Starting phenix.real_space_refine on Wed Mar 12 01:29:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7a91_11681/03_2025/7a91_11681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a91_11681/03_2025/7a91_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_2025/7a91_11681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2025/7a91_11681.map" model { file = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2025/7a91_11681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a91_11681/03_2025/7a91_11681.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 7.40, per 1000 atoms: 1.07 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: 1.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.78 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: 1.79 Time building geometry restraints manager: 2.02 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: 4.310 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.990 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.920 ------------------------------------------------------------------------------- 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 7102 Z= 0.403 Angle : 0.793 9.714 9653 Z= 0.426 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (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 TRP 0.036 0.003 TRP D 594 HIS 0.007 0.002 HIS D 241 PHE 0.024 0.002 PHE A 543 TYR 0.018 0.002 TYR A 421 ARG 0.010 0.001 ARG D 245 *********************** 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 : 0.754 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: 0.6107 (m-30) outliers start: 6 outliers final: 4 residues processed: 104 average time/residue: 0.1741 time to fit residues: 25.3192 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 : 0.775 ------------------------------------------------------------------------------- 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 70 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 42 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 0.0770 chunk 75 optimal weight: 0.9980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 24 GLN D 287 GLN A 334 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.149556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.138010 restraints weight = 15895.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.132795 restraints weight = 23337.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.130513 restraints weight = 14213.823| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7102 Z= 0.192 Angle : 0.625 7.335 9653 Z= 0.323 Chirality : 0.045 0.273 1049 Planarity : 0.005 0.093 1236 Dihedral : 8.019 55.907 1107 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.62 % Allowed : 9.04 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.27), residues: 833 helix: -0.63 (0.26), residues: 375 sheet: -0.13 (0.52), residues: 80 loop : -1.90 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 594 HIS 0.003 0.001 HIS D 535 PHE 0.009 0.001 PHE D 525 TYR 0.015 0.001 TYR D 183 ARG 0.004 0.000 ARG D 518 *********************** 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 97 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 168 TRP cc_start: 0.8229 (t-100) cc_final: 0.7990 (t-100) REVERT: D 277 ASN cc_start: 0.8535 (m-40) cc_final: 0.8114 (m110) REVERT: D 350 ASP cc_start: 0.8063 (t0) cc_final: 0.7784 (p0) REVERT: D 597 ASP cc_start: 0.6339 (m-30) cc_final: 0.6062 (m-30) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 0.1291 time to fit residues: 18.5827 Evaluate side-chains 83 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.0170 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 24 optimal weight: 0.0000 chunk 61 optimal weight: 0.0870 chunk 73 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.2800 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.150026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.138375 restraints weight = 15446.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.133757 restraints weight = 24654.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.131054 restraints weight = 15340.455| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7102 Z= 0.180 Angle : 0.577 7.243 9653 Z= 0.297 Chirality : 0.043 0.221 1049 Planarity : 0.005 0.090 1236 Dihedral : 7.313 54.991 1105 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.16 % Allowed : 11.07 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.27), residues: 833 helix: -0.18 (0.27), residues: 374 sheet: -0.04 (0.52), residues: 79 loop : -1.70 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.003 0.001 HIS D 241 PHE 0.009 0.001 PHE D 504 TYR 0.013 0.001 TYR D 183 ARG 0.005 0.000 ARG D 204 *********************** 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: 16 poor density : 75 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8419 (m-40) cc_final: 0.8061 (m110) REVERT: D 350 ASP cc_start: 0.8135 (t0) cc_final: 0.7896 (p0) REVERT: D 597 ASP cc_start: 0.6342 (m-30) cc_final: 0.5996 (m-30) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1331 time to fit residues: 17.7907 Evaluate side-chains 85 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 77 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3540 r_free = 0.3540 target = 0.146474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.134573 restraints weight = 13479.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.130686 restraints weight = 22149.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.127999 restraints weight = 16262.938| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7102 Z= 0.272 Angle : 0.622 6.972 9653 Z= 0.320 Chirality : 0.045 0.203 1049 Planarity : 0.005 0.086 1236 Dihedral : 7.265 55.360 1105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.43 % Allowed : 11.74 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), residues: 833 helix: -0.14 (0.27), residues: 376 sheet: -0.18 (0.54), residues: 69 loop : -1.73 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.005 0.001 HIS D 374 PHE 0.011 0.002 PHE D 504 TYR 0.019 0.001 TYR D 183 ARG 0.005 0.001 ARG D 204 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1666 Ramachandran restraints generated. 