Starting phenix.real_space_refine on Thu Jul 2 05:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.cif" model { file = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a91_11681/07_2026/7a91_11681.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.046 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4417 2.51 5 N 1137 2.21 5 O 1321 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6915 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 4815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 588, 4801 Classifications: {'peptide': 588} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 562} Chain breaks: 1 bond proxies already assigned to first conformer: 4917 Chain: "A" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1973 Classifications: {'peptide': 251} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 236} Chain breaks: 1 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.35 Number of scatterers: 6915 At special positions: 0 Unit cell: (76.538, 98.098, 137.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 39 16.00 O 1321 8.00 N 1137 7.00 C 4417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 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 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 701 " - " ASN A 343 " " NAG A 702 " - " ASN A 331 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG J 1 " - " ASN D 546 " Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 388.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 706 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 374 " pdb="ZN ZN D 706 " - pdb=" NE2 HIS D 378 " 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1582 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 50.2% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.517A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 81 removed outlier: 3.537A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.794A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.866A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.528A pdb=" N LEU D 162 " --> pdb=" O TYR D 158 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.701A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.603A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N HIS D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.508A pdb=" N TYR D 237 " --> pdb=" O ILE D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 3.816A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 4.126A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.908A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.575A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 412 removed outlier: 3.853A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.552A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.718A pdb=" N TRP D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.696A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG D 482 " --> pdb=" O TRP D 478 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 483 " --> pdb=" O GLU D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.519A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.951A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.978A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.540A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.791A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 343' Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.892A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.238A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 5.946A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.660A pdb=" N SER A 555 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.600A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 277 hydrogen bonds defined for protein. 