Starting phenix.real_space_refine on Thu Jul 31 23:30:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_22419.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_22419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_22419.map" model { file = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_22419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jpq_22419/07_2025/7jpq_22419.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.75, per 1000 atoms: 0.63 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: 3.35 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.41 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: 4.18 Time building geometry restraints manager: 4.01 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: 2.240 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.970 ------------------------------------------------------------------------------- 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 : 2.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.061 0.004 TRP B 443 HIS 0.013 0.003 HIS C 114 PHE 0.052 0.004 PHE D 138 TYR 0.044 0.003 TYR E 204 ARG 0.019 0.002 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.18174 ( 687) hydrogen bonds : angle 6.78891 ( 2013) covalent geometry : bond 0.00772 (14155) covalent geometry : angle 1.13767 (19159) *********************** 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 : 1.516 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: 0.7820 (p) REVERT: B 497 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7831 (mtmm) REVERT: B 498 TYR cc_start: 0.8132 (t80) cc_final: 0.7906 (t80) REVERT: C 189 MET cc_start: 0.7405 (mtp) cc_final: 0.7085 (ttp) REVERT: C 281 CYS cc_start: 0.7745 (m) cc_final: 0.7374 (m) REVERT: C 304 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7470 (pm20) REVERT: C 686 GLU cc_start: 0.6650 (mt-10) cc_final: 0.6434 (mt-10) REVERT: D 137 SER cc_start: 0.8633 (t) cc_final: 0.8278 (p) REVERT: E 6 ASN cc_start: 0.6643 (m-40) cc_final: 0.6377 (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: 0.5730 (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: 0.6440 (mptt) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2767 time to fit residues: 88.1232 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 : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 260 HIS C 500 GLN C 576 HIS C 677 HIS D 19 GLN D 36 ASN D 61 ASN D 212 HIS 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 = 0.3555 r_free = 0.3555 target = 0.132157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108090 restraints weight = 20363.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.109050 restraints weight = 18121.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110132 restraints weight = 15571.893| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1572 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= 0.127 Angle : 0.557 5.683 19159 Z= 0.298 Chirality : 0.040 0.151 2188 Planarity : 0.004 0.065 2410 Dihedral : 7.635 78.394 1875 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.89 % Allowed : 6.00 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 1653 helix: 0.37 (0.16), residues: 951 sheet: -0.81 (0.42), residues: 131 loop : -1.78 (0.22), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.009 0.001 HIS C 576 PHE 0.019 0.001 PHE C 548 TYR 0.019 0.001 TYR C 429 ARG 0.005 0.001 ARG B 540 Details of bonding type rmsd hydrogen bonds : bond 0.04735 ( 687) hydrogen bonds : angle 4.54097 ( 2013) covalent geometry : bond 0.00274 (14155) covalent geometry : angle 0.55726 (19159) *********************** 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 151 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.508 Fit side-chains REVERT: B 498 TYR cc_start: 0.8262 (t80) cc_final: 0.7976 (t80) REVERT: C 179 TYR cc_start: 0.6135 (m-80) cc_final: 0.5929 (m-80) REVERT: C 560 ASP cc_start: 0.7919 (t0) cc_final: 0.7451 (t0) REVERT: C 686 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6323 (mt-10) REVERT: D 137 SER cc_start: 0.8666 (t) cc_final: 0.8430 (p) REVERT: E 6 ASN cc_start: 0.6677 (m-40) cc_final: 0.6462 (p0) REVERT: E 189 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8178 (tttp) REVERT: E 248 ARG cc_start: 0.6822 (tpp-160) cc_final: 0.6064 (ttm-80) REVERT: E 263 LYS cc_start: 0.7079 (mmtm) cc_final: 0.6830 (ttmm) REVERT: E 398 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.5697 (t70) outliers start: 14 outliers final: 12 residues processed: 146 average time/residue: 0.2747 time to fit residues: 60.9887 Evaluate side-chains 131 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.0470 chunk 136 optimal weight: 0.8980 chunk 75 optimal weight: 0.0040 chunk 157 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 166 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.4690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3578 r_free = 0.3578 target = 0.134251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110349 restraints weight = 20189.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112675 restraints weight = 16082.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113423 restraints weight = 12419.671| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14155 Z= 0.105 Angle : 0.488 5.464 19159 Z= 0.260 Chirality : 0.038 0.156 2188 Planarity : 0.004 0.049 2410 Dihedral : 7.057 72.455 1875 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.77 % Allowed : 7.