Starting phenix.real_space_refine on Tue Mar 3 16:19:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a91_11681/03_2026/7a91_11681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a91_11681/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2026/7a91_11681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2026/7a91_11681.map" model { file = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2026/7a91_11681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2026/7a91_11681.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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: 0.62 Conformation dependent library (CDL) restraints added in 393.8 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: 0.20 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: 0.84 Time building geometry restraints manager: 0.80 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: 3827 17.98 - 35.97: 366 35.97 - 53.95: 102 53.95 - 71.94: 13 71.94 - 89.92: 10 Dihedral angle restraints: 4318 sinusoidal: 1854 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 4315 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 15.419 89.919 2712 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 covalent geometry : bond 0.00634 ( 7102) covalent geometry : angle 0.79256 ( 9653) SS BOND : bond 0.00394 ( 8) SS BOND : angle 1.31975 ( 16) hydrogen bonds : bond 0.15567 ( 277) hydrogen bonds : angle 6.36562 ( 777) metal coordination : bond 0.00245 ( 2) link_BETA1-4 : bond 0.00052 ( 1) link_BETA1-4 : angle 1.64894 ( 3) link_NAG-ASN : bond 0.00460 ( 8) link_NAG-ASN : angle 3.05226 ( 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 : 0.225 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: 0.0686 time to fit residues: 9.9719 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 : 0.181 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3922 r_free = 0.3922 target = 0.177920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.160648 restraints weight = 16972.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160488 restraints weight = 34396.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.160021 restraints weight = 16277.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.159639 restraints weight = 13786.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.159967 restraints weight = 13058.734| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1225 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= 0.128 Angle : 0.632 7.427 9696 Z= 0.323 Chirality : 0.044 0.277 1049 Planarity : 0.005 0.093 1236 Dihedral : 7.984 55.772 1107 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.62 % Allowed : 8.77 % Favored : 89.61 % 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: -1.70 (0.27), residues: 833 helix: -0.61 (0.26), residues: 378 sheet: -0.19 (0.52), residues: 81 loop : -1.84 (0.28), residues: 374 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 0.009 0.001 PHE D 504 TRP 0.012 0.001 TRP D 459 HIS 0.003 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 7102) covalent geometry : angle 0.61720 ( 9653) SS BOND : bond 0.00266 ( 8) SS BOND : angle 1.33466 ( 16) hydrogen bonds : bond 0.04897 ( 277) hydrogen bonds : angle 4.65991 ( 777) metal coordination : bond 0.00058 ( 2) link_BETA1-4 : bond 0.00815 ( 1) link_BETA1-4 : angle 1.67565 ( 3) link_NAG-ASN : bond 0.00687 ( 8) link_NAG-ASN : angle 2.55448 ( 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 101 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 168 TRP cc_start: 0.8182 (t-100) cc_final: 0.7975 (t-100) REVERT: D 277 ASN cc_start: 0.8352 (m-40) cc_final: 0.7986 (m110) REVERT: D 350 ASP cc_start: 0.8058 (t0) cc_final: 0.7822 (p0) REVERT: D 597 ASP cc_start: 0.6269 (m-30) cc_final: 0.5983 (m-30) outliers start: 12 outliers final: 9 residues processed: 98 average time/residue: 0.0534 time to fit residues: 8.0327 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 : 0.171 ------------------------------------------------------------------------------- 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: 0.0980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.154972 restraints weight = 14895.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.145317 restraints weight = 29904.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.141081 restraints weight = 18970.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.141904 restraints weight = 15324.