777 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: 0.86 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2198 1.34 - 1.46: 1706 1.46 - 1.58: 3138 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 7102 Sorted by residual: bond pdb=" C1 NAG A 702 " pdb=" O5 NAG A 702 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C1 NAG D 701 " pdb=" O5 NAG D 701 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG D 703 " pdb=" O5 NAG D 703 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C1 NAG D 705 " pdb=" O5 NAG D 705 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.70e+00 ... (remaining 7097 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 9332 1.94 - 3.89: 278 3.89 - 5.83: 31 5.83 - 7.77: 11 7.77 - 9.71: 1 Bond angle restraints: 9653 Sorted by residual: angle pdb=" CA LEU D 439 " pdb=" CB LEU D 439 " pdb=" CG LEU D 439 " ideal model delta sigma weight residual 116.30 106.59 9.71 3.50e+00 8.16e-02 7.70e+00 angle pdb=" C GLY A 526 " pdb=" N PRO A 527 " pdb=" CD PRO A 527 " ideal model delta sigma weight residual 120.60 126.69 -6.09 2.20e+00 2.07e-01 7.66e+00 angle pdb=" CG ARG D 518 " pdb=" CD ARG D 518 " pdb=" NE ARG D 518 " ideal model delta sigma weight residual 112.00 117.86 -5.86 2.20e+00 2.07e-01 7.10e+00 angle pdb=" C ASN D 322 " pdb=" CA ASN D 322 " pdb=" CB ASN D 322 " ideal model delta sigma weight residual 111.30 105.58 5.72 2.23e+00 2.01e-01 6.58e+00 angle pdb=" C PHE D 523 " pdb=" N GLN D 524 " pdb=" CA GLN D 524 " ideal model delta sigma weight residual 120.68 116.37 4.31 1.70e+00 3.46e-01 6.44e+00 ... (remaining 9648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3664 17.98 - 35.97: 358 35.97 - 53.95: 90 53.95 - 71.94: 7 71.94 - 89.92: 10 Dihedral angle restraints: 4129 sinusoidal: 1665 harmonic: 2464 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -36.01 -49.99 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA SER D 425 " pdb=" C SER D 425 " pdb=" N PRO D 426 " pdb=" CA PRO D 426 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 131.56 -38.56 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 4126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 675 0.044 - 0.088: 273 0.088 - 0.132: 83 0.132 - 0.176: 15 0.176 - 0.220: 3 Chirality restraints: 1049 Sorted by residual: chirality pdb=" C1 NAG D 705 " pdb=" ND2 ASN D 432 " pdb=" C2 NAG D 705 " pdb=" O5 NAG D 705 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1 NAG A 702 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A 702 " pdb=" O5 NAG A 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1046 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 451 " -0.016 2.00e-02 2.50e+03 3.09e-02 9.52e+00 pdb=" C PRO D 451 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO D 451 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE D 452 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 161 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.63e+00 pdb=" C ARG D 161 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG D 161 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU D 162 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 368 " 0.011 2.00e-02 2.50e+03 2.27e-02 5.16e+00 pdb=" C ASP D 368 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP D 368 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE D 369 " 0.013 2.00e-02 2.50e+03 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 653 2.74 - 3.28: 6614 3.28 - 3.82: 10378 3.82 - 4.36: 12686 4.36 - 4.90: 22387 Nonbonded interactions: 52718 Sorted by model distance: nonbonded pdb=" OD1 ASP A 578 " pdb=" N GLU A 583 " model vdw 2.194 3.120 nonbonded pdb=" OG SER D 19 " pdb=" OE1 GLU D 23 " model vdw 2.223 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.227 3.040 nonbonded pdb=" O ASP D 225 " pdb=" OG1 THR D 229 " model vdw 2.229 3.040 nonbonded pdb=" O LEU D 85 " pdb=" NZ LYS D 94 " model vdw 2.269 3.120 ... (remaining 52713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 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 : 0.006 0.059 7121 Z= 0.271 Angle : 0.808 9.714 9696 Z= 0.429 Chirality : 0.051 0.220 1049 Planarity : 0.006 0.054 1236 Dihedral : 15.317 89.919 2523 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.81 % Allowed : 5.13 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.81 (0.26), residues: 833 helix: -1.71 (0.24), residues: 376 sheet: -0.91 (0.48), residues: 89 loop : -2.18 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 245 TYR 0.018 0.002 TYR A 421 PHE 0.024 0.002 PHE A 543 TRP 0.036 0.003 TRP D 594 HIS 0.007 0.002 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00634 / 0.27 ( 7102) covalent geometry : angle 0.79256 / 0.43 ( 9653) SS BOND : bond 0.00394 / 0.27 ( 8) SS BOND : angle 1.31975 / 0.82 ( 16) hydrogen bonds : bond 0.15567 / 10.22 ( 277) hydrogen bonds : angle 6.36562 / 4.50 ( 777) metal coordination : bond 0.00245 / 0.13 ( 2) link_BETA1-4 : bond 0.00052 / 0.03 ( 1) link_BETA1-4 : angle 1.64894 / 0.87 ( 3) link_NAG-ASN : bond 0.00460 / 0.36 ( 8) link_NAG-ASN : angle 3.05226 / 2.