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1653 helix: 0.93 (0.17), residues: 952 sheet: -0.72 (0.41), residues: 140 loop : -1.67 (0.23), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.013 0.001 HIS E 195 PHE 0.012 0.001 PHE C 652 TYR 0.013 0.001 TYR C 429 ARG 0.005 0.000 ARG C 564 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 687) hydrogen bonds : angle 4.15877 ( 2013) covalent geometry : bond 0.00215 (14155) covalent geometry : angle 0.48820 (19159) *********************** 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 148 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.455 Fit side-chains REVERT: C 179 TYR cc_start: 0.6234 (m-80) cc_final: 0.5944 (m-80) REVERT: D 111 LEU cc_start: 0.9093 (tp) cc_final: 0.8718 (tp) REVERT: E 6 ASN cc_start: 0.6729 (m-40) cc_final: 0.6492 (p0) REVERT: E 189 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8164 (tttp) REVERT: E 248 ARG cc_start: 0.6866 (tpp-160) cc_final: 0.6158 (ttm-80) REVERT: E 263 LYS cc_start: 0.7150 (mmtm) cc_final: 0.6920 (ttmm) outliers start: 12 outliers final: 6 residues processed: 143 average time/residue: 0.2403 time to fit residues: 53.1830 Evaluate side-chains 122 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 537 THR 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 49 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 D 358 GLN 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 = 0.3552 r_free = 0.3552 target = 0.132256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108583 restraints weight = 20172.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110192 restraints weight = 17801.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111190 restraints weight = 14609.674| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2143 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= 0.134 Angle : 0.497 5.418 19159 Z= 0.264 Chirality : 0.040 0.167 2188 Planarity : 0.004 0.046 2410 Dihedral : 6.905 72.029 1875 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.47 % Allowed : 8.43 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.20), residues: 1653 helix: 1.19 (0.17), residues: 959 sheet: -0.51 (0.41), residues: 132 loop : -1.56 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS E 38 PHE 0.015 0.002 PHE C 548 TYR 0.015 0.001 TYR C 429 ARG 0.004 0.000 ARG C 552 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 687) hydrogen bonds : angle 4.03263 ( 2013) covalent geometry : bond 0.00316 (14155) covalent geometry : angle 0.49727 (19159) *********************** 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 144 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 1.436 Fit side-chains REVERT: B 465 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.7064 (tt) REVERT: C 422 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6481 (t80) REVERT: D 111 LEU cc_start: 0.9153 (tp) cc_final: 0.8759 (tp) REVERT: D 287 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8389 (tp) REVERT: E 6 ASN cc_start: 0.6873 (m-40) cc_final: 0.6626 (p0) REVERT: E 189 LYS cc_start: 0.8585 (ttmt) cc_final: 0.8210 (tttp) REVERT: E 248 ARG cc_start: 0.6891 (tpp-160) cc_final: 0.6239 (ttm-80) outliers start: 23 outliers final: 17 residues processed: 137 average time/residue: 0.2353 time to fit residues: 49.3055 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 : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 399 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 101 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 159 optimal weight: 0.0040 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108848 restraints weight = 20315.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110536 restraints weight = 17110.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111805 restraints weight = 13456.256| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14155 Z= 0.115 Angle : 0.472 5.208 19159 Z= 0.251 Chirality : 0.039 0.181 2188 Planarity : 0.003 0.046 2410 Dihedral : 6.739 71.114 1875 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.47 % Allowed : 9.39 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.21), residues: 1653 helix: 1.36 (0.17), residues: 961 sheet: -0.44 (0.41), residues: 132 loop : -1.50 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS E 38 PHE 0.027 0.001 PHE B 569 TYR 0.011 0.001 TYR C 429 ARG 0.003 0.000 ARG C 552 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 687) hydrogen bonds : angle 3.91921 ( 2013) covalent geometry : bond 0.00262 (14155) covalent geometry : angle 0.47244 (19159) *********************** 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 139 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 1.558 Fit side-chains REVERT: B 465 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7222 (tt) REVERT: B 522 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: C 422 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6351 (t80) REVERT: D 111 LEU cc_start: 0.9125 (tp) cc_final: 0.8697 (tp) REVERT: E 6 ASN cc_start: 0.6993 (m-40) cc_final: 0.6635 (p0) REVERT: E 189 LYS cc_start: 0.8571 (ttmt) cc_final: 0.8143 (tttp) REVERT: E 248 ARG cc_start: 0.6904 (tpp-160) cc_final: 0.6158 (ttm-80) outliers start: 23 outliers final: 16 residues processed: 133 average time/residue: 0.2381 time to fit residues: 48.3971 Evaluate side-chains 129 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 268 SER 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 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 31 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.0670 chunk 28 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 118 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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 = 0.3571 r_free = 0.3571 target = 0.133706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109737 restraints weight = 20342.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110748 restraints weight = 18143.