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.141872 restraints weight = 12687.973| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1489 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= 0.155 Angle : 0.622 7.344 9696 Z= 0.316 Chirality : 0.045 0.223 1049 Planarity : 0.005 0.090 1236 Dihedral : 7.493 56.013 1105 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.29 % Allowed : 10.80 % Favored : 86.91 % 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: -1.45 (0.27), residues: 833 helix: -0.31 (0.27), residues: 379 sheet: -0.16 (0.56), residues: 69 loop : -1.76 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 518 TYR 0.017 0.001 TYR D 183 PHE 0.010 0.001 PHE D 504 TRP 0.013 0.002 TRP D 594 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 7102) covalent geometry : angle 0.60868 ( 9653) SS BOND : bond 0.00284 ( 8) SS BOND : angle 1.21881 ( 16) hydrogen bonds : bond 0.04959 ( 277) hydrogen bonds : angle 4.45617 ( 777) metal coordination : bond 0.00148 ( 2) link_BETA1-4 : bond 0.00516 ( 1) link_BETA1-4 : angle 1.65965 ( 3) link_NAG-ASN : bond 0.00648 ( 8) link_NAG-ASN : angle 2.42758 ( 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 91 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 168 TRP cc_start: 0.8288 (t-100) cc_final: 0.8069 (t-100) REVERT: D 277 ASN cc_start: 0.8425 (m-40) cc_final: 0.7995 (m110) REVERT: D 350 ASP cc_start: 0.8063 (t0) cc_final: 0.7806 (p0) REVERT: D 597 ASP cc_start: 0.6465 (m-30) cc_final: 0.6132 (m-30) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.0537 time to fit residues: 7.1664 Evaluate side-chains 84 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.249 ------------------------------------------------------------------------------- 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 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 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 582 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: 0.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 0.0980 chunk 23 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 60 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.174508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.153516 restraints weight = 17006.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154141 restraints weight = 31304.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.154145 restraints weight = 17448.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.154423 restraints weight = 14331.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.154418 restraints weight = 11170.154| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3562 r_free = 0.3562 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7121 Z= 0.144 Angle : 0.598 6.808 9696 Z= 0.304 Chirality : 0.044 0.194 1049 Planarity : 0.005 0.088 1236 Dihedral : 7.105 55.188 1105 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.70 % Allowed : 11.34 % Favored : 85.96 % 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: -1.16 (0.27), residues: 833 helix: 0.01 (0.27), residues: 372 sheet: -0.19 (0.54), residues: 69 loop : -1.64 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 204 TYR 0.015 0.001 TYR D 183 PHE 0.010 0.001 PHE D 504 TRP 0.013 0.001 TRP D 477 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 7102) covalent geometry : angle 0.58466 ( 9653) SS BOND : bond 0.00188 ( 8) SS BOND : angle 1.04185 ( 16) hydrogen bonds : bond 0.04573 ( 277) hydrogen bonds : angle 4.32753 ( 777) metal coordination : bond 0.00109 ( 2) link_BETA1-4 : bond 0.00546 ( 1) link_BETA1-4 : angle 1.60841 ( 3) link_NAG-ASN : bond 0.00727 ( 8) link_NAG-ASN : angle 2.38728 ( 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 95 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8410 (m-40) cc_final: 0.7970 (m110) REVERT: D 350 ASP cc_start: 0.8114 (t0) cc_final: 0.7873 (p0) REVERT: D 597 ASP cc_start: 0.6369 (m-30) cc_final: 0.6034 (m-30) REVERT: A 581 THR cc_start: 0.7274 (OUTLIER) cc_final: 0.6716 (p) outliers start: 20 outliers final: 16 residues processed: 90 average time/residue: 0.0479 time to fit residues: 7.0135 Evaluate side-chains 88 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 376 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 23 optimal weight: 0.0050 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 75 optimal weight: 0.0870 chunk 60 optimal weight: 0.8980 chunk 36 optimal weight: 0.0170 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 overall best weight: 0.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS B 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 = 0.3867 r_free = 0.3867 target = 0.173233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.165146 restraints weight = 16318.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.154883 restraints weight = 29975.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.151086 restraints weight = 17357.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.151606 restraints weight = 14481.