833 Oldfield, 0 Emsley, 833 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 187 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7981 (mmtt) REVERT: D 277 ASN cc_start: 0.8346 (m-40) cc_final: 0.7893 (m110) REVERT: D 350 ASP cc_start: 0.8110 (t0) cc_final: 0.7891 (p0) REVERT: D 597 ASP cc_start: 0.6445 (m-30) cc_final: 0.6098 (m-30) REVERT: A 581 THR cc_start: 0.7296 (OUTLIER) cc_final: 0.6681 (p) outliers start: 18 outliers final: 14 residues processed: 94 average time/residue: 0.1537 time to fit residues: 21.1301 Evaluate side-chains 84 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.755 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 44 optimal weight: 0.0870 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.174255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.162971 restraints weight = 15951.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.155542 restraints weight = 31111.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.152578 restraints weight = 17077.987| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7102 Z= 0.183 Angle : 0.562 6.813 9653 Z= 0.290 Chirality : 0.043 0.232 1049 Planarity : 0.005 0.087 1236 Dihedral : 6.823 55.080 1105 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.97 % Allowed : 12.55 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.28), residues: 833 helix: 0.10 (0.27), residues: 372 sheet: -0.17 (0.55), residues: 69 loop : -1.60 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 168 HIS 0.003 0.001 HIS D 265 PHE 0.013 0.001 PHE D 315 TYR 0.013 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 *********************** 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 99 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8388 (m-40) cc_final: 0.8031 (m110) REVERT: D 350 ASP cc_start: 0.8053 (t0) cc_final: 0.7841 (p0) REVERT: D 597 ASP cc_start: 0.6359 (m-30) cc_final: 0.5972 (m-30) REVERT: A 581 THR cc_start: 0.7198 (OUTLIER) cc_final: 0.6575 (p) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 0.1342 time to fit residues: 18.8440 Evaluate side-chains 87 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 0.8980 chunk 61 optimal weight: 0.0050 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.176761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.150062 restraints weight = 16206.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.150238 restraints weight = 21180.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.151546 restraints weight = 19482.783| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7102 Z= 0.241 Angle : 0.586 6.693 9653 Z= 0.302 Chirality : 0.045 0.221 1049 Planarity : 0.005 0.088 1236 Dihedral : 6.776 54.918 1105 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.83 % Allowed : 13.09 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.27), residues: 833 helix: 0.08 (0.27), residues: 369 sheet: -0.07 (0.55), residues: 70 loop : -1.62 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 168 HIS 0.004 0.001 HIS D 374 PHE 0.028 0.002 PHE D 314 TYR 0.017 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 *********************** 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 97 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 187 LYS cc_start: 0.8123 (mmtt) cc_final: 0.7879 (mmtp) REVERT: D 277 ASN cc_start: 0.8372 (m-40) cc_final: 0.7930 (m110) REVERT: D 350 ASP cc_start: 0.8135 (t0) cc_final: 0.7914 (p0) REVERT: D 597 ASP cc_start: 0.6503 (m-30) cc_final: 0.6118 (m-30) REVERT: A 581 THR cc_start: 0.7160 (OUTLIER) cc_final: 0.6456 (p) outliers start: 21 outliers final: 17 residues processed: 91 average time/residue: 0.1456 time to fit residues: 19.5778 Evaluate side-chains 89 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135497 restraints weight = 17611.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.132120 restraints weight = 26240.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.128670 restraints weight = 14629.112| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7102 Z= 0.186 Angle : 0.554 6.827 9653 Z= 0.286 Chirality : 0.043 0.223 1049 Planarity : 0.004 0.081 1236 Dihedral : 6.549 54.865 1105 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.10 % Allowed : 13.23 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.28), residues: 833 helix: 0.23 (0.27), residues: 372 sheet: -0.04 (0.56), residues: 70 loop : -1.58 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.030 0.001 PHE D 314 TYR 0.012 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 *********************** 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 98 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8525 (m-40) cc_final: 0.8163 (m110) REVERT: D 350 ASP cc_start: 0.8091 (t0) cc_final: 0.7882 (p0) REVERT: D 597 ASP cc_start: 0.6415 (m-30) cc_final: 0.6021 (m-30) REVERT: A 581 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6578 (p) outliers start: 23 outliers final: 18 residues processed: 89 average time/residue: 0.1485 time to fit residues: 19.2876 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 : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 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 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 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.0670 chunk 54 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.178183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.156265 restraints weight = 11995.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.156112 restraints weight = 17084.