Starting phenix.real_space_refine on Sun Feb 8 08:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dxk_47290/02_2026/9dxk_47290.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dxk_47290/02_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_47290/02_2026/9dxk_47290.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dxk_47290/02_2026/9dxk_47290.map" model { file = "/net/cci-nas-00/data/ceres_data/9dxk_47290/02_2026/9dxk_47290.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dxk_47290/02_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-2.0-5952/lib/python3.9/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: 7.98, per 1000 atoms: 0.19 Number of scatterers: 42020 At special positions: 0 Unit cell: (143.775, 197.025, 126.735, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 76 16.00 P 216 15.00 O 4664 8.00 N 3790 7.00 C 13096 6.00 H 20174 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.57 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 320 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 353 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 358 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 323 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 320 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 353 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 358 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 323 " pdb=" ZN I 601 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 320 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 353 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 358 " pdb="ZN ZN I 601 " - pdb=" SG CYS I 323 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 320 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 358 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 353 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 323 " Number of angles added : 24 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 23 sheets defined 55.0% alpha, 11.2% beta 96 base pairs and 186 stacking pairs defined. Time for finding SS restraints: 7.19 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: 9.79 Time building geometry restraints manager: 6.21 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: 76600 7.57 - 15.15: 1094 15.15 - 22.72: 2 22.72 - 30.29: 0 30.29 - 37.86: 12 Bond angle restraints: 77708 Sorted by residual: 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 angle pdb=" C ALA I 217 " pdb=" CA ALA I 217 " pdb=" HA ALA I 217 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+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: 2247 0.151 - 0.301: 131 0.301 - 0.451: 214 0.451 - 0.602: 681 0.602 - 0.752: 215 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.610 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 55.560 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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= 1.736 Angle : 2.681 13.908 31402 Z= 1.698 Chirality : 0.310 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 covalent geometry : bond 0.03357 (22636) covalent geometry : angle 2.68026 (31378) hydrogen bonds : bond 0.16947 ( 1211) hydrogen bonds : angle 7.46598 ( 3320) metal coordination : bond 0.02863 ( 16) metal coordination : angle 3.52843 ( 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 : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9134 (pp20) REVERT: C 409 MET cc_start: 0.4882 (OUTLIER) cc_final: 0.3680 (ptm) REVERT: I 145 GLU cc_start: 0.9452 (OUTLIER) cc_final: 0.9138 (mm-30) REVERT: K 403 MET cc_start: 0.6323 (mtm) cc_final: 0.6045 (mmp) REVERT: K 477 VAL cc_start: 0.0816 (OUTLIER) cc_final: -0.0021 (t) outliers start: 101 outliers final: 63 residues processed: 269 average time/residue: 0.3984 time to fit residues: 156.5351 Evaluate side-chains 188 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 121 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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: 5.9990 chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS C 293 GLN C 422 ASN C 489 HIS C 498 ASN K 293 GLN ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.093595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.076014 restraints weight = 712211.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.073169 restraints weight = 273875.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.073314 restraints weight = 219736.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.072875 restraints weight = 210635.