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.151925 restraints weight = 10883.969| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2321 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= 0.100 Angle : 0.537 6.813 9696 Z= 0.272 Chirality : 0.041 0.247 1049 Planarity : 0.004 0.081 1236 Dihedral : 6.325 55.231 1105 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.02 % Allowed : 13.09 % Favored : 84.89 % 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: -0.72 (0.28), residues: 833 helix: 0.46 (0.28), residues: 371 sheet: -0.02 (0.56), residues: 69 loop : -1.48 (0.28), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.008 0.001 TYR D 127 PHE 0.006 0.001 PHE D 504 TRP 0.017 0.001 TRP D 168 HIS 0.002 0.000 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 7102) covalent geometry : angle 0.52354 ( 9653) SS BOND : bond 0.00132 ( 8) SS BOND : angle 0.67919 ( 16) hydrogen bonds : bond 0.03175 ( 277) hydrogen bonds : angle 4.08487 ( 777) metal coordination : bond 0.00027 ( 2) link_BETA1-4 : bond 0.00585 ( 1) link_BETA1-4 : angle 1.55266 ( 3) link_NAG-ASN : bond 0.00695 ( 8) link_NAG-ASN : angle 2.37688 ( 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 110 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 123 MET cc_start: 0.7062 (mtt) cc_final: 0.6763 (mtt) REVERT: D 277 ASN cc_start: 0.8354 (m-40) cc_final: 0.8132 (m110) REVERT: D 597 ASP cc_start: 0.6380 (m-30) cc_final: 0.5988 (m-30) REVERT: A 581 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6479 (p) outliers start: 15 outliers final: 12 residues processed: 106 average time/residue: 0.0608 time to fit residues: 9.4366 Evaluate side-chains 91 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 432 ASN 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 358 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 6 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 25 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.0370 chunk 5 optimal weight: 0.2980 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.150967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.139223 restraints weight = 14307.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138728 restraints weight = 23202.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137865 restraints weight = 18116.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.137593 restraints weight = 12748.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.137823 restraints weight = 10716.379| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3438 r_free = 0.3438 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7121 Z= 0.121 Angle : 0.554 6.734 9696 Z= 0.284 Chirality : 0.043 0.228 1049 Planarity : 0.004 0.077 1236 Dihedral : 6.284 54.566 1105 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.70 % Allowed : 14.71 % 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: -0.75 (0.28), residues: 833 helix: 0.43 (0.27), residues: 377 sheet: -0.09 (0.55), residues: 71 loop : -1.51 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.011 0.001 TYR D 183 PHE 0.012 0.001 PHE D 315 TRP 0.019 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 7102) covalent geometry : angle 0.54061 ( 9653) SS BOND : bond 0.00151 ( 8) SS BOND : angle 0.85926 ( 16) hydrogen bonds : bond 0.03827 ( 277) hydrogen bonds : angle 4.00482 ( 777) metal coordination : bond 0.00121 ( 2) link_BETA1-4 : bond 0.00395 ( 1) link_BETA1-4 : angle 1.57000 ( 3) link_NAG-ASN : bond 0.00605 ( 8) link_NAG-ASN : angle 2.40300 ( 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 101 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8379 (m-40) cc_final: 0.8101 (m110) REVERT: D 597 ASP cc_start: 0.6356 (m-30) cc_final: 0.5965 (m-30) REVERT: A 581 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6661 (p) outliers start: 20 outliers final: 17 residues processed: 95 average time/residue: 0.0490 time to fit residues: 7.2665 Evaluate side-chains 92 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 SER 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 299 ASP Chi-restraints excluded: chain D residue 432 ASN 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 376 THR 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: 2.9990 chunk 26 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 41 optimal weight: 0.1980 chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 34 HIS B A 334 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.147098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136388 restraints weight = 19040.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.131976 restraints weight = 24358.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.129061 restraints weight = 20007.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.130215 restraints weight = 17465.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.130157 restraints weight = 10221.836| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3563 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3563 r_free = 0.3563 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3563 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7121 Z= 0.169 Angle : 0.610 6.693 9696 Z= 0.312 Chirality : 0.045 0.209 1049 Planarity : 0.005 0.075 1236 Dihedral : 6.504 54.899 1105 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 15.38 % Favored : 81.78 % 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: -0.87 (0.28), residues: 833 helix: 0.28 (0.27), residues: 373 sheet: -0.14 (0.54), residues: 71 loop : -1.50 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 