Starting phenix.real_space_refine on Mon Aug 10 06:22:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxk_47290/08_2026/9dxk_47290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxk_47290/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dxk_47290/08_2026/9dxk_47290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxk_47290/08_2026/9dxk_47290.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxk_47290/08_2026/9dxk_47290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxk_47290/08_2026/9dxk_47290.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 7.37, 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: 3.87 Conformation dependent library (CDL) restraints added in 1.1 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: 7.22 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: 10.49 Time building geometry restraints manager: 5.47 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: 3.350 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: 0.120 Process input model: 53.950 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.490 ------------------------------------------------------------------------------- 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= 1.877 Angle : 2.690 14.208 31402 Z= 1.963 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 2.68885 / 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 : 0.879 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: A 148 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9137 (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: 0.9137 (mm-30) REVERT: I 154 MET cc_start: 0.9523 (mtm) cc_final: 0.9196 (mtm) REVERT: K 403 MET cc_start: 0.6323 (mtm) cc_final: 0.6044 (mmp) REVERT: K 477 VAL cc_start: 0.0816 (OUTLIER) cc_final: -0.0013 (t) outliers start: 101 outliers final: 63 residues processed: 269 average time/residue: 0.3918 time to fit residues: 157.6908 Evaluate side-chains 187 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 120 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 3.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.094413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.076884 restraints weight = 712060.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.073876 restraints weight = 275777.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.073967 restraints weight = 203191.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.073702 restraints weight = 194833.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.073662 restraints weight = 173601.393| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22652 Z= 0.241 Angle : 0.828 11.718 31402 Z= 0.489 Chirality : 0.052 0.362 3488 Planarity : 0.007 0.125 3280 Dihedral : 25.886 177.038 4792 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.97 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -0.46 (0.18), residues: 2132 helix: 0.56 (0.15), residues: 1098 sheet: -1.54 (0.27), residues: 317 loop : -0.87 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 268 TYR 0.028 0.002 TYR K 363 PHE 0.060 0.003 PHE C 147 TRP 0.010 0.002 TRP C 167 HIS 0.008 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.24 (22636) covalent geometry : angle 0.81757 / 0.49 (31378) hydrogen bonds : bond 0.08624 / 5.90 ( 1211) hydrogen bonds : angle 6.46135 / 4.56 ( 3320) metal coordination : bond 0.00608 / 0.34 ( 16) metal coordination : angle 4.70277 / 2.51 ( 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 152 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.056 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 138 PHE cc_start: 0.9293 (p90) cc_final: 0.8931 (p90) REVERT: C 139 GLU cc_start: 0.9453 (tm-30) cc_final: 0.9187 (tp30) REVERT: C 142 MET cc_start: 0.9574 (mtp) cc_final: 0.9221 (mtt) REVERT: C 409 MET cc_start: 0.4383 (tpt) cc_final: 0.3139 (ptp) REVERT: I 25 ASP cc_start: 0.9150 (m-30) cc_final: 0.8794 (t0) REVERT: I 44 MET cc_start: 0.9754 (mmm) cc_final: 0.9348 (mmm) REVERT: I 154 MET cc_start: 0.9508 (mtm) cc_final: 0.9158 (mtm) REVERT: I 318 CYS cc_start: 0.6443 (m) cc_final: 0.6175 (m) REVERT: K 142 MET cc_start: 0.9512 (mmp) cc_final: 0.9296 (mmm) REVERT: K 403 MET cc_start: 0.6166 (mtm) cc_final: 0.5835 (mmp) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.4293 time to fit residues: 96.1099 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 : 1.075 ------------------------------------------------------------------------------- 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: 5.9990 chunk 204 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 178 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS 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 = 0.3968 r_free = 0.3968 target = 0.082143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.045889 restraints weight = 458978.