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8425 (m-40) cc_final: 0.7896 (m110) REVERT: D 350 ASP cc_start: 0.8268 (t0) cc_final: 0.7938 (p0) REVERT: D 597 ASP cc_start: 0.6349 (m-30) cc_final: 0.6108 (m-30) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.0709 time to fit residues: 10.4645 Evaluate side-chains 77 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.1980 chunk 74 optimal weight: 0.0670 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 24 GLN A 334 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.151123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139220 restraints weight = 17631.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.134870 restraints weight = 25356.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.131877 restraints weight = 16407.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.132850 restraints weight = 15304.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.133310 restraints weight = 9150.745| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7121 Z= 0.126 Angle : 0.628 7.492 9696 Z= 0.320 Chirality : 0.044 0.274 1049 Planarity : 0.005 0.092 1236 Dihedral : 5.621 46.270 918 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.62 % Allowed : 8.91 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.63 (0.27), residues: 833 helix: -0.55 (0.26), residues: 375 sheet: -0.18 (0.52), residues: 81 loop : -1.80 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.012 0.001 TYR D 183 PHE 0.008 0.001 PHE D 504 TRP 0.012 0.001 TRP D 459 HIS 0.003 0.001 HIS D 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 7102) covalent geometry : angle 0.61375 / 0.32 ( 9653) SS BOND : bond 0.00275 / 0.15 ( 8) SS BOND : angle 1.26181 / 1.00 ( 16) hydrogen bonds : bond 0.04716 / 3.03 ( 277) hydrogen bonds : angle 4.62754 / 3.28 ( 777) metal coordination : bond 0.00072 / 0.04 ( 2) link_BETA1-4 : bond 0.00707 / 0.37 ( 1) link_BETA1-4 : angle 1.69837 / 0.90 ( 3) link_NAG-ASN : bond 0.00674 / 0.48 ( 8) link_NAG-ASN : angle 2.50023 / 1.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 168 TRP cc_start: 0.8185 (t-100) cc_final: 0.7961 (t-100) REVERT: D 277 ASN cc_start: 0.8362 (m-40) cc_final: 0.8001 (m110) REVERT: D 350 ASP cc_start: 0.8036 (t0) cc_final: 0.7795 (p0) REVERT: D 597 ASP cc_start: 0.6299 (m-30) cc_final: 0.6009 (m-30) outliers start: 12 outliers final: 9 residues processed: 99 average time/residue: 0.0568 time to fit residues: 8.6198 Evaluate side-chains 85 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 40 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 78 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.175268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.147421 restraints weight = 14171.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.148217 restraints weight = 16034.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.149047 restraints weight = 17934.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.150116 restraints weight = 13236.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.150320 restraints weight = 12145.167| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7121 Z= 0.185 Angle : 0.655 7.244 9696 Z= 0.333 Chirality : 0.046 0.194 1049 Planarity : 0.005 0.090 1236 Dihedral : 5.613 45.429 916 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.29 % Allowed : 11.20 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.55 (0.27), residues: 833 helix: -0.40 (0.26), residues: 379 sheet: -0.21 (0.55), residues: 69 loop : -1.81 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 518 TYR 0.020 0.002 TYR D 183 PHE 0.012 0.002 PHE D 504 TRP 0.015 0.002 TRP D 594 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 ( 7102) covalent geometry : angle 0.64213 / 0.33 ( 9653) SS BOND : bond 0.00246 / 0.18 ( 8) SS BOND : angle 1.33037 / 1.00 ( 16) hydrogen bonds : bond 0.05391 / 3.48 ( 277) hydrogen bonds : angle 4.53552 / 3.21 ( 777) metal coordination : bond 0.00216 / 0.11 ( 2) link_BETA1-4 : bond 0.00430 / 0.23 ( 1) link_BETA1-4 : angle 1.60420 / 0.85 ( 3) link_NAG-ASN : bond 0.00621 / 0.47 ( 8) link_NAG-ASN : angle 2.44573 / 1.67 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 168 TRP cc_start: 0.8298 (t-100) cc_final: 0.8074 (t-100) REVERT: D 277 ASN cc_start: 0.8464 (m-40) cc_final: 0.8040 (m110) REVERT: D 350 ASP cc_start: 0.8123 (t0) cc_final: 0.7819 (p0) REVERT: D 597 ASP cc_start: 0.6536 (m-30) cc_final: 0.6214 (m-30) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0577 time to fit residues: 7.7198 Evaluate side-chains 83 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 22 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 73 optimal weight: 0.0060 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 67 optimal weight: 0.0870 overall best weight: 0.1632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** A 439 ASN ** 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 = 0.3943 r_free = 0.3943 target = 0.180941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.151883 restraints weight = 17327.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.157147 restraints weight = 19211.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.156462 restraints weight = 16978.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.156672 restraints weight = 13732.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.156779 restraints weight = 12745.753| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7121 Z= 0.106 Angle : 0.559 6.688 9696 Z= 0.285 Chirality : 0.042 0.188 1049 Planarity : 0.004 0.087 1236 Dihedral : 5.171 45.211 916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.56 % Allowed : 11.88 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.09 (0.28), residues: 833 helix: 0.06 (0.27), residues: 374 sheet: -0.09 (0.55), residues: 69 loop : -1.62 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.010 0.001 TYR D 127 PHE 0.007 0.001 PHE D 504 TRP 0.010 0.001 TRP D 477 HIS 0.002 0.001 HIS D 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 ( 7102) covalent geometry : angle 0.54620 / 0.28 ( 9653) SS BOND : bond 0.00152 / 0.10 ( 8) SS BOND : angle 0.87738 / 0.70 ( 16) hydrogen bonds : bond 0.03899 / 2.50 ( 277) hydrogen bonds : angle 4.20537 / 2.96 ( 777) metal coordination : bond 0.00044 / 0.02 ( 2) link_BETA1-4 : bond 0.00470 / 0.25 ( 1) link_BETA1-4 : angle 1.45264 / 0.78 ( 3) link_NAG-ASN : bond 0.00685 / 0.51 ( 8) link_NAG-ASN : angle 2.34500 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8393 (m-40) cc_final: 0.8093 (m110) REVERT: D 350 ASP cc_start: 0.8107 (t0) cc_final: 0.7857 (p0) REVERT: D 597 ASP cc_start: 0.6455 (m-30) cc_final: 0.6080 (m-30) REVERT: A 581 THR cc_start: 0.6841 (OUTLIER) cc_final: 0.6202 (p) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.0516 time to fit residues: 7.6019 Evaluate side-chains 86 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 0.0030 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 24 GLN ** A 439 ASN ** 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 = 0.3527 r_free = 0.3527 target = 0.145521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.135478 restraints weight = 16363.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.128157 restraints weight = 25541.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.125280 restraints weight = 19646.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.126465 restraints weight = 17207.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.127181 restraints weight = 11400.793| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7121 Z= 0.190 Angle : 0.638 7.401 9696 Z= 0.324 Chirality : 0.046 0.199 1049 Planarity : 0.005 0.086 1236 Dihedral : 5.550 44.744 916 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.70 % Allowed : 12.82 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.25 (0.27), residues: 833 helix: -0.08 (0.27), residues: 373 sheet: -0.12 (0.54), residues: 70 loop : -1.70 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 245 TYR 0.020 0.002 TYR D 183 PHE 0.029 0.002 PHE D 314 TRP 0.022 0.002 TRP D 168 HIS 0.005 0.001 HIS D 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 7102) covalent geometry : angle 0.62595 / 0.32 ( 9653) SS BOND : bond 0.00238 / 0.17 ( 8) SS BOND : angle 1.08193 / 0.82 ( 