204 TYR 0.017 0.001 TYR D 183 PHE 0.011 0.002 PHE D 315 TRP 0.019 0.002 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 7102) covalent geometry : angle 0.59985 ( 9653) SS BOND : bond 0.00204 ( 8) SS BOND : angle 0.96553 ( 16) hydrogen bonds : bond 0.04581 ( 277) hydrogen bonds : angle 4.15186 ( 777) metal coordination : bond 0.00164 ( 2) link_BETA1-4 : bond 0.00317 ( 1) link_BETA1-4 : angle 1.60881 ( 3) link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 2.13419 ( 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 95 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8409 (m-40) cc_final: 0.8034 (m110) REVERT: D 597 ASP cc_start: 0.6471 (m-30) cc_final: 0.6080 (m-30) REVERT: A 581 THR cc_start: 0.7147 (OUTLIER) cc_final: 0.6631 (p) outliers start: 21 outliers final: 18 residues processed: 88 average time/residue: 0.0527 time to fit residues: 7.1105 Evaluate side-chains 89 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 SER 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 299 ASP Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 544 ILE 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 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: 0.6980 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 80 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.146015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135529 restraints weight = 20460.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.132089 restraints weight = 22975.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.129944 restraints weight = 22493.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.130990 restraints weight = 16526.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.130510 restraints weight = 10147.036| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2238 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= 0.177 Angle : 0.616 7.069 9696 Z= 0.315 Chirality : 0.045 0.216 1049 Planarity : 0.005 0.074 1236 Dihedral : 6.613 54.856 1105 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.10 % Allowed : 15.52 % Favored : 81.38 % 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: -1.01 (0.28), residues: 833 helix: 0.16 (0.27), residues: 372 sheet: -0.15 (0.55), residues: 71 loop : -1.59 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 204 TYR 0.019 0.001 TYR D 183 PHE 0.012 0.002 PHE D 230 TRP 0.020 0.002 TRP D 168 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00424 ( 7102) covalent geometry : angle 0.60667 ( 9653) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.98033 ( 16) hydrogen bonds : bond 0.04741 ( 277) hydrogen bonds : angle 4.22482 ( 777) metal coordination : bond 0.00166 ( 2) link_BETA1-4 : bond 0.00485 ( 1) link_BETA1-4 : angle 1.61446 ( 3) link_NAG-ASN : bond 0.00460 ( 8) link_NAG-ASN : angle 2.13292 ( 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 96 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8487 (m-40) cc_final: 0.8038 (m110) REVERT: D 597 ASP cc_start: 0.6477 (m-30) cc_final: 0.6079 (m-30) REVERT: A 581 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.6802 (p) outliers start: 23 outliers final: 19 residues processed: 88 average time/residue: 0.0561 time to fit residues: 7.4429 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 SER 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 299 ASP Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 544 ILE 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 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: 0.4980 chunk 70 optimal weight: 0.0980 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.0010 chunk 4 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 77 optimal weight: 0.8980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.139224 restraints weight = 16327.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.132055 restraints weight = 24792.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.129747 restraints weight = 14875.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.130268 restraints weight = 13517.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.130884 restraints weight = 9711.615| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2458 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= 0.119 Angle : 0.554 6.959 9696 Z= 0.285 Chirality : 0.042 0.222 1049 Planarity : 0.004 0.072 1236 Dihedral : 6.376 54.880 1105 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.56 % Allowed : 15.92 % Favored : 81.51 % 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: -0.81 (0.28), residues: 833 helix: 0.36 (0.27), residues: 372 sheet: -0.16 (0.54), residues: 71 loop : -1.50 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.012 0.001 TYR D 183 PHE 0.010 0.001 PHE D 315 TRP 0.018 0.001 TRP D 168 HIS 0.003 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7102) covalent geometry : angle 0.54458 ( 9653) SS BOND : bond 0.00140 ( 8) SS BOND : angle 0.82217 ( 16) hydrogen bonds : bond 0.03832 ( 277) hydrogen bonds : angle 