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.046648 restraints weight = 207338.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.047098 restraints weight = 136236.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.047399 restraints weight = 116341.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.047440 restraints weight = 108586.253| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22652 Z= 0.269 Angle : 0.770 12.691 31402 Z= 0.456 Chirality : 0.049 0.371 3488 Planarity : 0.006 0.073 3280 Dihedral : 26.069 179.644 4792 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.91 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % 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: -0.59 (0.18), residues: 2132 helix: 0.50 (0.15), residues: 1095 sheet: -1.69 (0.27), residues: 319 loop : -0.98 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 516 TYR 0.024 0.002 TYR A 346 PHE 0.044 0.003 PHE C 147 TRP 0.010 0.002 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.27 (22636) covalent geometry : angle 0.75538 / 0.46 (31378) hydrogen bonds : bond 0.08287 / 5.67 ( 1211) hydrogen bonds : angle 6.30327 / 4.43 ( 3320) metal coordination : bond 0.00844 / 0.46 ( 16) metal coordination : angle 5.38108 / 2.86 ( 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 134 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 1.132 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: I 139 GLU cc_start: 0.9678 (tp30) cc_final: 0.9436 (mm-30) REVERT: K 142 MET cc_start: 0.9471 (mmp) cc_final: 0.9264 (mmm) REVERT: K 403 MET cc_start: 0.6063 (mtm) cc_final: 0.5852 (mmp) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.4033 time to fit residues: 79.8712 Evaluate side-chains 110 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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: 50.0000 chunk 185 optimal weight: 2.9990 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 167 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 193 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS I 24 GLN I 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.081414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.045032 restraints weight = 461286.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.045741 restraints weight = 206645.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.046262 restraints weight = 137578.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.046644 restraints weight = 117165.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.046713 restraints weight = 109829.601| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22652 Z= 0.261 Angle : 0.743 11.570 31402 Z= 0.440 Chirality : 0.048 0.373 3488 Planarity : 0.006 0.088 3280 Dihedral : 26.163 179.838 4792 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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: -0.61 (0.18), residues: 2132 helix: 0.52 (0.15), residues: 1100 sheet: -1.77 (0.28), residues: 307 loop : -1.02 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG K 478 TYR 0.028 0.002 TYR C 122 PHE 0.037 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 0.00457 / 0.26 (22636) covalent geometry : angle 0.72498 / 0.44 (31378) hydrogen bonds : bond 0.08038 / 5.52 ( 1211) hydrogen bonds : angle 6.12801 / 4.31 ( 3320) metal coordination : bond 0.01105 / 0.63 ( 16) metal coordination : angle 5.87017 / 3.17 ( 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 : 1.068 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: C 409 MET cc_start: 0.4550 (tpt) cc_final: 0.3337 (ptp) REVERT: I 44 MET cc_start: 0.9708 (mmm) cc_final: 0.9299 (mmm) REVERT: I 139 GLU cc_start: 0.9655 (tp30) cc_final: 0.9417 (mm-30) REVERT: K 135 GLN cc_start: 0.9524 (tp40) cc_final: 0.8827 (tm-30) REVERT: K 142 MET cc_start: 0.9471 (mmp) cc_final: 0.9165 (mmm) REVERT: K 403 MET cc_start: 0.6130 (mtm) cc_final: 0.5871 (mmp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4255 time to fit residues: 79.6670 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 : 1.083 ------------------------------------------------------------------------------- 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: 7.9990 chunk 163 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 197 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 223 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 144 optimal weight: 7.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.081389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.046456 restraints weight = 455859.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.046929 restraints weight = 215692.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.046806 restraints weight = 132684.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046748 restraints weight = 128623.