Starting phenix.real_space_refine on Tue Nov 18 14:22:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.cif Found real_map, /net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.map" model { file = "/net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5oof_3839/11_2025/5oof_3839.cif" } resolution = 3.4 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= -0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.87, per 1000 atoms: 0.20 Number of scatterers: 14640 At special positions: 0 Unit cell: (98.04, 91.2, 190.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 6.00 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: 1.43 Conformation dependent library (CDL) restraints added in 756.8 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 52.3% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.879A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 295 removed outlier: 4.680A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.878A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 295 removed outlier: 4.681A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.878A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.680A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.878A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 295 removed outlier: 4.680A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.879A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 295 removed outlier: 4.680A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 349 Processing helix chain 'E' and resid 350 through 356 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.514A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.923A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.514A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 5.924A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.514A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.923A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.514A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 5.923A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.513A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 5.922A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 765 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3328 1.32 - 1.44: 3451 1.44 - 1.56: 7996 1.56 - 1.69: 0 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA SER C 155 " pdb=" C SER C 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.86e+01 bond pdb=" CA SER B 155 " pdb=" C SER B 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.84e+01 bond pdb=" CA SER E 155 " pdb=" C SER E 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.81e+01 bond pdb=" CA SER D 155 " pdb=" C SER D 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.79e+01 bond pdb=" CA SER A 155 " pdb=" C SER A 155 " ideal model delta sigma weight residual 1.533 1.492 0.041 9.60e-03 1.09e+04 1.79e+01 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 19238 2.91 - 5.82: 879 5.82 - 8.73: 148 8.73 - 11.64: 35 11.64 - 14.55: 5 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.84 129.55 -9.71 1.25e+00 6.40e-01 6.04e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.84 129.54 -9.70 1.25e+00 6.40e-01 6.02e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.84 129.53 -9.69 1.25e+00 6.40e-01 6.02e+01 angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.84 129.53 -9.69 1.25e+00 6.40e-01 6.00e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.84 129.48 -9.64 1.25e+00 6.40e-01 5.95e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.52: 8835 29.52 - 59.04: 135 59.04 - 88.56: 20 88.56 - 118.08: 0 118.08 - 147.61: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.61 -147.61 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.57 -147.57 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 87.56 -147.56 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 907 0.047 - 0.094: 909 0.094 - 0.140: 308 0.140 - 0.187: 93 0.187 - 0.234: 38 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA ASP A 157 " pdb=" N ASP A 157 " pdb=" C ASP A 157 " pdb=" CB ASP A 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ASP B 157 " pdb=" N ASP B 157 " pdb=" C ASP B 157 " pdb=" CB ASP B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA ASP E 157 " pdb=" N ASP E 157 " pdb=" C ASP E 157 " pdb=" CB ASP E 157 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 375 " -0.033 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE D 375 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE D 375 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE D 375 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " 0.032 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C PHE E 375 " -0.114 2.00e-02 2.50e+03 pdb=" O PHE E 375 " 0.041 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " -0.032 2.00e-02 2.50e+03 6.57e-02 4.31e+01 pdb=" C PHE B 375 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE B 375 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " -0.040 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 71 2.59 - 3.17: 13898 3.17 - 3.74: 22255 3.74 - 4.32: 34236 4.32 - 4.90: 53454 Nonbonded interactions: 123914 Sorted by model distance: nonbonded pdb=" O1B ADP D 401 " pdb="MG MG D 402 " model vdw 2.010 2.170 nonbonded pdb=" O1B ADP A 401 " pdb="MG MG A 402 " model vdw 2.010 2.170 nonbonded pdb=" O1B ADP C 401 " pdb="MG MG C 402 " model vdw 2.011 2.170 nonbonded pdb=" O1B ADP E 401 " pdb="MG MG E 402 " model vdw 2.011 2.170 nonbonded pdb=" O1B ADP B 401 " pdb="MG MG B 402 " model vdw 2.011 2.170 ... (remaining 123909 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.760 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.015 0.052 14960 Z= 0.964 Angle : 1.532 14.555 20305 Z= 0.993 Chirality : 0.075 0.234 2255 Planarity : 0.016 0.143 2595 Dihedral : 11.806 147.605 5565 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 2.73 % Allowed : 6.28 % Favored : 90.98 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 1830 helix: -1.44 (0.16), residues: 780 sheet: -1.22 (0.28), residues: 235 loop : -0.01 (0.25), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 183 TYR 0.030 0.005 TYR B 69 PHE 0.013 0.003 PHE C 375 TRP 0.031 0.006 TRP C 340 HIS 0.010 0.002 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.01535 (14960) covalent geometry : angle 1.53219 (20305) hydrogen bonds : bond 0.17424 ( 755) hydrogen bonds : angle 7.38131 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 76 ILE cc_start: 0.9238 (mt) cc_final: 0.8981 (mp) REVERT: A 176 MET cc_start: 0.8871 (mmm) cc_final: 0.8640 (mmt) REVERT: A 283 MET cc_start: 0.9192 (mmp) cc_final: 0.8962 (mmt) REVERT: A 328 LYS cc_start: 0.8714 (tttt) cc_final: 0.8452 (tttm) REVERT: A 355 MET cc_start: 0.8432 (mmm) cc_final: 0.8217 (mmm) REVERT: B 47 MET cc_start: 0.5700 (mtm) cc_final: 0.5438 (tpt) REVERT: C 123 MET cc_start: 0.8724 (mmp) cc_final: 0.8483 (mmt) REVERT: D 51 ASP cc_start: 0.7474 (p0) cc_final: 0.6841 (p0) REVERT: D 113 LYS cc_start: 0.8803 (mttt) cc_final: 0.8113 (mtpp) REVERT: E 12 ASN cc_start: 0.8292 (t0) cc_final: 0.8005 (p0) REVERT: E 78 ASN cc_start: 0.8630 (t0) cc_final: 0.8177 (t0) REVERT: E 269 MET cc_start: 0.8429 (tpp) cc_final: 0.8210 (mmt) REVERT: E 354 GLN cc_start: 0.8334 (pt0) cc_final: 0.7932 (pt0) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.1602 time to fit residues: 90.2375 Evaluate side-chains 184 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 121 GLN B 314 GLN C 92 ASN C 162 ASN C 246 GLN D 162 ASN D 371 HIS E 162 ASN E 371 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.104252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.090215 restraints weight = 25305.764| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.21 r_work: 0.2981 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14960 Z= 0.148 Angle : 0.667 7.174 20305 Z= 0.344 Chirality : 0.045 0.157 2255 Planarity : 0.007 0.071 2595 Dihedral : 7.206 87.025 2085 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.61 % Favored : 95.85 % Rotamer: Outliers : 1.41 % Allowed : 7.60 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.20), residues: 1830 helix: 0.38 (0.19), residues: 770 sheet: -0.99 (0.30), residues: 235 loop : 0.44 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 28 TYR 0.016 0.001 TYR D 306 PHE 0.024 0.001 PHE A 352 TRP 0.009 0.001 TRP E 79 HIS 0.006 0.002 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00330 (14960) covalent geometry : angle 0.66726 (20305) hydrogen bonds : bond 0.04328 ( 755) hydrogen bonds : angle 5.17073 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 269 time to evaluate : 0.541 Fit side-chains REVERT: A 151 ILE cc_start: 0.9145 (mm) cc_final: 0.8795 (tp) REVERT: A 246 GLN cc_start: 0.8358 (mt0) cc_final: 0.8122 (mt0) REVERT: A 285 CYS cc_start: 0.7198 (m) cc_final: 0.6822 (m) REVERT: A 355 MET cc_start: 0.8776 (mmm) cc_final: 0.8323 (mmm) REVERT: A 362 TYR cc_start: 0.8507 (t80) cc_final: 0.8250 (t80) REVERT: B 9 VAL cc_start: 0.9186 (t) cc_final: 0.8864 (m) REVERT: B 107 GLU cc_start: 0.7990 (pt0) cc_final: 0.7750 (pt0) REVERT: B 123 MET cc_start: 0.8952 (mmp) cc_final: 0.8730 (mmp) REVERT: B 192 ILE cc_start: 0.9178 (mm) cc_final: 0.8761 (pt) REVERT: B 226 GLU cc_start: 0.8504 (tt0) cc_final: 0.8193 (tt0) REVERT: B 355 MET cc_start: 0.7734 (tpp) cc_final: 0.7483 (mmt) REVERT: C 10 CYS cc_start: 0.8783 (t) cc_final: 0.8523 (t) REVERT: C 118 LYS cc_start: 0.8981 (mttt) cc_final: 0.8521 (mmmt) REVERT: C 269 MET cc_start: 0.8668 (tpt) cc_final: 0.8206 (tpt) REVERT: D 47 MET cc_start: 0.4082 (mmt) cc_final: 0.0782 (mmp) REVERT: D 51 ASP cc_start: 0.8181 (p0) cc_final: 0.7621 (p0) REVERT: D 82 MET cc_start: 0.9256 (tpt) cc_final: 0.8724 (tpt) REVERT: D 113 LYS cc_start: 0.8672 (mttt) cc_final: 0.8386 (mttp) REVERT: D 227 MET cc_start: 0.8628 (tpp) cc_final: 0.8422 (mtp) REVERT: E 11 ASP cc_start: 0.8807 (t0) cc_final: 0.8520 (t70) REVERT: E 113 LYS cc_start: 0.8565 (mttt) cc_final: 0.8271 (mtpm) REVERT: E 248 ILE cc_start: 0.9209 (mt) cc_final: 0.8942 (tt) outliers start: 22 outliers final: 10 residues processed: 284 average time/residue: 0.1260 time to fit residues: 52.8879 Evaluate side-chains 196 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 162 ASN C 246 GLN C 371 HIS D 12 ASN D 40 HIS E 40 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.096929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.083205 restraints weight = 26442.000| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.19 r_work: 0.2867 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14960 Z= 0.247 Angle : 0.683 6.278 20305 Z= 0.349 Chirality : 0.047 0.157 2255 Planarity : 0.006 0.048 2595 Dihedral : 6.468 66.021 2085 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.88 % Favored : 95.57 % Rotamer: Outliers : 2.24 % Allowed : 9.58 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1830 helix: 0.70 (0.19), residues: 760 sheet: -0.44 (0.29), residues: 265 loop : 0.51 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 147 TYR 0.013 0.002 TYR D 294 PHE 0.013 0.002 PHE A 255 TRP 0.018 0.002 TRP D 79 HIS 0.007 0.001 HIS D 40 Details of bonding type rmsd covalent geometry : bond 0.00581 (14960) covalent geometry : angle 0.68319 (20305) hydrogen bonds : bond 0.04803 ( 755) hydrogen bonds : angle 4.92338 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 299 MET cc_start: 0.9214 (mmm) cc_final: 0.8916 (mmm) REVERT: B 9 VAL cc_start: 0.9429 (t) cc_final: 0.9102 (m) REVERT: B 71 ILE cc_start: 0.9394 (mt) cc_final: 0.9155 (mt) REVERT: B 192 ILE cc_start: 0.9218 (mm) cc_final: 0.8729 (pt) REVERT: C 353 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8073 (mm-40) REVERT: D 9 VAL cc_start: 0.9479 (t) cc_final: 0.9156 (m) REVERT: D 47 MET cc_start: 0.3672 (mmt) cc_final: 0.0174 (mmp) REVERT: D 51 ASP cc_start: 0.8194 (p0) cc_final: 0.7721 (p0) REVERT: D 82 MET cc_start: 0.9323 (tpt) cc_final: 0.8783 (tpt) REVERT: D 263 GLN cc_start: 0.8852 (mt0) cc_final: 0.8560 (mt0) REVERT: E 120 THR cc_start: 0.9415 (m) cc_final: 0.9160 (p) REVERT: E 123 MET cc_start: 0.9385 (mmp) cc_final: 0.9166 (mmt) REVERT: E 313 MET cc_start: 0.8654 (ttp) cc_final: 0.8370 (ttp) outliers start: 35 outliers final: 21 residues processed: 216 average time/residue: 0.1111 time to fit residues: 37.4936 Evaluate side-chains 182 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 239 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 98 optimal weight: 0.4980 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 12 ASN D 40 HIS E 40 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.097724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.084030 restraints weight = 26259.766| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.19 r_work: 0.2883 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14960 Z= 0.179 Angle : 0.627 6.019 20305 Z= 0.314 Chirality : 0.045 0.153 2255 Planarity : 0.005 0.042 2595 Dihedral : 6.152 57.331 2085 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.33 % Favored : 96.12 % Rotamer: Outliers : 2.49 % Allowed : 11.44 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1830 helix: 0.90 (0.20), residues: 765 sheet: -0.29 (0.30), residues: 265 loop : 0.45 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 147 TYR 0.010 0.001 TYR C 306 PHE 0.008 0.001 PHE A 255 TRP 0.012 0.001 TRP D 79 HIS 0.007 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00416 (14960) covalent geometry : angle 0.62693 (20305) hydrogen bonds : bond 0.04056 ( 