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.156089 restraints weight = 15246.484| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3266 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3266 r_free = 0.3266 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3266 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7102 Z= 0.204 Angle : 0.568 6.828 9653 Z= 0.293 Chirality : 0.044 0.239 1049 Planarity : 0.004 0.079 1236 Dihedral : 6.505 54.669 1105 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.83 % Allowed : 14.04 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 833 helix: 0.26 (0.27), residues: 369 sheet: -0.02 (0.56), residues: 70 loop : -1.59 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 168 HIS 0.004 0.001 HIS D 374 PHE 0.026 0.001 PHE D 314 TYR 0.014 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 *********************** 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 93 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 72 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8338 (m-40) cc_final: 0.7985 (m110) REVERT: D 350 ASP cc_start: 0.8081 (t0) cc_final: 0.7874 (p0) REVERT: D 597 ASP cc_start: 0.6366 (m-30) cc_final: 0.6004 (m-30) REVERT: A 581 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6563 (p) outliers start: 21 outliers final: 19 residues processed: 85 average time/residue: 0.1372 time to fit residues: 17.5635 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 : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 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 72 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 20 optimal weight: 0.0060 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.176354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.148281 restraints weight = 23652.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.152103 restraints weight = 29015.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.151293 restraints weight = 21349.027| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7102 Z= 0.242 Angle : 0.589 6.770 9653 Z= 0.303 Chirality : 0.045 0.259 1049 Planarity : 0.004 0.078 1236 Dihedral : 6.589 54.709 1105 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.83 % Allowed : 14.04 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.28), residues: 833 helix: 0.19 (0.27), residues: 369 sheet: 0.01 (0.56), residues: 69 loop : -1.62 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.004 0.001 HIS D 374 PHE 0.024 0.002 PHE D 314 TYR 0.017 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 *********************** 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 95 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8466 (m-40) cc_final: 0.8030 (m110) REVERT: D 350 ASP cc_start: 0.8215 (t0) cc_final: 0.7985 (p0) REVERT: D 597 ASP cc_start: 0.6479 (m-30) cc_final: 0.6081 (m-30) REVERT: A 581 THR cc_start: 0.7228 (OUTLIER) cc_final: 0.6612 (p) outliers start: 21 outliers final: 19 residues processed: 86 average time/residue: 0.1421 time to fit residues: 18.6230 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 : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 80 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 43 optimal weight: 0.4980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.149508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.137250 restraints weight = 13708.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.136911 restraints weight = 21282.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.136301 restraints weight = 18133.944| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7102 Z= 0.170 Angle : 0.547 6.992 9653 Z= 0.282 Chirality : 0.043 0.239 1049 Planarity : 0.004 0.077 1236 Dihedral : 6.394 54.733 1105 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.56 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.28), residues: 833 helix: 0.35 (0.27), residues: 372 sheet: -0.02 (0.56), residues: 70 loop : -1.52 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 168 HIS 0.003 0.001 HIS D 265 PHE 0.025 0.001 PHE D 314 TYR 0.012 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 ********************** 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 91 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 277 ASN cc_start: 0.8392 (m-40) cc_final: 0.8084 (m110) REVERT: D 597 ASP cc_start: 0.6354 (m-30) cc_final: 0.5984 (m-30) REVERT: A 581 THR cc_start: 0.7132 (OUTLIER) cc_final: 0.6664 (p) outliers start: 19 outliers final: 18 residues processed: 83 average time/residue: 0.1345 time to fit residues: 17.0952 Evaluate side-chains 92 residues out of total 737 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 514 ARG Chi-restraints excluded: chain D residue 540 HIS Chi-restraints excluded: chain D residue 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 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 68 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.0970 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 36 optimal weight: 0.0270 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.177065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.154514 restraints weight = 17013.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.152350 restraints weight = 19495.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.152937 restraints weight = 17279.231| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7102 Z= 0.249 Angle : 0.586 6.789 9653 Z= 0.303 Chirality : 0.045 0.218 1049 Planarity : 0.005 0.078 1236 Dihedral : 6.521 54.566 1105 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.56 % Allowed : 14.98 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.28), residues: 833 helix: 0.25 (0.27), residues: 369 sheet: -0.03 (0.55), residues: 72 loop : -1.55 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 168 HIS 0.004 0.001 HIS D 374 PHE 0.023 0.002 PHE D 314 TYR 0.017 0.001 TYR D 183 ARG 0.004 0.000 ARG D 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2571.35 seconds wall clock time: 45 minutes 8.89 seconds (2708.89 seconds total)