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.046569 restraints weight = 125881.752| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22652 Z= 0.243 Angle : 0.726 11.031 31402 Z= 0.430 Chirality : 0.048 0.372 3488 Planarity : 0.006 0.106 3280 Dihedral : 26.230 178.705 4792 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: -0.56 (0.18), residues: 2132 helix: 0.58 (0.15), residues: 1100 sheet: -1.93 (0.29), residues: 279 loop : -1.02 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 21 TYR 0.024 0.002 TYR A 101 PHE 0.032 0.002 PHE C 147 TRP 0.007 0.002 TRP A 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.24 (22636) covalent geometry : angle 0.70938 / 0.43 (31378) hydrogen bonds : bond 0.07659 / 5.26 ( 1211) hydrogen bonds : angle 6.03320 / 4.23 ( 3320) metal coordination : bond 0.00909 / 0.53 ( 16) metal coordination : angle 5.55680 / 3.01 ( 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 123 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.276 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: 0.4530 (tpt) cc_final: 0.3086 (ptm) REVERT: I 44 MET cc_start: 0.9698 (mmm) cc_final: 0.9281 (mmm) REVERT: I 154 MET cc_start: 0.9478 (mtm) cc_final: 0.9049 (mtm) REVERT: K 135 GLN cc_start: 0.9378 (tp40) cc_final: 0.8893 (tm-30) REVERT: K 139 GLU cc_start: 0.9521 (mm-30) cc_final: 0.8966 (mm-30) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.4095 time to fit residues: 75.5062 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 : 1.012 ------------------------------------------------------------------------------- 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: 9.9990 chunk 171 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 123 optimal weight: 0.9990 chunk 207 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 chunk 115 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.092766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.074709 restraints weight = 716774.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.070692 restraints weight = 272335.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.070847 restraints weight = 205946.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.070481 restraints weight = 171269.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.070498 restraints weight = 153499.247| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22652 Z= 0.176 Angle : 0.679 10.671 31402 Z= 0.402 Chirality : 0.048 0.373 3488 Planarity : 0.005 0.049 3280 Dihedral : 26.242 178.384 4792 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: -0.17 (0.18), residues: 2132 helix: 0.94 (0.15), residues: 1101 sheet: -1.85 (0.29), residues: 277 loop : -0.86 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 153 TYR 0.018 0.002 TYR A 101 PHE 0.023 0.002 PHE C 147 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 0.00301 / 0.18 (22636) covalent geometry : angle 0.66366 / 0.40 (31378) hydrogen bonds : bond 0.06734 / 4.62 ( 1211) hydrogen bonds : angle 5.71735 / 4.02 ( 3320) metal coordination : bond 0.00772 / 0.42 ( 16) metal coordination : angle 5.15388 / 2.79 ( 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 126 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 1.125 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: A 1 MET cc_start: 0.7241 (ttm) cc_final: 0.6740 (ttm) REVERT: I 44 MET cc_start: 0.9769 (mmm) cc_final: 0.9341 (mmm) REVERT: I 138 PHE cc_start: 0.8982 (p90) cc_final: 0.8332 (p90) REVERT: I 154 MET cc_start: 0.9530 (mtm) cc_final: 0.9162 (mtm) REVERT: K 154 MET cc_start: 0.9639 (mtm) cc_final: 0.9381 (mtm) REVERT: K 403 MET cc_start: 0.6074 (mtm) cc_final: 0.5738 (mmp) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.4065 time to fit residues: 76.7338 Evaluate side-chains 105 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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: 20.0000 chunk 6 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 196 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 118 optimal weight: 0.9990 chunk 210 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 8 ASN A 402 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.081363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.044451 restraints weight = 459086.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045523 restraints weight = 204340.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.045987 restraints weight = 136746.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.046269 restraints weight = 113592.