Starting phenix.real_space_refine on Tue Mar 3 23:28:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684.map" model { file = "/net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze5_14684/03_2026/7ze5_14684_neut.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 30 5.16 5 C 5796 2.51 5 N 1598 2.21 5 O 1645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9077 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 4421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4421 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "D" Number of atoms: 4592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4592 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 27, 'TRANS': 560} Chain: "C" 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: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.25 Number of scatterers: 9077 At special positions: 0 Unit cell: (117.18, 97.929, 102.951, 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 30 16.00 P 6 15.00 Mg 2 11.99 O 1645 8.00 N 1598 7.00 C 5796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 374.4 milliseconds 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 5 sheets defined 69.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'C' and resid 1 through 3 No H-bonds generated for 'chain 'C' and resid 1 through 3' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 13 removed outlier: 3.690A pdb=" N ARG C 13 " --> pdb=" O LEU C 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 13' Processing helix chain 'C' and resid 14 through 50 removed outlier: 3.593A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 Processing helix chain 'C' and resid 59 through 101 removed outlier: 3.532A pdb=" N ALA C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Proline residue: C 105 - end of helix No H-bonds generated for 'chain 'C' and resid 102 through 107' Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 115 through 125 Processing helix chain 'C' and resid 125 through 130 removed outlier: 3.566A pdb=" N LEU C 130 " --> pdb=" O ASP C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.579A pdb=" N TYR C 134 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 159 removed outlier: 3.503A pdb=" N LEU C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE C 157 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 175 Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 185 through 209 removed outlier: 3.526A pdb=" N GLY C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.727A pdb=" N ILE C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 216 " --> pdb=" O GLU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 267 removed outlier: 3.638A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 291 removed outlier: 3.776A pdb=" N CYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 3.826A pdb=" N PHE C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 319 removed outlier: 3.501A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 313 " --> pdb=" O ALA C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 429 through 435 Processing helix chain 'C' and resid 442 through 454 Processing helix chain 'C' and resid 455 through 460 Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.553A pdb=" N ASN C 465 " --> pdb=" O ALA C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 492 removed outlier: 3.567A pdb=" N ARG C 482 " --> pdb=" O GLY C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 521 Processing helix chain 'C' and resid 555 through 563 Processing helix chain 'C' and resid 564 through 571 removed outlier: 3.631A pdb=" N GLN C 568 " --> pdb=" O GLY C 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 17 through 19 No H-bonds generated for 'chain 'D' and resid 17 through 19' Processing helix chain 'D' and resid 20 through 54 Processing helix chain 'D' and resid 63 through 110 removed outlier: 3.719A pdb=" N GLY D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 133 through 139 Processing helix chain 'D' and resid 139 through 157 removed outlier: 4.690A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL D 148 " --> pdb=" O MET D 144 " (cutoff:3.500A) Proline residue: D 151 - end of helix removed outlier: 3.564A pdb=" N ALA D 157 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 173 removed outlier: 3.714A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 184 removed outlier: 3.512A pdb=" N LEU D 178 " --> pdb=" O PRO D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 211 Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.650A pdb=" N LEU D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 274 removed outlier: 3.631A pdb=" N LEU D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 330 removed outlier: 3.675A pdb=" N ALA D 297 " --> pdb=" O ALA D 293 " (cutoff:3.500A) Proline residue: D 298 - end of helix removed outlier: 3.757A pdb=" N PHE D 301 " --> pdb=" O ALA D 297 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.743A pdb=" N HIS D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 313 " --> pdb=" O THR D 309 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER D 323 " --> pdb=" O GLY D 319 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU D 324 " --> pdb=" O ALA D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 397 Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 463 through 467 removed outlier: 3.753A pdb=" N GLU D 466 " --> pdb=" O TRP D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.855A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 477 " --> pdb=" O GLY D 474 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 473 through 477' Processing helix chain 'D' and resid 487 through 502 removed outlier: 3.565A pdb=" N ALA D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN D 502 " --> pdb=" O ARG D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 533 removed outlier: 3.877A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 533 " --> pdb=" O ASN D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 572 removed outlier: 4.134A pdb=" N VAL D 572 " --> pdb=" O ALA D 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 584 removed outlier: 3.709A pdb=" N ALA D 578 " --> pdb=" O GLY D 574 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS D 583 " --> pdb=" O THR D 579 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 584 " --> pdb=" O LEU D 580 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 363 removed outlier: 6.749A pdb=" N LYS C 357 " --> pdb=" O GLN C 345 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLN C 345 " --> pdb=" O LYS C 357 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE C 359 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419 removed outlier: 6.386A pdb=" N SER C 417 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASP C 499 " --> pdb=" O SER C 417 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL C 419 " --> pdb=" O ASP C 499 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL C 496 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL C 529 " --> pdb=" O VAL C 496 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C 498 " --> pdb=" O VAL C 529 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N HIS C 368 " --> pdb=" O GLN C 541 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ILE C 543 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 370 " --> pdb=" O ILE C 543 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N MET C 545 " --> pdb=" O ALA C 370 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU C 372 " --> pdb=" O MET C 545 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.643A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER D 401 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 364 through 373 removed outlier: 6.643A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY D 367 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU D 355 " --> pdb=" O GLY D 367 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU D 369 " --> pdb=" O GLU D 353 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 353 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N PHE D 371 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 351 " --> pdb=" O PHE D 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 425 through 428 removed outlier: 6.914A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG D 378 " --> pdb=" O VAL D 552 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N TRP D 554 " --> pdb=" O ARG D 378 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL D 380 " --> pdb=" O TRP D 554 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N MET D 556 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL D 382 " --> pdb=" O MET D 556 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.00 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: 2143 1.33 - 1.45: 1811 1.45 - 1.57: 5235 1.57 - 1.69: 10 1.69 - 1.81: 58 Bond restraints: 9257 Sorted by residual: bond pdb=" C4 ATP C 602 " pdb=" C5 ATP C 602 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" O3A ANP D 602 " pdb=" PB ANP D 602 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C5 ATP C 602 " pdb=" C6 ATP C 602 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.82e+01 bond pdb=" N3B ANP D 602 " pdb=" PG ANP D 602 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C5 ATP C 602 " pdb=" N7 ATP C 602 " ideal model delta sigma weight residual 1.387 1.343 0.044 1.00e-02 1.00e+04 1.93e+01 ... (remaining 9252 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 12542 4.09 - 8.17: 38 8.17 - 12.26: 5 12.26 - 16.34: 2 16.34 - 20.43: 1 Bond angle restraints: 12588 Sorted by residual: angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 119.44 20.43 1.00e+00 1.00e+00 4.17e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 121.12 15.71 1.00e+00 1.00e+00 2.47e+02 angle pdb=" C5 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 126.80 118.78 8.02 1.00e+00 1.00e+00 6.44e+01 angle pdb=" N3 ATP C 602 " pdb=" C4 ATP C 602 " pdb=" N9 ATP C 602 " ideal model delta sigma weight residual 127.04 135.02 -7.98 1.15e+00 7.59e-01 4.83e+01 angle pdb=" N1 ATP C 602 " pdb=" C2 ATP C 602 " pdb=" N3 ATP C 602 " ideal model delta sigma weight residual 128.69 123.67 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 12583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 5090 19.76 - 39.51: 372 39.51 - 59.27: 67 59.27 - 79.02: 26 79.02 - 98.78: 5 