Starting phenix.real_space_refine on Tue Jul 7 04:19:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxk_47290/07_2026/9dxk_47290.map" } resolution = 4.81 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= 0.016 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 216 5.49 5 S 76 5.16 5 C 13096 2.51 5 N 3790 2.21 5 O 4664 1.98 5 H 20174 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42020 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 8782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8782 Classifications: {'peptide': 535} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "C" Number of atoms: 8782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8782 Classifications: {'peptide': 535} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "I" Number of atoms: 8782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8782 Classifications: {'peptide': 535} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "K" Number of atoms: 8782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 8782 Classifications: {'peptide': 535} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 17, 'TRANS': 517} Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 895 Classifications: {'DNA': 28} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 27} Chain: "F" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 859 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 831 Classifications: {'DNA': 26} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 795 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "M" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 895 Classifications: {'DNA': 28} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 27} Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 859 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "O" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 895 Classifications: {'DNA': 28} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 27} Chain: "P" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 859 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5240 SG CYS A 320 35.240 45.766 38.685 1.00779.26 S ATOM 5284 SG CYS A 323 37.855 46.895 40.962 1.00732.29 S ATOM 5772 SG CYS A 353 38.899 44.716 38.188 1.00734.92 S ATOM 5863 SG CYS A 358 36.837 43.303 41.122 1.00738.86 S ATOM 14022 SG CYS C 320 105.581 41.562 80.896 1.00897.09 S ATOM 14066 SG CYS C 323 102.827 43.330 79.340 1.00861.45 S ATOM 14554 SG CYS C 353 101.966 40.799 81.946 1.00855.73 S ATOM 14645 SG CYS C 358 103.276 39.638 78.552 1.00858.00 S ATOM 22804 SG CYS I 320 107.919 148.911 39.711 1.00647.10 S ATOM 22848 SG CYS I 323 105.336 147.367 41.890 1.00604.15 S ATOM 23336 SG CYS I 353 104.195 149.544 39.257 1.00613.28 S ATOM 23427 SG CYS I 358 106.042 151.184 42.114 1.00619.43 S ATOM 31586 SG CYS K 320 39.500 152.613 81.943 1.00943.09 S ATOM 31630 SG CYS K 323 42.172 150.686 80.394 1.00905.83 S ATOM 32118 SG CYS K 353 43.152 153.363 82.817 1.00908.96 S ATOM 32209 SG CYS K 358 41.748 154.432 79.523 1.00905.49 S Time building chain proxies: 7.47, per 1000 atoms: 0.18 Number of scatterers: 42020 At special positions: 0 Unit cell: (143.775, 197.025, 126.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 76 16.00 P 216 15.00 O 4664 8.00 N 3790 7.00 C 13096 6.00 H 20174 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.72 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 320 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 353 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 358 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 323 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 320 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 353 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 358 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 323 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 320 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 353 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 358 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 323 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 320 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 358 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 353 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 323 " Number of angles added : 24 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 55.0% alpha, 11.2% beta 96 base pairs and 186 stacking pairs defined. Time for finding SS restraints: 8.