 chunk 159 optimal weight: 0.7980 chunk 156 optimal weight: 0.6980 overall best weight: 0.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 GLN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112739 restraints weight = 20074.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114734 restraints weight = 17684.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115853 restraints weight = 13564.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.115969 restraints weight = 10924.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.116517 restraints weight = 9943.564| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3000 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= 0.086 Angle : 0.435 5.702 19159 Z= 0.229 Chirality : 0.037 0.145 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.189 69.343 1875 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.02 % Allowed : 12.07 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.21), residues: 1653 helix: 1.88 (0.17), residues: 957 sheet: -0.15 (0.42), residues: 132 loop : -1.21 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.014 0.001 TYR B 498 PHE 0.016 0.001 PHE B 569 TRP 0.005 0.001 TRP C 51 HIS 0.005 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00177 (14155) covalent geometry : angle 0.43451 (19159) hydrogen bonds : bond 0.02855 ( 687) hydrogen bonds : angle 3.53292 ( 2013) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.55 seconds wall clock time: 33 minutes 26.50 seconds (2006.50 seconds total)