Dihedral angle restraints: 5560 sinusoidal: 2233 harmonic: 3327 Sorted by residual: dihedral pdb=" CA LEU D 425 " pdb=" C LEU D 425 " pdb=" N SER D 426 " pdb=" CA SER D 426 " ideal model delta harmonic sigma weight residual 180.00 161.30 18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA LEU C 106 " pdb=" C LEU C 106 " pdb=" N SER C 107 " pdb=" CA SER C 107 " ideal model delta harmonic sigma weight residual 180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA THR C 530 " pdb=" C THR C 530 " pdb=" N HIS C 531 " pdb=" CA HIS C 531 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1206 0.054 - 0.107: 215 0.107 - 0.161: 32 0.161 - 0.215: 3 0.215 - 0.269: 3 Chirality restraints: 1459 Sorted by residual: chirality pdb=" CB THR C 530 " pdb=" CA THR C 530 " pdb=" OG1 THR C 530 " pdb=" CG2 THR C 530 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C3' ANP D 602 " pdb=" C2' ANP D 602 " pdb=" C4' ANP D 602 " pdb=" O3' ANP D 602 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ILE C 397 " pdb=" N ILE C 397 " pdb=" C ILE C 397 " pdb=" CB ILE C 397 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 1456 not shown) Planarity restraints: 1602 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 114 " -0.013 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C TYR C 114 " 0.047 2.00e-02 2.50e+03 pdb=" O TYR C 114 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 115 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET C 177 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO C 178 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 178 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 178 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 527 " 0.007 2.00e-02 2.50e+03 1.49e-02 2.22e+00 pdb=" C LEU C 527 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU C 527 " 0.010 2.00e-02 2.50e+03 pdb=" N MET C 528 " 0.009 2.00e-02 2.50e+03 ... (remaining 1599 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 46 2.50 - 3.10: 6403 3.10 - 3.70: 14192 3.70 - 4.30: 21262 4.30 - 4.90: 35422 Nonbonded interactions: 77325 Sorted by model distance: nonbonded pdb=" OE1 GLN D 430 " pdb="MG MG D 601 " model vdw 1.901 2.170 nonbonded pdb=" OG SER D 390 " pdb="MG MG D 601 " model vdw 1.903 2.170 nonbonded pdb="MG MG D 601 " pdb=" O3G ANP D 602 " model vdw 1.907 2.170 nonbonded pdb="MG MG D 601 " pdb=" O2B ANP D 602 " model vdw 1.929 2.170 nonbonded pdb=" OE1 GLN C 421 " pdb="MG MG C 601 " model vdw 1.970 2.170 ... (remaining 77320 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 individual isotropic 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: 1.550 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 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 : 0.005 0.144 9257 Z= 0.308 Angle : 0.738 20.427 12588 Z= 0.476 Chirality : 0.044 0.269 1459 Planarity : 0.003 0.042 1602 Dihedral : 14.944 98.778 3414 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.24), residues: 1155 helix: -0.45 (0.19), residues: 685 sheet: -0.45 (0.64), residues: 62 loop : -0.33 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 238 TYR 0.016 0.001 TYR D 88 PHE 0.016 0.001 PHE C 539 TRP 0.017 0.002 TRP D 427 HIS 0.006 0.001 HIS D 542 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 9257) covalent geometry : angle 0.73751 (12588) hydrogen bonds : bond 0.24218 ( 562) hydrogen bonds : angle 7.77046 ( 1644) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8500 (tttm) cc_final: 0.8137 (ttmt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.7966 time to fit residues: 95.4601 Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0570 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 198 GLN C 208 GLN C 228 ASN ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN D 433 GLN D 543 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.112658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.092485 restraints weight = 12136.171| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.60 r_work: 0.2916 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9257 Z= 0.262 Angle : 0.645 8.588 12588 Z= 0.331 Chirality : 0.045 0.203 1459 Planarity : 0.005 0.045 1602 Dihedral : 10.092 85.990 1329 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.23 % Allowed : 8.70 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.24), residues: 1155 helix: 0.96 (0.19), residues: 715 sheet: -0.27 (0.66), residues: 62 loop : -0.23 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 96 TYR 0.023 0.002 TYR D 88 PHE 0.023 0.002 PHE D 467 TRP 0.015 0.002 TRP D 163 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 9257) covalent geometry : angle 0.64507 (12588) hydrogen bonds : bond 0.06416 ( 562) hydrogen bonds : angle 4.47759 ( 1644) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8704 (tttm) cc_final: 0.8300 (ttmt) REVERT: C 394 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7556 (tm-30) REVERT: C 521 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8394 (mtp) REVERT: D 115 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7785 (tt0) REVERT: D 226 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.7877 (tm-30) outliers start: 21 outliers final: 7 residues processed: 