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.072792 restraints weight = 175459.158| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22652 Z= 0.229 Angle : 0.719 12.578 31402 Z= 0.419 Chirality : 0.046 0.361 3488 Planarity : 0.006 0.121 3280 Dihedral : 25.950 173.621 4792 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.47 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.18), residues: 2132 helix: 0.60 (0.15), residues: 1098 sheet: -1.56 (0.27), residues: 305 loop : -0.79 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 21 TYR 0.026 0.002 TYR K 363 PHE 0.033 0.002 PHE C 147 TRP 0.010 0.002 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00471 (22636) covalent geometry : angle 0.70578 (31378) hydrogen bonds : bond 0.07007 ( 1211) hydrogen bonds : angle 6.11942 ( 3320) metal coordination : bond 0.00668 ( 16) metal coordination : angle 5.09845 ( 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 142 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.061 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: A 403 MET cc_start: 0.2138 (mtp) cc_final: 0.1747 (ttt) REVERT: C 101 TYR cc_start: 0.9299 (m-80) cc_final: 0.8920 (m-80) REVERT: C 142 MET cc_start: 0.9561 (mtp) cc_final: 0.9253 (tmm) REVERT: C 409 MET cc_start: 0.4308 (tpt) cc_final: 0.2973 (ptm) REVERT: K 88 ILE cc_start: 0.9423 (pt) cc_final: 0.9211 (mp) REVERT: K 138 PHE cc_start: 0.9629 (t80) cc_final: 0.9402 (t80) REVERT: K 142 MET cc_start: 0.9481 (mmp) cc_final: 0.9265 (mmm) REVERT: K 403 MET cc_start: 0.6138 (mtm) cc_final: 0.5818 (mmp) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.4143 time to fit residues: 85.1263 Evaluate side-chains 114 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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: 10.0000 chunk 137 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 178 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 131 optimal weight: 4.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 293 GLN A 489 HIS I 8 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN I 222 ASN K 109 ASN K 204 ASN ** 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 = 0.3925 r_free = 0.3925 target = 0.079350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.043253 restraints weight = 466617.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.044366 restraints weight = 212462.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.044717 restraints weight = 144763.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.044906 restraints weight = 119894.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.045082 restraints weight = 111872.132| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22652 Z= 0.310 Angle : 0.743 13.595 31402 Z= 0.433 Chirality : 0.049 0.375 3488 Planarity : 0.006 0.070 3280 Dihedral : 26.192 176.726 4792 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.13 % Favored : 92.82 % Rotamer: Outliers : 0.05 % Allowed : 3.57 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.18), residues: 2132 helix: 0.47 (0.15), residues: 1102 sheet: -1.85 (0.29), residues: 280 loop : -1.03 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG A 21 TYR 0.031 0.002 TYR A 101 PHE 0.050 0.003 PHE I 452 TRP 0.016 0.002 TRP A 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00617 (22636) covalent geometry : angle 0.72587 (31378) hydrogen bonds : bond 0.08137 ( 1211) hydrogen bonds : angle 5.98473 ( 3320) metal coordination : bond 0.01195 ( 16) metal coordination : angle 5.71737 ( 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 133 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.986 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 138 PHE cc_start: 0.9668 (p90) cc_final: 0.9467 (p90) REVERT: A 142 MET cc_start: 0.9435 (mmp) cc_final: 0.9223 (mmm) REVERT: C 142 MET cc_start: 0.9385 (mtp) cc_final: 0.9173 (mmm) REVERT: C 409 MET cc_start: 0.4675 (tpt) cc_final: 0.3446 (ptp) REVERT: I 44 MET cc_start: 0.9765 (mmm) cc_final: 0.9305 (mmm) REVERT: I 154 MET cc_start: 0.9468 (mtm) cc_final: 0.9185 (mtm) REVERT: K 135 GLN cc_start: 0.9311 (tp40) cc_final: 0.8665 (tm-30) REVERT: K 138 PHE cc_start: 0.9541 (t80) cc_final: 0.9320 (t80) REVERT: K 142 MET cc_start: 0.9435 (mmp) cc_final: 0.9021 (mmm) outliers start: 1 outliers final: 1 residues processed: 133 average time/residue: 0.3992 time to fit residues: 76.3965 Evaluate side-chains 102 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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: 40.0000 chunk 212 optimal weight: 20.0000 chunk 185 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 211 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 167 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 ASN A 222 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS C 5 ASN ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 ASN ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.078332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.042128 restraints weight = 468931.