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 Processing helix chain 'A' and resid 22 through 33 removed outlier: 3.733A pdb=" N ARG A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 52 removed outlier: 3.541A pdb=" N GLU A 39 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 69 Processing helix chain 'A' and resid 70 through 82 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.658A pdb=" N LEU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 129 through 164 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.048A pdb=" N TYR A 248 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 Processing helix chain 'A' and resid 363 through 379 removed outlier: 3.917A pdb=" N ASP A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 392 Processing helix chain 'A' and resid 399 through 433 removed outlier: 7.343A pdb=" N THR A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LYS A 406 " --> pdb=" O ASN A 402 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 466 removed outlier: 3.848A pdb=" N GLU A 461 " --> pdb=" O ASN A 457 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LEU A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 464 " --> pdb=" O ASN A 460 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 474 removed outlier: 4.635A pdb=" N SER A 474 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 Processing helix chain 'A' and resid 493 through 504 Processing helix chain 'C' and resid 3 through 8 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 35 through 52 Processing helix chain 'C' and resid 70 through 82 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.696A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 Processing helix chain 'C' and resid 129 through 164 Processing helix chain 'C' and resid 188 through 205 Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 235 through 244 Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.607A pdb=" N TYR C 248 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 299 Processing helix chain 'C' and resid 363 through 380 removed outlier: 4.416A pdb=" N ASP C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 405 through 433 removed outlier: 3.986A pdb=" N MET C 409 " --> pdb=" O THR C 405 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS C 412 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 465 removed outlier: 4.141A pdb=" N LEU C 462 " --> pdb=" O ALA C 458 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASN C 463 " --> pdb=" O LYS C 459 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 491 removed outlier: 3.737A pdb=" N ARG C 478 " --> pdb=" O SER C 474 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 482 " --> pdb=" O ARG C 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 504 Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 23 through 32 removed outlier: 3.857A pdb=" N GLU I 27 " --> pdb=" O ARG I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 52 removed outlier: 3.519A pdb=" N GLU I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 69 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 92 through 97 removed outlier: 3.572A pdb=" N LEU I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 97 " --> pdb=" O ILE I 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 92 through 97' Processing helix chain 'I' and resid 101 through 115 Processing helix chain 'I' and resid 129 through 164 Processing helix chain 'I' and resid 188 through 205 Processing helix chain 'I' and resid 212 through 224 Processing helix chain 'I' and resid 235 through 244 Processing helix chain 'I' and resid 245 through 250 removed outlier: 3.880A pdb=" N TYR I 248 " --> pdb=" O ASN I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 299 Processing helix chain 'I' and resid 362 through 377 removed outlier: 3.526A pdb=" N LEU I 377 " --> pdb=" O TYR I 373 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 396 Processing helix chain 'I' and resid 396 through 401 Processing helix chain 'I' and resid 403 through 433 Processing helix chain 'I' and resid 437 through 464 Processing helix chain 'I' and resid 475 through 491 Processing helix chain 'I' and resid 493 through 504 Processing helix chain 'K' and resid 2 through 8 Processing helix chain 'K' and resid 22 through 33 Processing helix chain 'K' and resid 35 through 52 Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 92 through 97 removed outlier: 3.822A pdb=" N LEU K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER K 97 " --> pdb=" O ILE K 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 92 through 97' Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 129 through 164 Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 212 through 224 Processing helix chain 'K' and resid 235 through 244 Processing helix chain 'K' and resid 245 through 250 removed outlier: 3.622A pdb=" N TYR K 248 " --> pdb=" O ASN K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 299 Processing helix chain 'K' and resid 362 through 380 removed outlier: 3.987A pdb=" N ASN K 378 " --> pdb=" O LEU K 374 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP K 379 " --> pdb=" O SER K 375 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 380 " --> pdb=" O SER K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 397 Processing helix chain 'K' and resid 409 through 433 Processing helix chain 'K' and resid 437 through 465 removed outlier: 4.103A pdb=" N ASN K 463 " --> pdb=" O LYS K 459 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 491 Processing helix chain 'K' and resid 493 through 504 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 6.366A pdb=" N ILE A 15 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LYS A 58 " --> pdb=" O ILE A 15 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLY A 17 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU A 16 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 176 through 179 Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 254 Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 259 Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 320 Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 337 removed outlier: 3.766A pdb=" N SER A 328 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 352 " --> pdb=" O SER A 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AA8, first strand: chain 'C' and resid 176 through 179 Processing sheet with id=AA9, first strand: chain 'C' and resid 252 through 254 Processing sheet with id=AB1, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AB2, first strand: chain 'C' and resid 328 through 337 Processing sheet with id=AB3, first strand: chain 'I' and resid 55 through 59 Processing sheet with id=AB4, first strand: chain 'I' and resid 176 through 179 Processing sheet with id=AB5, first strand: chain 'I' and resid 252 through 254 Processing sheet with id=AB6, first strand: chain 'I' and resid 257 through 259 Processing sheet with id=AB7, first strand: chain 'I' and resid 319 through 320 removed outlier: 6.413A pdb=" N THR I 319 " --> pdb=" O VAL I 510 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N MET I 512 " --> pdb=" O THR I 319 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN I 523 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 328 through 337 Processing sheet with id=AB9, first strand: chain 'K' and resid 55 through 59 removed outlier: 3.532A pdb=" N ILE K 118 " --> pdb=" O TYR K 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 176 through 179 Processing sheet with id=AC2, first strand: chain 'K' and resid 252 through 254 Processing sheet with id=AC3, first strand: chain 'K' and resid 257 through 259 Processing sheet with id=AC4, first strand: chain 'K' and resid 318 through 320 Processing sheet with id=AC5, first strand: chain 'K' and resid 328 through 337 991 hydrogen bonds defined for protein. 2880 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 220 hydrogen bonds 440 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 186 stacking parallelities Total time for adding SS restraints: 10.23 Time building geometry restraints manager: 6.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9750 1.04 - 1.23: 12033 1.23 - 1.43: 10305 1.43 - 1.63: 10594 1.63 - 1.83: 128 Bond restraints: 42810 Sorted by residual: bond pdb=" CE1 HIS A 219 " pdb=" NE2 HIS A 219 " ideal model delta sigma weight residual 1.321 1.232 0.089 1.00e-02 1.00e+04 7.85e+01 bond pdb=" CE1 HIS A 280 " pdb=" NE2 HIS A 280 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.83e+01 bond pdb=" CE1 HIS C 219 " pdb=" NE2 HIS C 219 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.82e+01 bond pdb=" CE1 HIS K 280 " pdb=" NE2 HIS K 280 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.81e+01 bond pdb=" CE1 HIS C 280 " pdb=" NE2 HIS C 280 " ideal model delta sigma weight residual 1.321 1.233 0.088 1.00e-02 1.00e+04 7.78e+01 ... (remaining 42805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 76588 7.57 - 15.15: 1106 15.15 - 22.72: 2 22.72 - 30.29: 0 30.29 - 37.86: 12 Bond angle restraints: 77708 Sorted by residual: angle pdb=" O5' DA N 2 " pdb=" C5' DA N 2 " pdb=" C4' DA N 2 " ideal model delta sigma weight residual 109.40 119.91 -10.51 8.00e-01 1.56e+00 1.73e+02 angle pdb=" CB ALA A 217 " pdb=" CA ALA A 217 " pdb=" HA ALA A 217 " ideal model delta sigma weight residual 109.00 71.14 37.86 3.00e+00 1.11e-01 1.59e+02 angle pdb=" CB ALA I 217 " pdb=" CA ALA I 217 " pdb=" HA ALA I 217 " ideal model delta sigma weight residual 109.00 71.25 37.75 3.00e+00 1.11e-01 1.58e+02 angle pdb=" CB ALA C 217 " pdb=" CA ALA C 217 " pdb=" HA ALA C 217 " ideal model delta sigma weight residual 109.00 71.31 37.69 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C LYS C 271 " pdb=" CA LYS C 271 " pdb=" HA LYS C 271 " ideal model delta sigma weight residual 109.00 71.68 37.32 3.00e+00 1.11e-01 1.55e+02 ... (remaining 77703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 17928 35.88 - 71.76: 1266 71.76 - 107.65: 31 107.65 - 143.53: 3 143.53 - 179.41: 28 Dihedral angle restraints: 19256 sinusoidal: 12104 harmonic: 7152 Sorted by residual: dihedral pdb=" CA ARG K 98 " pdb=" C ARG K 98 " pdb=" N GLY K 99 " pdb=" CA GLY K 99 " ideal model delta harmonic sigma weight residual -180.00 -143.80 -36.20 0 5.00e+00 4.00e-02 5.24e+01 dihedral pdb=" CA ASN C 381 " pdb=" C ASN C 381 " pdb=" N ASP C 382 " pdb=" CA ASP C 382 " ideal model delta harmonic sigma weight residual -180.00 -146.13 -33.87 0 5.00e+00 4.00e-02 4.59e+01 dihedral pdb=" CA ARG C 98 " pdb=" C ARG C 98 " pdb=" N GLY C 99 " pdb=" CA GLY C 99 " ideal model delta harmonic sigma weight residual -180.00 -146.99 -33.01 0 5.00e+00 4.00e-02 4.36e+01 ... (remaining 19253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2176 0.151 - 0.301: 185 0.301 - 0.451: 228 0.451 - 0.602: 683 0.602 - 0.752: 216 Chirality restraints: 3488 Sorted by residual: chirality pdb=" CG LEU C 48 " pdb=" CB LEU C 48 " pdb=" CD1 LEU C 48 " pdb=" CD2 LEU C 48 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" CG