16) hydrogen bonds : bond 0.05110 / 3.29 ( 277) hydrogen bonds : angle 4.38300 / 3.09 ( 777) metal coordination : bond 0.00189 / 0.10 ( 2) link_BETA1-4 : bond 0.00462 / 0.24 ( 1) link_BETA1-4 : angle 1.50610 / 0.81 ( 3) link_NAG-ASN : bond 0.00633 / 0.48 ( 8) link_NAG-ASN : angle 2.39402 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 LYS cc_start: 0.8233 (mmtt) cc_final: 0.8009 (mmtt) REVERT: D 277 ASN cc_start: 0.8472 (m-40) cc_final: 0.8001 (m110) REVERT: D 597 ASP cc_start: 0.6455 (m-30) cc_final: 0.6101 (m-30) REVERT: A 581 THR cc_start: 0.7401 (OUTLIER) cc_final: 0.6792 (p) outliers start: 20 outliers final: 15 residues processed: 91 average time/residue: 0.0591 time to fit residues: 8.1493 Evaluate side-chains 81 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.0270 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 ASN ** A 439 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135571 restraints weight = 14379.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.129416 restraints weight = 22043.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.126646 restraints weight = 15679.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.127188 restraints weight = 15228.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.127597 restraints weight = 11384.744| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3251 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7121 Z= 0.147 Angle : 0.592 7.485 9696 Z= 0.301 Chirality : 0.044 0.205 1049 Planarity : 0.005 0.087 1236 Dihedral : 5.413 44.493 916 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.10 (0.27), residues: 833 helix: 0.08 (0.27), residues: 369 sheet: -0.09 (0.55), residues: 70 loop : -1.63 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 204 TYR 0.015 0.001 TYR D 183 PHE 0.026 0.001 PHE D 314 TRP 0.019 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 7102) covalent geometry : angle 0.57927 / 0.30 ( 9653) SS BOND : bond 0.00187 / 0.13 ( 8) SS BOND : angle 0.95054 / 0.73 ( 16) hydrogen bonds : bond 0.04481 / 2.88 ( 277) hydrogen bonds : angle 4.23708 / 2.99 ( 777) metal coordination : bond 0.00128 / 0.07 ( 2) link_BETA1-4 : bond 0.00442 / 0.23 ( 1) link_BETA1-4 : angle 1.44546 / 0.78 ( 3) link_NAG-ASN : bond 0.00619 / 0.47 ( 8) link_NAG-ASN : angle 2.35543 / 1.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8449 (m-40) cc_final: 0.7992 (m110) REVERT: D 350 ASP cc_start: 0.8162 (t0) cc_final: 0.7756 (p0) REVERT: D 597 ASP cc_start: 0.6490 (m-30) cc_final: 0.6096 (m-30) REVERT: A 581 THR cc_start: 0.7305 (OUTLIER) cc_final: 0.6645 (p) outliers start: 21 outliers final: 17 residues processed: 84 average time/residue: 0.0647 time to fit residues: 8.0908 Evaluate side-chains 85 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 5 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 45 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136582 restraints weight = 18885.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.132055 restraints weight = 22410.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.129509 restraints weight = 25519.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.130397 restraints weight = 20692.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129991 restraints weight = 13074.403| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7121 Z= 0.151 Angle : 0.593 7.548 9696 Z= 0.302 Chirality : 0.044 0.209 1049 Planarity : 0.004 0.081 1236 Dihedral : 5.399 44.158 916 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.97 % Allowed : 13.63 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.07 (0.28), residues: 833 helix: 0.08 (0.27), residues: 372 sheet: 0.06 (0.55), residues: 69 loop : -1.63 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.016 0.001 TYR D 183 PHE 0.023 0.001 PHE D 314 TRP 0.020 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7102) covalent geometry : angle 0.58290 / 0.30 ( 9653) SS BOND : bond 0.00181 / 0.13 ( 8) SS BOND : angle 0.94783 / 0.73 ( 16) hydrogen bonds : bond 0.04546 / 2.93 ( 277) hydrogen bonds : angle 4.21677 / 2.98 ( 777) metal coordination : bond 0.00142 / 0.07 ( 2) link_BETA1-4 : bond 0.00382 / 0.20 ( 1) link_BETA1-4 : angle 1.45612 / 0.78 ( 3) link_NAG-ASN : bond 0.00533 / 0.40 ( 8) link_NAG-ASN : angle 2.07822 