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.042945 restraints weight = 215095.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.043390 restraints weight = 145274.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.043712 restraints weight = 124104.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.043729 restraints weight = 115676.438| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22652 Z= 0.326 Angle : 0.752 15.056 31402 Z= 0.438 Chirality : 0.049 0.372 3488 Planarity : 0.006 0.061 3280 Dihedral : 26.328 179.674 4792 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.26 % Favored : 91.70 % Rotamer: Outliers : 0.36 % Allowed : 3.11 % Favored : 96.53 % 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: -0.98 (0.18), residues: 2132 helix: 0.24 (0.15), residues: 1101 sheet: -2.08 (0.30), residues: 256 loop : -1.27 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 28 TYR 0.034 0.002 TYR A 101 PHE 0.027 0.003 PHE C 147 TRP 0.010 0.002 TRP A 167 HIS 0.008 0.002 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00644 (22636) covalent geometry : angle 0.73366 (31378) hydrogen bonds : bond 0.07763 ( 1211) hydrogen bonds : angle 6.02180 ( 3320) metal coordination : bond 0.01141 ( 16) metal coordination : angle 6.05633 ( 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 128 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 1.076 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: 0.7500 (ttm) cc_final: 0.6900 (ttm) REVERT: A 26 MET cc_start: 0.9679 (mtt) cc_final: 0.9465 (mtp) REVERT: A 138 PHE cc_start: 0.9447 (p90) cc_final: 0.9034 (p90) REVERT: A 139 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9130 (mm-30) REVERT: A 142 MET cc_start: 0.9404 (mmp) cc_final: 0.9182 (mmm) REVERT: C 142 MET cc_start: 0.9554 (mtp) cc_final: 0.9161 (mmm) REVERT: I 1 MET cc_start: 0.7419 (mmm) cc_final: 0.7183 (mmm) REVERT: I 139 GLU cc_start: 0.9648 (tp30) cc_final: 0.9363 (tp30) REVERT: I 154 MET cc_start: 0.9460 (mtm) cc_final: 0.9110 (mtm) REVERT: K 262 ASP cc_start: 0.9583 (OUTLIER) cc_final: 0.8853 (t0) outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 0.3990 time to fit residues: 75.6809 Evaluate side-chains 106 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 23 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 87 optimal weight: 9.9990 chunk 105 optimal weight: 50.0000 chunk 144 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 402 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.090067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.072399 restraints weight = 719825.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.069003 restraints weight = 282373.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.068779 restraints weight = 238617.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.068531 restraints weight = 184658.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.068567 restraints weight = 156405.966| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22652 Z= 0.261 Angle : 0.690 13.082 31402 Z= 0.402 Chirality : 0.046 0.372 3488 Planarity : 0.005 0.053 3280 Dihedral : 26.356 179.845 4792 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.11 % Favored : 91.84 % 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: -0.64 (0.18), residues: 2132 helix: 0.53 (0.15), residues: 1101 sheet: -2.08 (0.31), residues: 247 loop : -1.10 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG K 153 TYR 0.029 0.002 TYR A 101 PHE 0.018 0.002 PHE I 138 TRP 0.007 0.002 TRP A 167 HIS 0.008 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00517 (22636) covalent geometry : angle 0.67023 (31378) hydrogen bonds : bond 0.06707 ( 1211) hydrogen bonds : angle 5.81220 ( 3320) metal coordination : bond 0.00973 ( 16) metal coordination : angle 5.95877 ( 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 : 0.878 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: A 1 MET cc_start: 0.7370 (ttm) cc_final: 0.6731 (ttm) REVERT: A 138 PHE cc_start: 0.9370 (p90) cc_final: 0.8964 (p90) REVERT: A 139 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9171 (mm-30) REVERT: A 142 MET cc_start: 0.9407 (mmp) cc_final: 0.9179 (mmm) REVERT: C 409 MET cc_start: 0.4531 (tpt) cc_final: 0.2956 (ptm) REVERT: I 1 MET cc_start: 0.7284 (mmm) cc_final: 0.7037 (mmm) REVERT: I 44 MET cc_start: 0.9796 (mmm) cc_final: 0.9380 (mmm) REVERT: I 154 MET cc_start: 0.9493 (mtm) cc_final: 0.9104 (mtm) REVERT: K 142 MET cc_start: 0.9504 (mmp) cc_final: 0.9214 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.3702 time to fit residues: 68.4363 Evaluate side-chains 99 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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: 0.9980 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 123 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.091021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.073147 restraints weight = 718072.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.069269 restraints weight = 279961.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.069469 restraints weight = 218555.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.069270 restraints weight = 188994.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.069340 restraints weight = 154066.966| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5009 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= 0.190 Angle : 0.629 11.669 31402 Z= 0.369 Chirality : 0.044 0.371 3488 Planarity : 0.005 0.077 3280 Dihedral : 26.291 178.771 4792 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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: -0.15 (0.19), residues: 2132 helix: 1.02 (0.15), residues: 1101 sheet: -2.01 (0.32), residues: 250 loop : -0.94 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 98 TYR 0.025 0.001 TYR A 396 PHE 0.014 0.002 PHE I 138 TRP 0.005 0.001 TRP C 234 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00384 (22636) covalent geometry : angle 0.61373 (31378) hydrogen bonds : bond 0.05644 ( 1211) hydrogen bonds : angle 5.49599 ( 3320) metal coordination : bond 0.00733 ( 16) metal coordination : angle 5.02534 ( 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 121 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.078 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: A 138 PHE cc_start: 0.9340 (p90) cc_final: 0.8911 (p90) REVERT: A 139 GLU cc_start: 0.9522 (mm-30) cc_final: 0.9216 (mm-30) REVERT: A 142 MET cc_start: 0.9413 (mmp) cc_final: 0.9193 (mmm) REVERT: C 142 MET cc_start: 0.9454 (mtp) cc_final: 0.9247 (mmm) REVERT: C 409 MET cc_start: 0.4407 (tpt) cc_final: 0.2814 (ptm) REVERT: I 1 MET cc_start: 0.7305 (mmm) cc_final: 0.7084 (mmm) REVERT: I 44 MET cc_start: 0.9780 (mmm) cc_final: 0.9371 (mmm) REVERT: I 154 MET cc_start: 0.9492 (mtm) cc_final: 0.9135 (mtm) REVERT: K 142 MET cc_start: 0.9431 (mmp) cc_final: 0.9107 (mmm) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.3715 time to fit residues: 67.0041 Evaluate side-chains 100 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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: 7.9990 chunk 6 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 196 optimal weight: 30.0000 chunk 25 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN ** I 482 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.088178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.047149 restraints weight = 461836.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.048773 restraints weight = 230278.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.048115 restraints weight = 140883.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.048332 restraints weight = 143956.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.048315 restraints weight = 132491.995| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22652 Z= 0.212 Angle : 0.638 12.596 31402 Z= 0.372 Chirality : 0.044 0.373 3488 Planarity : 0.005 0.047 3280 Dihedral : 26.267 178.874 4792 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 2132 helix: 1.03 (0.15), residues: 1109 sheet: -2.00 (0.31), residues: 260 loop : -0.90 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 98 TYR 0.027 0.001 TYR A 101 PHE 0.013 0.002 PHE I 73 TRP 0.006 0.001 TRP A 167 HIS 0.006 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00426 (22636) covalent geometry : angle 0.62125 (31378) hydrogen bonds : bond 0.05960 ( 1211) hydrogen bonds : angle 5.42413 ( 3320) metal coordination : bond 0.00815 ( 16) metal coordination : angle 5.30682 ( 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 117 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.286 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 138 PHE cc_start: 0.9367 (p90) cc_final: 0.8731 (p90) REVERT: A 139 