LEU K 48 " pdb=" CB LEU K 48 " pdb=" CD1 LEU K 48 " pdb=" CD2 LEU K 48 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CB ILE C 119 " pdb=" CA ILE C 119 " pdb=" CG1 ILE C 119 " pdb=" CG2 ILE C 119 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 3485 not shown) Planarity restraints: 5482 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT M -2 " -0.383 2.00e-02 2.50e+03 1.69e-01 8.58e+02 pdb=" N1 DT M -2 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT M -2 " 0.060 2.00e-02 2.50e+03 pdb=" O2 DT M -2 " 0.124 2.00e-02 2.50e+03 pdb=" N3 DT M -2 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DT M -2 " -0.075 2.00e-02 2.50e+03 pdb=" O4 DT M -2 " -0.323 2.00e-02 2.50e+03 pdb=" C5 DT M -2 " 0.075 2.00e-02 2.50e+03 pdb=" C7 DT M -2 " 0.070 2.00e-02 2.50e+03 pdb=" C6 DT M -2 " 0.106 2.00e-02 2.50e+03 pdb=" H3 DT M -2 " 0.163 2.00e-02 2.50e+03 pdb=" H6 DT M -2 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG P 15 " -0.000 2.00e-02 2.50e+03 1.46e-01 7.44e+02 pdb=" N9 DG P 15 " -0.088 2.00e-02 2.50e+03 pdb=" C8 DG P 15 " 0.085 2.00e-02 2.50e+03 pdb=" N7 DG P 15 " 0.046 2.00e-02 2.50e+03 pdb=" C5 DG P 15 " -0.095 2.00e-02 2.50e+03 pdb=" C6 DG P 15 " -0.118 2.00e-02 2.50e+03 pdb=" O6 DG P 15 " -0.120 2.00e-02 2.50e+03 pdb=" N1 DG P 15 " 0.020 2.00e-02 2.50e+03 pdb=" C2 DG P 15 " -0.041 2.00e-02 2.50e+03 pdb=" N2 DG P 15 " 0.226 2.00e-02 2.50e+03 pdb=" N3 DG P 15 " -0.224 2.00e-02 2.50e+03 pdb=" C4 DG P 15 " -0.166 2.00e-02 2.50e+03 pdb=" H8 DG P 15 " 0.245 2.00e-02 2.50e+03 pdb=" H1 DG P 15 " 0.230 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT F 12 " 0.278 2.00e-02 2.50e+03 1.47e-01 6.50e+02 pdb=" N1 DT F 12 " 0.098 2.00e-02 2.50e+03 pdb=" C2 DT F 12 " -0.049 2.00e-02 2.50e+03 pdb=" O2 DT F 12 " -0.194 2.00e-02 2.50e+03 pdb=" N3 DT F 12 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DT F 12 " 0.083 2.00e-02 2.50e+03 pdb=" O4 DT F 12 " 0.270 2.00e-02 2.50e+03 pdb=" C5 DT F 12 " -0.032 2.00e-02 2.50e+03 pdb=" C7 DT F 12 " -0.145 2.00e-02 2.50e+03 pdb=" C6 DT F 12 " -0.034 2.00e-02 2.50e+03 pdb=" H3 DT F 12 " -0.109 2.00e-02 2.50e+03 pdb=" H6 DT F 12 " -0.130 2.00e-02 2.50e+03 ... (remaining 5479 not shown) Histogram of nonbonded interaction distances: 1.32 - 1.97: 809 1.97 - 2.63: 50282 2.63 - 3.29: 131859 3.29 - 3.94: 164971 3.94 - 4.60: 253744 Nonbonded interactions: 601665 Sorted by model distance: nonbonded pdb=" OE1 GLU A 92 " pdb=" H THR A 94 " model vdw 1.315 2.450 nonbonded pdb=" O VAL I 504 " pdb=" H ARG I 531 " model vdw 1.367 2.450 nonbonded pdb=" O TYR A 248 " pdb=" H ILE A 283 " model vdw 1.408 2.450 nonbonded pdb=" H GLY C 175 " pdb=" OE1 GLU C 191 " model vdw 1.434 2.450 nonbonded pdb=" OG SER A 97 " pdb=" H GLY A 99 " model vdw 1.446 2.450 ... (remaining 601660 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' selection = chain 'K' } ncs_group { reference = (chain 'E' and resid -26 through -1) selection = chain 'G' selection = (chain 'M' and resid -26 through -1) selection = (chain 'O' and resid -26 through -1) } ncs_group { reference = (chain 'F' and resid 2 through 26) selection = chain 'H' selection = (chain 'N' and resid 2 through 26) selection = (chain 'P' and resid 2 through 26) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.250 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 57.340 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.090 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: 62.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.034 0.148 22652 Z= 1.876 Angle : 2.687 14.208 31402 Z= 1.960 Chirality : 0.312 0.752 3488 Planarity : 0.022 0.192 3280 Dihedral : 21.231 179.412 9448 Min Nonbonded Distance : 1.608 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.91 % Favored : 93.95 % Rotamer: Outliers : 5.15 % Allowed : 6.63 % Favored : 88.21 % Cbeta Deviations : 16.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.53 (0.18), residues: 2132 helix: -0.50 (0.15), residues: 1066 sheet: -1.79 (0.26), residues: 330 loop : -1.12 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG K 31 TYR 0.161 0.013 TYR K 18 PHE 0.109 0.010 PHE C 147 TRP 0.118 0.019 TRP C 167 HIS 0.005 0.001 HIS I 280 Details of bonding type rmsd/Z covalent geometry : bond 0.03361 / 1.88 (22636) covalent geometry : angle 2.68644 / 1.96 (31378) hydrogen bonds : bond 0.16947 / 11.16 ( 1211) hydrogen bonds : angle 7.46598 / 5.30 ( 3320) metal coordination : bond 0.02863 / 1.92 ( 16) metal coordination : angle 3.52843 / 1.94 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 182 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9134 (pp20) REVERT: C 409 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.3680 (ptm) REVERT: I 145 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9138 (mm-30) REVERT: K 403 MET cc_start: 0.6323 (mtm) cc_final: 0.6045 (mmp) REVERT: K 477 VAL cc_start: 0.0816 (OUTLIER) cc_final: -0.0021 (t) outliers start: 101 outliers final: 63 residues processed: 269 average time/residue: 0.4028 time to fit residues: 161.2424 Evaluate side-chains 188 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 293 GLN ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN C 422 ASN C 489 HIS C 498 ASN I 422 ASN ** K 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.094223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.076766 restraints weight = 712399.