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8415 (m-40) cc_final: 0.7966 (m110) REVERT: D 350 ASP cc_start: 0.8194 (t0) cc_final: 0.7819 (p0) REVERT: D 597 ASP cc_start: 0.6474 (m-30) cc_final: 0.6094 (m-30) REVERT: A 581 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.6828 (p) outliers start: 22 outliers final: 19 residues processed: 89 average time/residue: 0.0634 time to fit residues: 8.4467 Evaluate side-chains 90 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 18 optimal weight: 0.0670 chunk 75 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.146831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.135878 restraints weight = 21496.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.130249 restraints weight = 26232.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.127744 restraints weight = 19182.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.129041 restraints weight = 15438.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.128940 restraints weight = 9920.074| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7121 Z= 0.157 Angle : 0.596 7.586 9696 Z= 0.304 Chirality : 0.044 0.205 1049 Planarity : 0.004 0.079 1236 Dihedral : 5.420 44.143 916 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.83 % Allowed : 14.57 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.06 (0.28), residues: 833 helix: 0.09 (0.27), residues: 372 sheet: 0.05 (0.56), residues: 69 loop : -1.63 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.017 0.001 TYR D 183 PHE 0.020 0.001 PHE D 314 TRP 0.020 0.002 TRP D 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7102) covalent geometry : angle 0.58606 / 0.30 ( 9653) SS BOND : bond 0.00174 / 0.12 ( 8) SS BOND : angle 0.97922 / 0.75 ( 16) hydrogen bonds : bond 0.04613 / 2.97 ( 277) hydrogen bonds : angle 4.22307 / 2.99 ( 777) metal coordination : bond 0.00161 / 0.08 ( 2) link_BETA1-4 : bond 0.00374 / 0.20 ( 1) link_BETA1-4 : angle 1.45381 / 0.78 ( 3) link_NAG-ASN : bond 0.00494 / 0.37 ( 8) link_NAG-ASN : angle 2.08887 / 1.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8445 (m-40) cc_final: 0.7980 (m110) REVERT: D 350 ASP cc_start: 0.8171 (t0) cc_final: 0.7810 (p0) REVERT: D 597 ASP cc_start: 0.6508 (m-30) cc_final: 0.6120 (m-30) REVERT: A 581 THR cc_start: 0.7383 (OUTLIER) cc_final: 0.6791 (p) outliers start: 21 outliers final: 19 residues processed: 86 average time/residue: 0.0599 time to fit residues: 7.8697 Evaluate side-chains 92 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 15 optimal weight: 0.0870 chunk 56 optimal weight: 0.3980 chunk 77 optimal weight: 0.6980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 58 ASN ** A 439 ASN ** 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 = 0.3915 r_free = 0.3915 target = 0.178149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.151442 restraints weight = 16031.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.151305 restraints weight = 19601.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.152151 restraints weight = 17686.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.152464 restraints weight = 16196.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.153105 restraints weight = 15659.574| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7121 Z= 0.126 Angle : 0.570 7.634 9696 Z= 0.290 Chirality : 0.043 0.208 1049 Planarity : 0.004 0.076 1236 Dihedral : 5.249 43.996 916 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 14.84 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.94 (0.28), residues: 833 helix: 0.23 (0.27), residues: 372 sheet: -0.08 (0.56), residues: 70 loop : -1.57 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.013 0.001 TYR D 183 PHE 0.021 0.001 PHE D 314 TRP 0.019 0.001 TRP D 168 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7102) covalent geometry : angle 0.56033 / 0.29 ( 9653) SS BOND : bond 0.00159 / 0.11 ( 8) SS BOND : angle 0.87076 / 0.66 ( 16) hydrogen bonds : bond 0.04171 / 2.68 ( 277) hydrogen bonds : angle 4.12191 / 2.91 ( 777) metal coordination : bond 0.00093 / 0.05 ( 2) link_BETA1-4 : bond 0.00373 / 0.20 ( 1) link_BETA1-4 : angle 1.41823 / 0.77 ( 3) link_NAG-ASN : bond 0.00511 / 0.38 ( 8) link_NAG-ASN : angle 2.06716 / 1.