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.046565 restraints weight = 106088.893| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3776 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= 0.221 Angle : 0.689 12.728 31402 Z= 0.407 Chirality : 0.047 0.375 3488 Planarity : 0.005 0.047 3280 Dihedral : 26.282 178.062 4792 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -0.20 (0.18), residues: 2132 helix: 0.94 (0.15), residues: 1101 sheet: -1.89 (0.29), residues: 277 loop : -0.92 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 268 TYR 0.022 0.002 TYR A 101 PHE 0.019 0.002 PHE C 147 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 0.00382 / 0.22 (22636) covalent geometry : angle 0.67255 / 0.41 (31378) hydrogen bonds : bond 0.07014 / 4.81 ( 1211) hydrogen bonds : angle 5.68545 / 3.99 ( 3320) metal coordination : bond 0.00865 / 0.49 ( 16) metal coordination : angle 5.41060 / 2.90 ( 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 121 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.016 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: A 1 MET cc_start: 0.7369 (ttm) cc_final: 0.6543 (ttm) REVERT: C 409 MET cc_start: 0.4582 (tpt) cc_final: 0.3245 (ptm) REVERT: I 44 MET cc_start: 0.9723 (mmm) cc_final: 0.9256 (mmm) REVERT: I 138 PHE cc_start: 0.8828 (p90) cc_final: 0.8213 (p90) REVERT: I 139 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9102 (mm-30) REVERT: I 154 MET cc_start: 0.9514 (mtm) cc_final: 0.9143 (mtm) REVERT: K 135 GLN cc_start: 0.9639 (tp40) cc_final: 0.9437 (tm-30) REVERT: K 403 MET cc_start: 0.6060 (mtm) cc_final: 0.5771 (mmp) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3531 time to fit residues: 64.4665 Evaluate side-chains 105 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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: 0.9990 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 137 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 199 optimal weight: 0.9980 chunk 191 optimal weight: 30.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.082344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.045336 restraints weight = 456091.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.046020 restraints weight = 208883.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.046552 restraints weight = 137073.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.046773 restraints weight = 114071.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.046941 restraints weight = 106442.156| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22652 Z= 0.176 Angle : 0.663 12.465 31402 Z= 0.393 Chirality : 0.047 0.372 3488 Planarity : 0.005 0.046 3280 Dihedral : 26.295 179.155 4792 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 0.00 (0.19), residues: 2132 helix: 1.15 (0.16), residues: 1095 sheet: -1.89 (0.29), residues: 277 loop : -0.83 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 257 TYR 0.020 0.002 TYR A 101 PHE 0.033 0.002 PHE C 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 0.00302 / 0.18 (22636) covalent geometry : angle 0.64703 / 0.39 (31378) hydrogen bonds : bond 0.06415 / 4.39 ( 1211) hydrogen bonds : angle 5.53289 / 3.88 ( 3320) metal coordination : bond 0.00769 / 0.42 ( 16) metal coordination : angle 5.29254 / 2.84 ( 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 119 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.140 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: A 1 MET cc_start: 0.7386 (ttm) cc_final: 0.6854 (ttm) REVERT: C 409 MET cc_start: 0.4679 (tpt) cc_final: 0.3308 (ptm) REVERT: I 44 MET cc_start: 0.9734 (mmm) cc_final: 0.9251 (mmm) REVERT: I 154 MET cc_start: 0.9505 (mtm) cc_final: 0.9109 (mtm) REVERT: K 403 MET cc_start: 0.6047 (mtm) cc_final: 0.5769 (mmp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.3546 time to fit residues: 63.8951 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: 10.0000 chunk 174 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.081767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.044769 restraints weight = 454283.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.045603 restraints weight = 202963.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.046201 restraints weight = 134903.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.046481 restraints weight = 112057.