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.073733 restraints weight = 306599.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.074060 restraints weight = 231041.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.073743 restraints weight = 201639.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.073716 restraints weight = 172448.193| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 22652 Z= 0.246 Angle : 0.825 11.802 31402 Z= 0.489 Chirality : 0.052 0.352 3488 Planarity : 0.007 0.126 3280 Dihedral : 25.923 177.070 4792 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.02 % Favored : 94.93 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -0.52 (0.18), residues: 2132 helix: 0.52 (0.15), residues: 1099 sheet: -1.55 (0.27), residues: 317 loop : -0.92 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 21 TYR 0.028 0.002 TYR K 363 PHE 0.059 0.003 PHE C 147 TRP 0.011 0.002 TRP C 167 HIS 0.006 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.25 (22636) covalent geometry : angle 0.81529 / 0.49 (31378) hydrogen bonds : bond 0.08676 / 5.93 ( 1211) hydrogen bonds : angle 6.46515 / 4.57 ( 3320) metal coordination : bond 0.00599 / 0.34 ( 16) metal coordination : angle 4.74635 / 2.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 149 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 138 PHE cc_start: 0.9315 (p90) cc_final: 0.8938 (p90) REVERT: C 139 GLU cc_start: 0.9448 (tm-30) cc_final: 0.9183 (tp30) REVERT: C 142 MET cc_start: 0.9574 (mtp) cc_final: 0.9218 (mtt) REVERT: C 409 MET cc_start: 0.4369 (tpt) cc_final: 0.3120 (ptp) REVERT: I 44 MET cc_start: 0.9755 (mmm) cc_final: 0.9352 (mmm) REVERT: I 318 CYS cc_start: 0.6504 (m) cc_final: 0.6253 (m) REVERT: K 142 MET cc_start: 0.9520 (mmp) cc_final: 0.9287 (mmm) REVERT: K 403 MET cc_start: 0.6173 (mtm) cc_final: 0.5838 (mmp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.4229 time to fit residues: 92.4883 Evaluate side-chains 115 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 34 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 204 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 122 optimal weight: 4.9990 chunk 178 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 GLN K 498 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.080791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.044947 restraints weight = 457908.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.045637 restraints weight = 211767.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.046231 restraints weight = 142126.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.046413 restraints weight = 117917.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.046461 restraints weight = 109830.002| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 22652 Z= 0.314 Angle : 0.804 13.042 31402 Z= 0.475 Chirality : 0.049 0.362 3488 Planarity : 0.006 0.078 3280 Dihedral : 26.163 178.672 4792 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 23.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.71 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.88 (0.18), residues: 2132 helix: 0.23 (0.15), residues: 1095 sheet: -1.73 (0.27), residues: 315 loop : -1.09 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 516 TYR 0.027 0.003 TYR A 101 PHE 0.045 0.003 PHE I 452 TRP 0.012 0.002 TRP A 167 HIS 0.007 0.002 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.31 (22636) covalent geometry : angle 0.78888 / 0.47 (31378) hydrogen bonds : bond 0.08940 / 6.12 ( 1211) hydrogen bonds : angle 6.41045 / 4.51 ( 3320) metal coordination : bond 0.00980 / 0.54 ( 16) metal coordination : angle 5.60731 / 3.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 MET cc_start: 0.4494 (tpt) cc_final: 0.3273 (ptp) REVERT: K 135 GLN cc_start: 0.9361 (tp40) cc_final: 0.9152 (tm-30) REVERT: K 142 MET cc_start: 0.9446 (mmp) cc_final: 0.9232 (mmm) REVERT: K 403 MET cc_start: 0.6084 (mtm) cc_final: 0.5854 (mmp) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.4403 time to fit residues: 84.4716 Evaluate side-chains 107 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 152 optimal weight: 30.0000 chunk 212 optimal weight: 40.0000 chunk 185 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 211 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN I 109 ASN K 135 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.081624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.046905 restraints weight = 455636.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.047131 restraints weight = 222359.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047436 restraints weight = 136043.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.047137 restraints weight = 127921.