108 average time/residue: 0.7854 time to fit residues: 89.3737 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 321 LYS Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain D residue 465 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093307 restraints weight = 11891.352| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.72 r_work: 0.2925 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9257 Z= 0.145 Angle : 0.536 6.595 12588 Z= 0.274 Chirality : 0.040 0.178 1459 Planarity : 0.004 0.043 1602 Dihedral : 8.744 76.298 1329 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.12 % Allowed : 10.62 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1155 helix: 1.84 (0.20), residues: 700 sheet: 0.07 (0.67), residues: 62 loop : -0.15 (0.32), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.024 0.001 TYR D 88 PHE 0.018 0.001 PHE C 89 TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9257) covalent geometry : angle 0.53565 (12588) hydrogen bonds : bond 0.05111 ( 562) hydrogen bonds : angle 4.05001 ( 1644) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8692 (tttm) cc_final: 0.8291 (ttpt) REVERT: C 323 GLU cc_start: 0.8324 (tt0) cc_final: 0.8076 (mt-10) REVERT: C 394 GLN cc_start: 0.7842 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 521 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8364 (mtp) REVERT: D 115 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: D 226 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: D 336 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7866 (tm-30) REVERT: D 523 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8501 (mmt90) outliers start: 20 outliers final: 4 residues processed: 108 average time/residue: 0.7404 time to fit residues: 84.2372 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 91 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093453 restraints weight = 12052.554| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.73 r_work: 0.2928 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9257 Z= 0.136 Angle : 0.523 6.796 12588 Z= 0.265 Chirality : 0.040 0.226 1459 Planarity : 0.004 0.041 1602 Dihedral : 8.100 71.900 1329 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.34 % Allowed : 12.21 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.25), residues: 1155 helix: 2.17 (0.20), residues: 703 sheet: 0.32 (0.67), residues: 62 loop : -0.02 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 560 TYR 0.022 0.001 TYR D 88 PHE 0.018 0.001 PHE C 89 TRP 0.015 0.001 TRP D 81 HIS 0.005 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9257) covalent geometry : angle 0.52342 (12588) hydrogen bonds : bond 0.04687 ( 562) hydrogen bonds : angle 3.87083 ( 1644) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: C 171 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8352 (mp) REVERT: C 186 LYS cc_start: 0.8605 (tttm) cc_final: 0.8297 (ttpt) REVERT: C 323 GLU cc_start: 0.8303 (tt0) cc_final: 0.8069 (mt-10) REVERT: C 394 GLN cc_start: 0.7831 (tm-30) cc_final: 0.7535 (tm-30) REVERT: C 521 MET cc_start: 0.9039 (OUTLIER) cc_final: 0.8331 (mtp) REVERT: C 534 ARG cc_start: 0.8659 (ttt90) cc_final: 0.8356 (ttt-90) REVERT: D 115 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: D 222 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8124 (mp0) REVERT: D 226 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7728 (tm-30) outliers start: 22 outliers final: 5 residues processed: 110 average time/residue: 0.7224 time to fit residues: 83.9297 Evaluate side-chains 101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 115 GLN Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 84 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.090703 restraints weight = 11981.662| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.63 r_work: 0.2912 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9257 Z= 0.193 Angle : 0.569 8.320 12588 Z= 0.283 Chirality : 0.042 0.211 1459 Planarity : 0.004 0.054 1602 Dihedral : 8.003 76.197 1329 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.34 % Allowed : 13.16 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1155 helix: 2.21 (0.19), residues: 703 sheet: 0.33 (0.65), residues: 62 loop : -0.02 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 560 TYR 0.022 0.001 TYR D 88 PHE 0.018 0.002 PHE D 467 TRP 0.014 0.002 TRP D 81 HIS 0.006 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 9257) covalent geometry : angle 0.56872 (12588) hydrogen bonds : bond 0.04950 ( 562) hydrogen bonds : angle 3.89509 ( 1644) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 171 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (mp) REVERT: C 186 LYS cc_start: 0.8619 (tttm) cc_final: 0.8304 (ttpt) REVERT: C 394 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7188 (tm-30) REVERT: C 519 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8379 (tp30) REVERT: C 521 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: C 534 ARG cc_start: 0.8683 (ttt90) cc_final: 0.8376 (ttt-90) REVERT: D 144 MET cc_start: 0.8515 (tpt) cc_final: 0.7610 (mtm) REVERT: D 226 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: D 423 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8643 (mttm) REVERT: D 523 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8475 (mmt90) outliers start: 22 outliers final: 5 residues processed: 104 average time/residue: 0.7890 time to fit residues: 86.3927 Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 423 LYS Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093466 restraints weight = 11995.466| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.75 r_work: 0.2937 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9257 Z= 0.133 Angle : 0.516 7.747 12588 Z= 0.260 Chirality : 0.039 0.181 1459 Planarity : 0.004 0.056 1602 Dihedral : 7.534 74.847 1329 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.02 % Allowed : 13.80 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.25), residues: 1155 helix: 2.42 (0.19), residues: 702 sheet: 0.50 (0.66), residues: 62 loop : -0.01 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 560 TYR 0.020 0.001 TYR D 88 PHE 0.017 0.001 PHE C 89 TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9257) covalent geometry : angle 0.51583 (12588) hydrogen bonds : bond 0.04499 ( 562) hydrogen bonds : angle 3.76472 ( 1644) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8568 (tttm) cc_final: 0.8246 (ttpt) REVERT: C 323 GLU cc_start: 0.8296 (tt0) cc_final: 0.8047 (mt-10) REVERT: C 394 GLN cc_start: 0.7751 (tm-30) cc_final: 0.7164 (tm-30) REVERT: C 521 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: C 534 ARG cc_start: 0.8711 (ttt90) cc_final: 0.8416 (ttt-90) REVERT: D 144 MET cc_start: 0.8524 (tpt) cc_final: 0.7553 (mtm) REVERT: D 226 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7706 (tm-30) REVERT: D 523 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8484 (mmt90) outliers start: 19 outliers final: 6 residues processed: 101 average time/residue: 0.7538 time to fit residues: 80.2699 Evaluate side-chains 97 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.0060 chunk 82 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 531 HIS D 92 GLN D 115 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.094412 restraints weight = 11915.147| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.75 r_work: 0.2938 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9257 Z= 0.122 Angle : 0.506 8.166 12588 Z= 0.254 Chirality : 0.039 0.139 1459 Planarity : 0.004 0.053 1602 Dihedral : 7.274 77.315 1329 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.44 % Allowed : 13.16 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.25), residues: 1155 helix: 2.55 (0.19), residues: 703 sheet: 0.52 (0.67), residues: 62 loop : 0.06 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 560 TYR 0.018 0.001 TYR D 88 PHE 0.017 0.001 PHE C 89 TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9257) covalent geometry : angle 0.50550 (12588) hydrogen bonds : bond 0.04292 ( 562) hydrogen bonds : angle 3.66507 ( 1644) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8509 (tttm) cc_final: 0.8247 (ttpt) REVERT: C 323 GLU cc_start: 0.8255 (tt0) cc_final: 0.8044 (mt-10) REVERT: C 394 GLN cc_start: 0.7764 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 521 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8306 (mtp) REVERT: C 534 ARG cc_start: 0.8714 (ttt90) cc_final: 0.8409 (ttt-90) REVERT: D 226 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: D 336 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7633 (tm-30) REVERT: D 523 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8481 (mmt90) outliers start: 23 outliers final: 8 residues processed: 109 average time/residue: 0.7984 time to fit residues: 91.7555 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 7 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.092457 restraints weight = 11898.663| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.72 r_work: 0.2914 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9257 Z= 0.182 Angle : 0.549 7.155 12588 Z= 0.275 Chirality : 0.041 0.141 1459 Planarity : 0.004 0.063 1602 Dihedral : 7.470 81.305 1329 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.34 % Allowed : 13.59 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.25), residues: 1155 helix: 2.39 (0.19), residues: 711 sheet: 0.45 (0.68), residues: 62 loop : 0.07 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 560 TYR 0.018 0.001 TYR D 88 PHE 0.018 0.001 PHE D 467 TRP 0.013 0.002 TRP D 81 HIS 0.006 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 9257) covalent geometry : angle 0.54866 (12588) hydrogen bonds : bond 0.04675 ( 562) hydrogen bonds : angle 3.74595 ( 1644) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8530 (tttm) cc_final: 0.8232 (ttpt) REVERT: C 323 GLU cc_start: 0.8281 (tt0) cc_final: 0.8045 (mt-10) REVERT: C 394 GLN cc_start: 0.7738 (tm-30) cc_final: 0.7175 (tm-30) REVERT: C 521 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8294 (mtt) REVERT: C 534 ARG cc_start: 0.8723 (ttt90) cc_final: 0.8432 (ttt-90) REVERT: D 226 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: D 336 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: D 523 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8464 (mmt90) outliers start: 22 outliers final: 