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8428 (m-40) cc_final: 0.7988 (m110) REVERT: D 350 ASP cc_start: 0.8178 (t0) cc_final: 0.7935 (p0) REVERT: D 597 ASP cc_start: 0.6435 (m-30) cc_final: 0.6041 (m-30) REVERT: A 581 THR cc_start: 0.7002 (OUTLIER) cc_final: 0.6318 (p) outliers start: 21 outliers final: 19 residues processed: 86 average time/residue: 0.0628 time to fit residues: 8.1731 Evaluate side-chains 93 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 59 optimal weight: 0.0470 chunk 39 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.137709 restraints weight = 16612.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.131678 restraints weight = 26577.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.129092 restraints weight = 16529.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.129692 restraints weight = 14125.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.130776 restraints weight = 9134.490| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7121 Z= 0.132 Angle : 0.570 7.593 9696 Z= 0.291 Chirality : 0.043 0.203 1049 Planarity : 0.004 0.076 1236 Dihedral : 5.226 44.091 916 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.97 % Allowed : 14.84 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.89 (0.28), residues: 833 helix: 0.27 (0.27), residues: 372 sheet: -0.01 (0.56), residues: 70 loop : -1.55 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.014 0.001 TYR D 183 PHE 0.020 0.001 PHE D 314 TRP 0.021 0.001 TRP D 168 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7102) covalent geometry : angle 0.56037 / 0.29 ( 9653) SS BOND : bond 0.00166 / 0.12 ( 8) SS BOND : angle 0.87696 / 0.68 ( 16) hydrogen bonds : bond 0.04226 / 2.72 ( 277) hydrogen bonds : angle 4.11434 / 2.90 ( 777) metal coordination : bond 0.00139 / 0.07 ( 2) link_BETA1-4 : bond 0.00364 / 0.19 ( 1) link_BETA1-4 : angle 1.42112 / 0.77 ( 3) link_NAG-ASN : bond 0.00478 / 0.35 ( 8) link_NAG-ASN : angle 2.07872 / 1.50 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8434 (m-40) cc_final: 0.8053 (m110) REVERT: D 350 ASP cc_start: 0.8128 (t0) cc_final: 0.7881 (p0) REVERT: D 597 ASP cc_start: 0.6446 (m-30) cc_final: 0.6038 (m-30) REVERT: A 581 THR cc_start: 0.7195 (OUTLIER) cc_final: 0.6566 (p) outliers start: 22 outliers final: 19 residues processed: 85 average time/residue: 0.0640 time to fit residues: 8.2536 Evaluate side-chains 88 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 55 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.0050 chunk 59 optimal weight: 0.0670 chunk 38 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 overall best weight: 0.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.151300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.140915 restraints weight = 23995.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135584 restraints weight = 25091.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.132549 restraints weight = 25098.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.134373 restraints weight = 19260.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.134386 restraints weight = 10532.192| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7121 Z= 0.106 Angle : 0.544 7.634 9696 Z= 0.277 Chirality : 0.042 0.281 1049 Planarity : 0.004 0.074 1236 Dihedral : 4.983 44.046 916 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.43 % Allowed : 15.25 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.69 (0.28), residues: 833 helix: 0.47 (0.28), residues: 372 sheet: 0.09 (0.56), residues: 69 loop : -1.48 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.009 0.001 TYR D 183 PHE 0.021 0.001 PHE D 314 TRP 0.018 0.001 TRP D 168 HIS 0.002 0.001 HIS D 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 7102) covalent geometry : angle 0.53552 / 0.28 ( 9653) SS BOND : bond 0.00136 / 0.09 ( 8) SS BOND : angle 0.74957 / 0.59 ( 16) hydrogen bonds : bond 0.03591 / 2.31 ( 277) hydrogen bonds : angle 3.98731 / 2.80 ( 777) metal coordination : bond 0.00062 / 0.03 ( 2) link_BETA1-4 : bond 0.00387 / 0.20 ( 1) link_BETA1-4 : angle 1.38793 / 0.76 ( 3) link_NAG-ASN : bond 0.00772 / 0.58 ( 8) link_NAG-ASN : angle 1.89234 / 1.37 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.41 seconds wall clock time: 24 minutes 41.70 seconds (1481.70 seconds total)