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9202 (mm-30) REVERT: A 142 MET cc_start: 0.9348 (mmp) cc_final: 0.9073 (mmm) REVERT: I 44 MET cc_start: 0.9742 (mmm) cc_final: 0.9300 (mmm) REVERT: I 154 MET cc_start: 0.9505 (mtm) cc_final: 0.9170 (mtm) REVERT: K 142 MET cc_start: 0.9415 (mmp) cc_final: 0.9130 (mmm) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3786 time to fit residues: 66.5195 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 : 0.998 ------------------------------------------------------------------------------- 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: 5.9990 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 167 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 460 ASN I 511 ASN ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.077085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.041310 restraints weight = 482092.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042049 restraints weight = 218642.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.042510 restraints weight = 145057.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.042707 restraints weight = 120566.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.042870 restraints weight = 113082.868| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22652 Z= 0.334 Angle : 0.740 14.413 31402 Z= 0.433 Chirality : 0.049 0.375 3488 Planarity : 0.006 0.082 3280 Dihedral : 26.511 177.923 4792 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: -0.85 (0.18), residues: 2132 helix: 0.38 (0.15), residues: 1108 sheet: -2.15 (0.32), residues: 254 loop : -1.25 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 153 TYR 0.036 0.002 TYR A 101 PHE 0.021 0.002 PHE I 138 TRP 0.012 0.002 TRP A 167 HIS 0.007 0.002 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00661 (22636) covalent geometry : angle 0.72093 (31378) hydrogen bonds : bond 0.08038 ( 1211) hydrogen bonds : angle 5.85240 ( 3320) metal coordination : bond 0.01124 ( 16) metal coordination : angle 6.10610 ( 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 108 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.077 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: A 142 MET cc_start: 0.9370 (mmp) cc_final: 0.9166 (mmm) REVERT: C 142 MET cc_start: 0.9516 (mmp) cc_final: 0.9313 (mmm) REVERT: I 44 MET cc_start: 0.9711 (mmm) cc_final: 0.9271 (mmm) REVERT: I 154 MET cc_start: 0.9508 (mtm) cc_final: 0.9101 (mtm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3819 time to fit residues: 62.3054 Evaluate side-chains 93 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.096 ------------------------------------------------------------------------------- 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: 3.9990 chunk 197 optimal weight: 0.5980 chunk 174 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.089962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.072406 restraints weight = 725849.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.069381 restraints weight = 298560.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.069575 restraints weight = 243885.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.069103 restraints weight = 205894.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.069144 restraints weight = 164470.768| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22652 Z= 0.202 Angle : 0.640 12.692 31402 Z= 0.373 Chirality : 0.044 0.372 3488 Planarity : 0.005 0.052 3280 Dihedral : 26.442 179.063 4792 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.35 (0.18), residues: 2132 helix: 0.84 (0.15), residues: 1109 sheet: -2.03 (0.33), residues: 242 loop : -1.10 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 257 TYR 0.022 0.002 TYR A 101 PHE 0.018 0.002 PHE I 147 TRP 0.005 0.001 TRP A 167 HIS 0.007 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00407 (22636) covalent geometry : angle 0.62280 (31378) hydrogen bonds : bond 0.05622 ( 1211) hydrogen bonds : angle 5.48919 ( 3320) metal coordination : bond 0.00814 ( 16) metal coordination : angle 5.37044 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4264 Ramachandran restraints generated. 