9 residues processed: 103 average time/residue: 0.6970 time to fit residues: 75.5893 Evaluate side-chains 102 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 384 GLN D 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093567 restraints weight = 11889.219| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.72 r_work: 0.2933 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9257 Z= 0.138 Angle : 0.520 7.000 12588 Z= 0.263 Chirality : 0.039 0.159 1459 Planarity : 0.004 0.068 1602 Dihedral : 7.361 80.781 1329 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.02 % Allowed : 14.12 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.25), residues: 1155 helix: 2.50 (0.19), residues: 710 sheet: 0.45 (0.68), residues: 62 loop : 0.10 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 560 TYR 0.019 0.001 TYR D 88 PHE 0.017 0.001 PHE C 89 TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9257) covalent geometry : angle 0.52021 (12588) hydrogen bonds : bond 0.04439 ( 562) hydrogen bonds : angle 3.68929 ( 1644) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8511 (tttm) cc_final: 0.8251 (ttpt) REVERT: C 323 GLU cc_start: 0.8273 (tt0) cc_final: 0.8051 (mt-10) REVERT: C 394 GLN cc_start: 0.7730 (tm-30) cc_final: 0.7191 (tm-30) REVERT: C 521 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: C 534 ARG cc_start: 0.8704 (ttt90) cc_final: 0.8428 (ttt-90) REVERT: D 144 MET cc_start: 0.8192 (tpt) cc_final: 0.7505 (mtm) REVERT: D 226 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: D 523 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8492 (mmt90) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.8137 time to fit residues: 84.8282 Evaluate side-chains 99 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 523 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 79 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 500 GLN D 115 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093900 restraints weight = 11825.162| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.74 r_work: 0.2945 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9257 Z= 0.131 Angle : 0.516 6.932 12588 Z= 0.260 Chirality : 0.039 0.185 1459 Planarity : 0.004 0.069 1602 Dihedral : 7.276 80.416 1329 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.17 % Allowed : 15.07 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.25), residues: 1155 helix: 2.56 (0.19), residues: 710 sheet: 0.35 (0.71), residues: 57 loop : 0.07 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 560 TYR 0.017 0.001 TYR D 88 PHE 0.017 0.001 PHE C 89 TRP 0.014 0.001 TRP D 81 HIS 0.004 0.001 HIS D 312 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9257) covalent geometry : angle 0.51551 (12588) hydrogen bonds : bond 0.04350 ( 562) hydrogen bonds : angle 3.65028 ( 1644) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2310 Ramachandran restraints generated. 1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: C 186 LYS cc_start: 0.8541 (tttm) cc_final: 0.8272 (ttpt) REVERT: C 323 GLU cc_start: 0.8266 (tt0) cc_final: 0.8055 (mt-10) REVERT: C 394 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7205 (tm-30) REVERT: C 521 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8359 (mtt) REVERT: C 534 ARG cc_start: 0.8692 (ttt90) cc_final: 0.8412 (ttt-90) REVERT: D 144 MET cc_start: 0.8156 (tpt) cc_final: 0.7485 (mtm) REVERT: D 226 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7775 (tm-30) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.8246 time to fit residues: 84.3331 Evaluate side-chains 100 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 359 ILE Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 457 LYS Chi-restraints excluded: chain C residue 521 MET Chi-restraints excluded: chain D residue 149 SER Chi-restraints excluded: chain D residue 226 GLU Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain D residue 342 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 18 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 84 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 0.0170 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.5232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094386 restraints weight = 11784.122| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.63 r_work: 0.2973 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9257 Z= 0.114 Angle : 0.497 6.754 12588 Z= 0.252 Chirality : 0.038 0.164 1459 Planarity : 0.004 0.068 1602 Dihedral : 7.081 82.200 1329 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.38 % Allowed : 14.86 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.25), residues: 1155 helix: 2.70 (0.20), residues: 705 sheet: 0.40 (0.71), residues: 57 loop : 0.08 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 560 TYR 0.016 0.001 TYR D 88 PHE 0.016 0.001 PHE C 89 TRP 0.015 0.001 TRP D 81 HIS 0.004 0.001 HIS C 132 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9257) covalent geometry : angle 0.49732 (12588) hydrogen bonds : bond 0.04123 ( 562) hydrogen bonds : angle 3.58923 ( 1644) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.99 seconds wall clock time: 51 minutes 52.19 seconds (3112.19 seconds total)