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111831 restraints weight = 15411.243| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2461 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= 0.094 Angle : 0.448 5.309 19159 Z= 0.238 Chirality : 0.038 0.183 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.563 70.405 1875 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.21), residues: 1653 helix: 1.54 (0.17), residues: 962 sheet: -0.39 (0.41), residues: 132 loop : -1.43 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 PHE 0.029 0.001 PHE B 569 TYR 0.010 0.001 TYR C 429 ARG 0.003 0.000 ARG C 552 Details of bonding type rmsd hydrogen bonds : bond 0.03403 ( 687) hydrogen bonds : angle 3.77609 ( 2013) covalent geometry : bond 0.00201 (14155) covalent geometry : angle 0.44791 (19159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 3.460 Fit side-chains REVERT: B 330 MET cc_start: 0.8887 (mmm) cc_final: 0.8663 (mmm) REVERT: B 465 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7187 (tt) REVERT: C 422 PHE cc_start: 0.7092 (OUTLIER) cc_final: 0.6446 (t80) REVERT: D 111 LEU cc_start: 0.9156 (tp) cc_final: 0.8712 (tp) REVERT: D 287 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8351 (tp) REVERT: E 163 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7618 (mm-30) REVERT: E 189 LYS cc_start: 0.8601 (ttmt) cc_final: 0.8198 (tttp) REVERT: E 248 ARG cc_start: 0.6918 (tpp-160) cc_final: 0.6216 (ttm-80) outliers start: 21 outliers final: 13 residues processed: 135 average time/residue: 0.3867 time to fit residues: 81.1039 Evaluate side-chains 127 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 399 MET 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 422 PHE Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain 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 13 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 4 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 157 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.109389 restraints weight = 20415.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.110644 restraints weight = 15111.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111223 restraints weight = 13801.866| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.2528 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= 0.112 Angle : 0.458 5.227 19159 Z= 0.244 Chirality : 0.038 0.191 2188 Planarity : 0.003 0.043 2410 Dihedral : 6.558 70.157 1875 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.47 % Allowed : 10.79 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1653 helix: 1.57 (0.17), residues: 962 sheet: -0.34 (0.41), residues: 132 loop : -1.42 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 319 PHE 0.023 0.001 PHE B 569 TYR 0.017 0.001 TYR C 429 ARG 0.005 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 687) hydrogen bonds : angle 3.77817 ( 2013) covalent geometry : bond 0.00261 (14155) covalent geometry : angle 0.45845 (19159) *********************** 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 134 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.499 Fit side-chains REVERT: B 330 MET cc_start: 0.8969 (mmm) cc_final: 0.8744 (mmm) REVERT: C 422 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6526 (t80) REVERT: D 111 LEU cc_start: 0.9160 (tp) cc_final: 0.8722 (tp) REVERT: D 287 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8372 (tp) REVERT: E 163 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7578 (mm-30) REVERT: E 189 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8184 (tttp) REVERT: E 248 ARG cc_start: 0.6929 (tpp-160) cc_final: 0.6213 (ttm-80) outliers start: 23 outliers final: 19 residues processed: 127 average time/residue: 0.2388 time to fit residues: 46.8644 Evaluate side-chains 131 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 399 MET 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 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 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 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 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 88 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 39 optimal weight: 0.0970 chunk 134 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1580 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.131330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107830 restraints weight = 20226.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.109715 restraints weight = 16189.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110458 restraints weight = 13919.288| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2595 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= 0.123 Angle : 0.472 5.318 19159 Z= 0.250 Chirality : 0.039 0.184 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.595 69.953 1875 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.92 % Allowed : 10.66 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1653 helix: 1.59 (0.17), residues: 964 sheet: -0.25 (0.42), residues: 132 loop : -1.45 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 PHE 0.021 0.001 PHE B 569 TYR 0.016 0.001 TYR C 429 ARG 0.006 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.03759 ( 687) hydrogen bonds : angle 3.82222 ( 2013) covalent geometry : bond 0.00289 (14155) covalent geometry : angle 0.47176 (19159) *********************** 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 147 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.528 Fit side-chains REVERT: B 330 MET cc_start: 0.9026 (mmm) cc_final: 0.8809 (mmm) REVERT: B 465 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7287 (tt) REVERT: C 422 PHE cc_start: 0.7066 (OUTLIER) cc_final: 0.6504 (t80) REVERT: D 287 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 373 MET cc_start: 0.8565 (tpp) cc_final: 0.8215 (tpp) REVERT: E 163 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: E 189 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8182 (tttp) REVERT: E 248 ARG cc_start: 0.6960 (tpp-160) cc_final: 0.6227 (ttm-80) outliers start: 30 outliers final: 21 residues processed: 136 average time/residue: 0.2936 time to fit residues: 60.9257 Evaluate side-chains 135 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 399 MET 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 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 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 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 163 GLU Chi-restraints excluded: chain E residue 282 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.106729 restraints weight = 20312.