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.047228 restraints weight = 123442.152| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22652 Z= 0.243 Angle : 0.733 11.858 31402 Z= 0.436 Chirality : 0.048 0.367 3488 Planarity : 0.006 0.071 3280 Dihedral : 26.205 179.604 4792 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.47 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.67 (0.18), residues: 2132 helix: 0.47 (0.15), residues: 1100 sheet: -1.85 (0.28), residues: 294 loop : -1.06 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG K 478 TYR 0.031 0.002 TYR C 122 PHE 0.036 0.002 PHE C 147 TRP 0.008 0.002 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.24 (22636) covalent geometry : angle 0.71476 / 0.43 (31378) hydrogen bonds : bond 0.07908 / 5.44 ( 1211) hydrogen bonds : angle 6.11956 / 4.30 ( 3320) metal coordination : bond 0.01072 / 0.60 ( 16) metal coordination : angle 5.98996 / 3.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9558 (mmp) cc_final: 0.9344 (mmm) REVERT: C 409 MET cc_start: 0.4559 (tpt) cc_final: 0.3328 (ptp) REVERT: I 44 MET cc_start: 0.9749 (mmm) cc_final: 0.9330 (mmm) REVERT: K 135 GLN cc_start: 0.9400 (tp-100) cc_final: 0.8916 (tm-30) REVERT: K 139 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8966 (mm-30) REVERT: K 142 MET cc_start: 0.9490 (mmp) cc_final: 0.9181 (mmm) REVERT: K 403 MET cc_start: 0.6131 (mtm) cc_final: 0.5856 (mmp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4414 time to fit residues: 81.2618 Evaluate side-chains 106 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 223 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 105 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.082341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.045271 restraints weight = 460533.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.046311 restraints weight = 208395.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.046775 restraints weight = 139842.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.047137 restraints weight = 120085.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.047145 restraints weight = 112249.762| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 22652 Z= 0.202 Angle : 0.699 11.628 31402 Z= 0.415 Chirality : 0.047 0.374 3488 Planarity : 0.005 0.071 3280 Dihedral : 26.254 179.426 4792 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.39 (0.18), residues: 2132 helix: 0.71 (0.15), residues: 1101 sheet: -1.84 (0.29), residues: 280 loop : -0.93 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG I 362 TYR 0.020 0.002 TYR A 101 PHE 0.031 0.002 PHE C 147 TRP 0.006 0.001 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.20 (22636) covalent geometry : angle 0.68226 / 0.41 (31378) hydrogen bonds : bond 0.07191 / 4.94 ( 1211) hydrogen bonds : angle 5.91227 / 4.15 ( 3320) metal coordination : bond 0.00840 / 0.49 ( 16) metal coordination : angle 5.56376 / 3.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 409 MET cc_start: 0.4618 (tpt) cc_final: 0.3237 (ptm) REVERT: I 44 MET cc_start: 0.9708 (mmm) cc_final: 0.9299 (mmm) REVERT: K 135 GLN cc_start: 0.9448 (tp-100) cc_final: 0.8916 (tm-30) REVERT: K 136 ILE cc_start: 0.9799 (mt) cc_final: 0.9518 (mt) REVERT: K 139 GLU cc_start: 0.9533 (mm-30) cc_final: 0.9007 (mm-30) REVERT: K 403 MET cc_start: 0.6045 (mtm) cc_final: 0.5777 (mmp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3943 time to fit residues: 70.2832 Evaluate side-chains 106 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 207 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.082439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.046151 restraints weight = 471002.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.047040 restraints weight = 209403.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.047617 restraints weight = 141880.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.047757 restraints weight = 118079.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 73)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.047562 restraints weight = 108998.477| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22652 Z= 0.194 Angle : 0.676 10.662 31402 Z= 0.403 Chirality : 0.047 0.373 3488 Planarity : 0.005 0.048 3280 Dihedral : 26.287 178.293 4792 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.16 (0.18), residues: 2132 helix: 0.93 (0.15), residues: 1101 sheet: -1.82 (0.29), residues: 280 loop : -0.85 (0.24), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 21 TYR 0.019 0.002 TYR A 122 PHE 0.028 0.002 PHE K 199 TRP 0.005 0.001 TRP A 167 HIS 0.009 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (22636) covalent geometry : angle 0.66085 / 0.40 (31378) hydrogen bonds : bond 0.06743 / 4.63 ( 1211) hydrogen bonds : angle 5.69835 / 4.00 ( 3320) metal coordination : bond 0.00791 / 0.44 ( 16) metal coordination : angle 5.12318 / 2.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7308 (ttm) cc_final: 0.6459 (ttm) REVERT: I 44 MET cc_start: 0.9702 (mmm) cc_final: 0.9276 (mmm) REVERT: I 154 MET cc_start: 0.9549 (mtm) cc_final: 0.9100 (mtm) REVERT: K 403 MET cc_start: 0.6035 (mtm) cc_final: 0.5756 (mmp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4253 time to fit residues: 77.9317 Evaluate side-chains 108 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 205 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 196 optimal weight: 20.0000 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 118 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 176 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 402 ASN ** I 24 GLN ** 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 = 0.3946 r_free = 0.3946 target = 0.080676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.044237 restraints weight = 456746.