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.046496 restraints weight = 104731.628| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22652 Z= 0.201 Angle : 0.669 14.597 31402 Z= 0.395 Chirality : 0.046 0.373 3488 Planarity : 0.005 0.058 3280 Dihedral : 26.316 179.167 4792 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: 0.02 (0.19), residues: 2132 helix: 1.13 (0.15), residues: 1104 sheet: -1.86 (0.30), residues: 267 loop : -0.84 (0.24), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 362 TYR 0.023 0.002 TYR A 101 PHE 0.019 0.002 PHE C 138 TRP 0.005 0.001 TRP K 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.20 (22636) covalent geometry : angle 0.65261 / 0.39 (31378) hydrogen bonds : bond 0.06502 / 4.45 ( 1211) hydrogen bonds : angle 5.50492 / 3.86 ( 3320) metal coordination : bond 0.01126 / 0.60 ( 16) metal coordination : angle 5.36362 / 2.89 ( 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 117 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.082 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: 0.7320 (ttm) cc_final: 0.6585 (ttm) REVERT: A 142 MET cc_start: 0.9450 (mmp) cc_final: 0.9246 (mmm) REVERT: C 101 TYR cc_start: 0.8999 (m-80) cc_final: 0.8707 (m-10) REVERT: C 409 MET cc_start: 0.4662 (tpt) cc_final: 0.3308 (ptm) REVERT: I 44 MET cc_start: 0.9717 (mmm) cc_final: 0.9234 (mmm) REVERT: I 154 MET cc_start: 0.9504 (mtm) cc_final: 0.9154 (mtm) REVERT: K 403 MET cc_start: 0.6056 (mtm) cc_final: 0.5775 (mmp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3554 time to fit residues: 64.2456 Evaluate side-chains 101 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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: 4.9990 chunk 220 optimal weight: 40.0000 chunk 211 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 81 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 46 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 219 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.079305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.042574 restraints weight = 478697.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.043547 restraints weight = 213234.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.044143 restraints weight = 142528.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.044354 restraints weight = 120605.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044405 restraints weight = 113849.717| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22652 Z= 0.286 Angle : 0.740 17.111 31402 Z= 0.435 Chirality : 0.047 0.374 3488 Planarity : 0.005 0.049 3280 Dihedral : 26.436 179.266 4792 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.50 (0.18), residues: 2132 helix: 0.70 (0.15), residues: 1107 sheet: -1.93 (0.29), residues: 276 loop : -1.12 (0.24), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 153 TYR 0.034 0.002 TYR A 101 PHE 0.017 0.002 PHE I 73 TRP 0.010 0.002 TRP K 167 HIS 0.008 0.002 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.29 (22636) covalent geometry : angle 0.72203 / 0.43 (31378) hydrogen bonds : bond 0.07847 / 5.38 ( 1211) hydrogen bonds : angle 5.75715 / 4.03 ( 3320) metal coordination : bond 0.00961 / 0.57 ( 16) metal coordination : angle 5.83537 / 3.17 ( 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 111 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.944 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: A 1 MET cc_start: 0.7436 (ttm) cc_final: 0.6728 (ttm) REVERT: C 409 MET cc_start: 0.4757 (tpt) cc_final: 0.3340 (ptm) REVERT: I 1 MET cc_start: 0.7401 (mmm) cc_final: 0.7193 (mmm) REVERT: I 44 MET cc_start: 0.9738 (mmm) cc_final: 0.9268 (mmm) REVERT: I 154 MET cc_start: 0.9494 (mtm) cc_final: 0.9120 (mtm) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.3311 time to fit residues: 57.3906 Evaluate side-chains 95 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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: 7.9990 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 3.9990 overall best weight: 2.5744 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.081937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.044746 restraints weight = 453393.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.045924 restraints weight = 199543.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.046597 restraints weight = 134044.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.046533 restraints weight = 112299.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.046651 restraints weight = 102844.030| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22652 Z= 0.168 Angle : 0.668 16.027 31402 Z= 0.391 Chirality : 0.047 0.366 3488 Planarity : 0.005 0.046 3280 Dihedral : 26.408 178.818 4792 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.03 (0.19), residues: 2132 helix: 1.14 (0.15), residues: 1092 sheet: -1.85 (0.30), residues: 276 loop : -0.90 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 268 TYR 0.022 0.002 TYR A 101 PHE 0.016 0.002 PHE C 138 TRP 0.005 0.001 TRP A 234 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (22636) covalent geometry : angle 0.64960 / 0.39 (31378) hydrogen bonds : bond 0.06128 / 4.18 ( 1211) hydrogen bonds : angle 5.49028 / 3.85 ( 3320) metal coordination : bond 0.00723 / 0.40 ( 16) metal coordination : angle 5.62402 / 3.04 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7717.60 seconds wall clock time: 132 minutes 34.18 seconds (7954.18 seconds total)