4.05286 ( 777) metal coordination : bond 0.00080 ( 2) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 1.57915 ( 3) link_NAG-ASN : bond 0.01022 ( 8) link_NAG-ASN : angle 1.94718 ( 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 90 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8369 (m-40) cc_final: 0.8018 (m110) REVERT: D 597 ASP cc_start: 0.6369 (m-30) cc_final: 0.5995 (m-30) REVERT: A 581 THR cc_start: 0.7185 (OUTLIER) cc_final: 0.6595 (p) outliers start: 19 outliers final: 17 residues processed: 84 average time/residue: 0.0568 time to fit residues: 7.2711 Evaluate side-chains 88 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 SER 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 299 ASP Chi-restraints excluded: chain D residue 514 ARG 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 376 THR 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: 0.0770 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 70 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.0170 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.151044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.139984 restraints weight = 16504.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.133402 restraints weight = 25960.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.131369 restraints weight = 14857.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.131798 restraints weight = 11976.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.132100 restraints weight = 8954.876| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2601 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= 0.111 Angle : 0.540 6.964 9696 Z= 0.278 Chirality : 0.042 0.247 1049 Planarity : 0.004 0.070 1236 Dihedral : 6.219 54.594 1105 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.43 % Allowed : 16.60 % Favored : 80.97 % 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: -0.71 (0.28), residues: 833 helix: 0.46 (0.27), residues: 372 sheet: -0.06 (0.55), residues: 71 loop : -1.46 (0.29), 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 183 PHE 0.009 0.001 PHE D 315 TRP 0.025 0.001 TRP D 168 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 7102) covalent geometry : angle 0.53178 ( 9653) SS BOND : bond 0.00144 ( 8) SS BOND : angle 0.78740 ( 16) hydrogen bonds : bond 0.03725 ( 277) hydrogen bonds : angle 3.97935 ( 777) metal coordination : bond 0.00081 ( 2) link_BETA1-4 : bond 0.00416 ( 1) link_BETA1-4 : angle 1.55468 ( 3) link_NAG-ASN : bond 0.00726 ( 8) link_NAG-ASN : angle 1.87663 ( 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 88 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8429 (m-40) cc_final: 0.8126 (m110) REVERT: D 597 ASP cc_start: 0.6416 (m-30) cc_final: 0.6024 (m-30) REVERT: A 581 THR cc_start: 0.7088 (OUTLIER) cc_final: 0.6495 (p) outliers start: 18 outliers final: 16 residues processed: 82 average time/residue: 0.0480 time to fit residues: 6.3090 Evaluate side-chains 85 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 218 SER 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 299 ASP 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 376 THR 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: 0.7980 chunk 56 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 59 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 0.1980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.149178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.138824 restraints weight = 24274.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.133983 restraints weight = 25451.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.130976 restraints weight = 22701.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.132490 restraints weight = 17762.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.132413 restraints weight = 9578.766| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2577 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= 0.129 Angle : 0.558 6.869 9696 Z= 0.286 Chirality : 0.043 0.217 1049 Planarity : 0.004 0.071 1236 Dihedral : 6.274 54.595 1105 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.70 % Allowed : 15.92 % Favored : 81.38 % 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: -0.73 (0.28), residues: 833 helix: 0.44 (0.27), residues: 372 sheet: -0.09 (0.55), residues: 71 loop : -1.48 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 204 TYR 0.013 0.001 TYR D 183 PHE 0.009 0.001 PHE D 315 TRP 0.031 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7102) covalent geometry : angle 0.54883 ( 9653) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.83749 ( 16) hydrogen bonds : bond 0.04004 ( 277) hydrogen bonds : angle 4.01881 ( 777) metal coordination : bond 0.00104 ( 2) link_BETA1-4 : bond 0.00487 ( 1) link_BETA1-4 : angle 1.55261 ( 3) link_NAG-ASN : bond 0.00590 ( 8) link_NAG-ASN : angle 1.92848 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.08 seconds wall clock time: 22 minutes 14.52 seconds (1334.52 seconds total)