2132 Oldfield, 0 Emsley, 2132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Residue SER 22 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 1.074 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: A 138 PHE cc_start: 0.9357 (p90) cc_final: 0.8676 (p90) REVERT: A 139 GLU cc_start: 0.9606 (mm-30) cc_final: 0.9204 (mm-30) REVERT: A 142 MET cc_start: 0.9471 (mmp) cc_final: 0.9185 (mmm) REVERT: C 142 MET cc_start: 0.9478 (mmp) cc_final: 0.9244 (mmm) REVERT: C 409 MET cc_start: 0.4284 (tpt) cc_final: 0.2565 (ptm) REVERT: I 25 ASP cc_start: 0.9206 (m-30) cc_final: 0.8723 (t0) REVERT: I 44 MET cc_start: 0.9787 (mmm) cc_final: 0.9316 (mmm) REVERT: I 154 MET cc_start: 0.9551 (mtm) cc_final: 0.9200 (mtm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3921 time to fit residues: 66.2383 Evaluate side-chains 97 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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: 6.9990 chunk 220 optimal weight: 20.0000 chunk 211 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 219 optimal weight: 10.0000 chunk 114 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.079418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.042849 restraints weight = 466391.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.043660 restraints weight = 205800.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.044113 restraints weight = 138113.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.044320 restraints weight = 115959.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.044480 restraints weight = 109473.746| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.6212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22652 Z= 0.199 Angle : 0.627 11.641 31402 Z= 0.368 Chirality : 0.044 0.372 3488 Planarity : 0.005 0.045 3280 Dihedral : 26.439 179.003 4792 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % 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 : 0.19 % 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: -0.11 (0.19), residues: 2132 helix: 1.07 (0.15), residues: 1106 sheet: -1.99 (0.33), residues: 252 loop : -0.98 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 153 TYR 0.024 0.002 TYR A 101 PHE 0.021 0.002 PHE I 138 TRP 0.005 0.001 TRP A 167 HIS 0.010 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00402 (22636) covalent geometry : angle 0.61094 (31378) hydrogen bonds : bond 0.05751 ( 1211) hydrogen bonds : angle 5.37501 ( 3320) metal coordination : bond 0.00788 ( 16) metal coordination : angle 5.10661 ( 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 109 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.090 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: A 138 PHE cc_start: 0.9242 (p90) cc_final: 0.8706 (p90) REVERT: A 139 GLU cc_start: 0.9563 (mm-30) cc_final: 0.9154 (mm-30) REVERT: A 142 MET cc_start: 0.9327 (mmp) cc_final: 0.9115 (mmm) REVERT: C 142 MET cc_start: 0.9446 (mmp) cc_final: 0.9246 (mmm) REVERT: I 25 ASP cc_start: 0.9215 (m-30) cc_final: 0.8755 (t0) REVERT: I 44 MET cc_start: 0.9709 (mmm) cc_final: 0.9167 (mmm) REVERT: I 154 MET cc_start: 0.9533 (mtm) cc_final: 0.9156 (mtm) outliers start: 0 outliers final: 0 residues processed: 109 average time/residue: 0.3840 time to fit residues: 63.2077 Evaluate side-chains 97 residues out of total 1960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 104 optimal weight: 20.0000 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 217 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 HIS ** I 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.080660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.043489 restraints weight = 460297.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.044641 restraints weight = 199636.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.044981 restraints weight = 136290.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.045199 restraints weight = 112952.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.045396 restraints weight = 106267.364| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22652 Z= 0.162 Angle : 0.600 10.244 31402 Z= 0.352 Chirality : 0.042 0.370 3488 Planarity : 0.004 0.047 3280 Dihedral : 26.352 178.548 4792 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % 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: 0.20 (0.19), residues: 2132 helix: 1.36 (0.16), residues: 1107 sheet: -1.98 (0.33), residues: 242 loop : -0.87 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 144 TYR 0.018 0.001 TYR A 101 PHE 0.017 0.002 PHE I 138 TRP 0.005 0.001 TRP K 234 HIS 0.006 0.001 HIS A 489 Details of bonding type rmsd covalent geometry : bond 0.00337 (22636) covalent geometry : angle 0.58684 (31378) hydrogen bonds : bond 0.05013 ( 1211) hydrogen bonds : angle 5.17109 ( 3320) metal coordination : bond 0.00656 ( 16) metal coordination : angle 4.53205 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7784.70 seconds wall clock time: 133 minutes 52.00 seconds (8032.00 seconds total)