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.045113 restraints weight = 207560.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.045420 restraints weight = 138739.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.045645 restraints weight = 115582.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.045843 restraints weight = 108131.449| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22652 Z= 0.248 Angle : 0.704 13.275 31402 Z= 0.418 Chirality : 0.046 0.375 3488 Planarity : 0.005 0.046 3280 Dihedral : 26.337 178.165 4792 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.38 (0.18), residues: 2132 helix: 0.77 (0.15), residues: 1107 sheet: -1.92 (0.29), residues: 280 loop : -0.99 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 134 TYR 0.026 0.002 TYR A 101 PHE 0.021 0.002 PHE C 147 TRP 0.008 0.002 TRP A 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.25 (22636) covalent geometry : angle 0.68651 / 0.42 (31378) hydrogen bonds : bond 0.07407 / 5.09 ( 1211) hydrogen bonds : angle 5.75712 / 4.04 ( 3320) metal coordination : bond 0.00946 / 0.53 ( 16) metal coordination : angle 5.63613 / 3.01 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7381 (ttm) cc_final: 0.6796 (ttm) REVERT: A 142 MET cc_start: 0.9491 (mmp) cc_final: 0.9269 (mmm) REVERT: I 44 MET cc_start: 0.9763 (mmm) cc_final: 0.9319 (mmm) REVERT: I 154 MET cc_start: 0.9484 (mtm) cc_final: 0.9189 (mtm) REVERT: K 138 PHE cc_start: 0.9567 (t80) cc_final: 0.9339 (t80) REVERT: K 403 MET cc_start: 0.6062 (mtm) cc_final: 0.5762 (mmp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3777 time to fit residues: 66.1493 Evaluate side-chains 106 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 22 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 137 optimal weight: 10.0000 chunk 167 optimal weight: 6.9990 chunk 32 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 191 optimal weight: 30.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** 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 = 0.3954 r_free = 0.3954 target = 0.081314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.044687 restraints weight = 453917.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.045403 restraints weight = 205235.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.046033 restraints weight = 137155.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.046232 restraints weight = 115151.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.046321 restraints weight = 108142.387| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22652 Z= 0.210 Angle : 0.681 13.100 31402 Z= 0.405 Chirality : 0.046 0.373 3488 Planarity : 0.005 0.047 3280 Dihedral : 26.395 179.490 4792 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.20 (0.18), residues: 2132 helix: 0.94 (0.15), residues: 1107 sheet: -1.88 (0.30), residues: 270 loop : -0.95 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 362 TYR 0.025 0.002 TYR A 101 PHE 0.018 0.002 PHE A 138 TRP 0.007 0.001 TRP A 167 HIS 0.009 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.21 (22636) covalent geometry : angle 0.66341 / 0.40 (31378) hydrogen bonds : bond 0.06801 / 4.66 ( 1211) hydrogen bonds : angle 5.62919 / 3.95 ( 3320) metal coordination : bond 0.00855 / 0.47 ( 16) metal coordination : angle 5.54875 / 2.98 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7355 (ttm) cc_final: 0.6614 (ttm) REVERT: A 142 MET cc_start: 0.9475 (mmp) cc_final: 0.9238 (mmm) REVERT: C 409 MET cc_start: 0.4646 (tpt) cc_final: 0.3308 (ptm) REVERT: I 44 MET cc_start: 0.9733 (mmm) cc_final: 0.9274 (mmm) REVERT: I 154 MET cc_start: 0.9447 (mtm) cc_final: 0.9018 (mtm) REVERT: K 135 GLN cc_start: 0.9576 (tp-100) cc_final: 0.9366 (tm-30) REVERT: K 138 PHE cc_start: 0.9521 (t80) cc_final: 0.9187 (t80) REVERT: K 403 MET cc_start: 0.6052 (mtm) cc_final: 0.5762 (mmp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.4028 time to fit residues: 71.2041 Evaluate side-chains 104 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 174 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 171 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 129 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.079463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.043117 restraints weight = 474070.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.043939 restraints weight = 211191.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.044477 restraints weight = 140269.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.044746 restraints weight = 116558.