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108561 restraints weight = 17480.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109397 restraints weight = 13574.241| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2612 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= 0.164 Angle : 0.517 5.426 19159 Z= 0.271 Chirality : 0.040 0.180 2188 Planarity : 0.004 0.043 2410 Dihedral : 6.730 71.206 1875 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.11 % Allowed : 10.73 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.21), residues: 1653 helix: 1.46 (0.17), residues: 964 sheet: -0.24 (0.42), residues: 132 loop : -1.55 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 51 HIS 0.005 0.001 HIS D 34 PHE 0.018 0.002 PHE B 569 TYR 0.015 0.001 TYR C 429 ARG 0.007 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 687) hydrogen bonds : angle 3.94944 ( 2013) covalent geometry : bond 0.00401 (14155) covalent geometry : angle 0.51684 (19159) *********************** 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 145 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 2.493 Fit side-chains REVERT: B 330 MET cc_start: 0.9011 (mmm) cc_final: 0.8791 (mmm) REVERT: B 465 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7326 (tt) REVERT: C 422 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6600 (t80) REVERT: D 111 LEU cc_start: 0.9209 (tp) cc_final: 0.8781 (tp) REVERT: D 287 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8375 (tp) REVERT: D 373 MET cc_start: 0.8564 (tpp) cc_final: 0.8185 (tpp) REVERT: E 163 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7564 (mm-30) REVERT: E 189 LYS cc_start: 0.8654 (ttmt) cc_final: 0.8211 (tttp) REVERT: E 248 ARG cc_start: 0.6991 (tpp-160) cc_final: 0.6235 (ttm-80) outliers start: 33 outliers final: 24 residues processed: 133 average time/residue: 0.3025 time to fit residues: 63.7613 Evaluate side-chains 136 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 399 MET 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 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 422 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 684 VAL Chi-restraints excluded: chain C residue 706 LEU Chi-restraints excluded: chain D residue 152 CYS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 401 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 122 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 636 HIS D 420 ASN E 383 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108357 restraints weight = 20326.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110125 restraints weight = 17093.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.111100 restraints weight = 13517.521| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14155 Z= 0.105 Angle : 0.470 6.414 19159 Z= 0.249 Chirality : 0.038 0.171 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.579 71.005 1875 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.85 % Allowed : 11.37 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1653 helix: 1.62 (0.17), residues: 963 sheet: -0.19 (0.42), residues: 132 loop : -1.46 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 PHE 0.020 0.001 PHE B 569 TYR 0.013 0.001 TYR C 429 ARG 0.007 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 687) hydrogen bonds : angle 3.78496 ( 2013) covalent geometry : bond 0.00236 (14155) covalent geometry : angle 0.47047 (19159) ********************** 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 141 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.588 Fit side-chains REVERT: B 465 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7292 (tt) REVERT: C 59 GLU cc_start: 0.7264 (pt0) cc_final: 0.6741 (mt-10) REVERT: C 422 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6579 (t80) REVERT: D 111 LEU cc_start: 0.9123 (tp) cc_final: 0.8705 (tp) REVERT: D 287 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8314 (tp) REVERT: D 373 MET cc_start: 0.8564 (tpp) cc_final: 0.8177 (tpp) REVERT: E 163 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: E 189 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8192 (tttp) REVERT: E 248 ARG cc_start: 0.6974 (tpp-160) cc_final: 0.6222 (ttm-80) outliers start: 29 outliers final: 20 residues processed: 131 average time/residue: 0.2561 time to fit residues: 52.2577 Evaluate side-chains 132 residues out of total 1566 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 399 MET 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 465 LEU Chi-restraints excluded: chain B residue 527 ASN Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 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 184 GLN 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 1 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN D 420 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108755 restraints weight = 20322.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.111227 restraints weight = 17124.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111991 restraints weight = 13575.716| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2737 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= 0.111 Angle : 0.472 6.765 19159 Z= 0.248 Chirality : 0.038 0.167 2188 Planarity : 0.003 0.042 2410 Dihedral : 6.541 70.788 1875 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.53 % Allowed : 11.81 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1653 helix: 1.66 (0.17), residues: 958 sheet: -0.18 (0.42), residues: 132 loop : -1.43 (0.25), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 51 HIS 0.004 0.001 HIS D 34 PHE 0.019 0.001 PHE B 569 TYR 0.013 0.001 TYR C 429 ARG 0.006 0.000 ARG D 397 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 687) hydrogen bonds : angle 3.76730 ( 2013) covalent geometry : bond 0.00255 (14155) covalent geometry : angle 0.47221 (19159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4107.50 seconds wall clock time: 75 minutes 43.39 seconds (4543.39 seconds total)