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.044805 restraints weight = 108766.524| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22652 Z= 0.279 Angle : 0.734 15.689 31402 Z= 0.432 Chirality : 0.047 0.376 3488 Planarity : 0.005 0.049 3280 Dihedral : 26.464 179.177 4792 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.56 (0.18), residues: 2132 helix: 0.61 (0.15), residues: 1107 sheet: -1.89 (0.30), residues: 268 loop : -1.12 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 153 TYR 0.033 0.002 TYR A 101 PHE 0.018 0.002 PHE A 138 TRP 0.011 0.002 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.28 (22636) covalent geometry : angle 0.71570 / 0.43 (31378) hydrogen bonds : bond 0.07787 / 5.35 ( 1211) hydrogen bonds : angle 5.78295 / 4.06 ( 3320) metal coordination : bond 0.01332 / 0.71 ( 16) metal coordination : angle 5.85990 / 3.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7412 (ttm) cc_final: 0.6687 (ttm) REVERT: A 142 MET cc_start: 0.9428 (mmp) cc_final: 0.9226 (mmm) REVERT: C 409 MET cc_start: 0.4723 (tpt) cc_final: 0.3302 (ptm) REVERT: I 1 MET cc_start: 0.7459 (mmm) cc_final: 0.6924 (mmm) REVERT: I 44 MET cc_start: 0.9753 (mmm) cc_final: 0.9293 (mmm) REVERT: I 154 MET cc_start: 0.9475 (mtm) cc_final: 0.9087 (mtm) REVERT: K 403 MET cc_start: 0.6062 (mtm) cc_final: 0.5793 (mmp) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3925 time to fit residues: 67.1811 Evaluate side-chains 97 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 3.9990 chunk 220 optimal weight: 40.0000 chunk 211 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 0.0980 chunk 46 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 114 optimal weight: 0.0980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 293 GLN ** 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 = 0.3958 r_free = 0.3958 target = 0.081502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.044530 restraints weight = 451977.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.045521 restraints weight = 201277.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.046015 restraints weight = 133461.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.046046 restraints weight = 112708.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.046117 restraints weight = 104523.148| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22652 Z= 0.177 Angle : 0.670 16.610 31402 Z= 0.396 Chirality : 0.047 0.366 3488 Planarity : 0.005 0.046 3280 Dihedral : 26.456 178.907 4792 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.18 (0.18), residues: 2132 helix: 1.00 (0.15), residues: 1098 sheet: -1.90 (0.30), residues: 270 loop : -0.96 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 531 TYR 0.023 0.002 TYR A 101 PHE 0.018 0.002 PHE A 138 TRP 0.004 0.001 TRP A 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 (22636) covalent geometry : angle 0.65124 / 0.40 (31378) hydrogen bonds : bond 0.06406 / 4.39 ( 1211) hydrogen bonds : angle 5.57654 / 3.91 ( 3320) metal coordination : bond 0.00712 / 0.40 ( 16) metal coordination : angle 5.68502 / 3.08 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7340 (ttm) cc_final: 0.6608 (ttm) REVERT: A 142 MET cc_start: 0.9372 (mmp) cc_final: 0.9162 (mmm) REVERT: C 101 TYR cc_start: 0.9039 (m-80) cc_final: 0.8813 (m-10) REVERT: I 1 MET cc_start: 0.7287 (mmm) cc_final: 0.7027 (mmm) REVERT: I 44 MET cc_start: 0.9715 (mmm) cc_final: 0.9223 (mmm) REVERT: I 154 MET cc_start: 0.9462 (mtm) cc_final: 0.9021 (mtm) REVERT: K 403 MET cc_start: 0.6059 (mtm) cc_final: 0.5796 (mmp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.3661 time to fit residues: 64.6829 Evaluate side-chains 98 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 104 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 20.0000 chunk 7 optimal weight: 0.3980 chunk 217 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 489 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.081824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.044556 restraints weight = 452681.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.045833 restraints weight = 199480.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.046122 restraints weight = 133774.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.046353 restraints weight = 111091.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046473 restraints weight = 104336.718| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22652 Z= 0.175 Angle : 0.651 14.890 31402 Z= 0.387 Chirality : 0.046 0.369 3488 Planarity : 0.005 0.045 3280 Dihedral : 26.422 178.964 4792 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: 0.09 (0.19), residues: 2132 helix: 1.22 (0.15), residues: 1098 sheet: -1.82 (0.31), residues: 269 loop : -0.84 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 153 TYR 0.023 0.002 TYR A 101 PHE 0.018 0.002 PHE K 289 TRP 0.005 0.001 TRP K 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (22636) covalent geometry : angle 0.63488 / 0.39 (31378) hydrogen bonds : bond 0.05971 / 4.08 ( 1211) hydrogen bonds : angle 5.43460 / 3.81 ( 3320) metal coordination : bond 0.00733 / 0.40 ( 16) metal coordination : angle 5.24894 / 2.84 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8087.16 seconds wall clock time: 138 minutes 57.39 seconds (8337.39 seconds total)