755) hydrogen bonds : angle 4.68531 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8474 (t160) REVERT: A 299 MET cc_start: 0.9208 (mmm) cc_final: 0.8944 (mmm) REVERT: A 305 MET cc_start: 0.9034 (mmt) cc_final: 0.8779 (tpp) REVERT: B 9 VAL cc_start: 0.9377 (t) cc_final: 0.9040 (m) REVERT: B 192 ILE cc_start: 0.9195 (mm) cc_final: 0.8813 (pt) REVERT: C 227 MET cc_start: 0.8369 (tpp) cc_final: 0.8073 (ttt) REVERT: D 9 VAL cc_start: 0.9427 (t) cc_final: 0.9067 (m) REVERT: D 47 MET cc_start: 0.3575 (mmt) cc_final: 0.0348 (mmp) REVERT: D 51 ASP cc_start: 0.8180 (p0) cc_final: 0.7729 (p0) REVERT: D 184 ASP cc_start: 0.8398 (m-30) cc_final: 0.8192 (m-30) REVERT: E 120 THR cc_start: 0.9429 (m) cc_final: 0.9038 (p) REVERT: E 313 MET cc_start: 0.8577 (ttp) cc_final: 0.8285 (ttp) outliers start: 39 outliers final: 27 residues processed: 214 average time/residue: 0.1146 time to fit residues: 37.8584 Evaluate side-chains 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 113 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 246 GLN D 12 ASN D 40 HIS E 40 HIS E 246 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085812 restraints weight = 25983.345| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.19 r_work: 0.2912 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14960 Z= 0.129 Angle : 0.593 5.922 20305 Z= 0.294 Chirality : 0.043 0.150 2255 Planarity : 0.004 0.040 2595 Dihedral : 5.871 51.870 2085 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.39 % Favored : 96.07 % Rotamer: Outliers : 2.17 % Allowed : 12.65 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1830 helix: 1.06 (0.20), residues: 765 sheet: -0.51 (0.29), residues: 295 loop : 0.73 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 372 TYR 0.012 0.001 TYR C 306 PHE 0.007 0.001 PHE C 31 TRP 0.009 0.001 TRP D 79 HIS 0.006 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00297 (14960) covalent geometry : angle 0.59266 (20305) hydrogen bonds : bond 0.03644 ( 755) hydrogen bonds : angle 4.51265 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8488 (t160) REVERT: B 9 VAL cc_start: 0.9355 (t) cc_final: 0.9025 (m) REVERT: B 192 ILE cc_start: 0.9169 (mm) cc_final: 0.8857 (pt) REVERT: B 355 MET cc_start: 0.8028 (tpp) cc_final: 0.7699 (mmt) REVERT: C 132 MET cc_start: 0.8708 (ttp) cc_final: 0.8438 (ttp) REVERT: C 325 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8676 (mmm) REVERT: D 9 VAL cc_start: 0.9390 (t) cc_final: 0.9021 (m) REVERT: D 47 MET cc_start: 0.2960 (mmt) cc_final: 0.0061 (mmt) REVERT: D 51 ASP cc_start: 0.8202 (p0) cc_final: 0.7520 (p0) REVERT: E 16 LEU cc_start: 0.9457 (mt) cc_final: 0.9239 (mp) REVERT: E 47 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.3342 (tpt) REVERT: E 120 THR cc_start: 0.9437 (m) cc_final: 0.9032 (p) REVERT: E 151 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8694 (tp) REVERT: E 246 GLN cc_start: 0.8789 (tt0) cc_final: 0.8277 (mt0) outliers start: 34 outliers final: 22 residues processed: 219 average time/residue: 0.1058 time to fit residues: 36.4680 Evaluate side-chains 208 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 184 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 246 GLN D 12 ASN D 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.096083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.082556 restraints weight = 26307.186| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.18 r_work: 0.2858 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14960 Z= 0.225 Angle : 0.654 11.215 20305 Z= 0.325 Chirality : 0.046 0.154 2255 Planarity : 0.005 0.037 2595 Dihedral : 6.019 52.119 2085 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.77 % Favored : 95.68 % Rotamer: Outliers : 3.13 % Allowed : 12.91 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.20), residues: 1830 helix: 0.99 (0.20), residues: 760 sheet: -0.14 (0.32), residues: 255 loop : 0.31 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 372 TYR 0.009 0.001 TYR D 166 PHE 0.015 0.001 PHE E 223 TRP 0.009 0.002 TRP B 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00531 (14960) covalent geometry : angle 0.65403 (20305) hydrogen bonds : bond 0.04216 ( 755) hydrogen bonds : angle 4.61812 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.607 Fit side-chains REVERT: A 12 ASN cc_start: 0.8866 (OUTLIER) cc_final: 0.8591 (t160) REVERT: A 299 MET cc_start: 0.9090 (mmm) cc_final: 0.8830 (mmt) REVERT: B 192 ILE cc_start: 0.9180 (mm) cc_final: 0.8805 (pt) REVERT: C 44 MET cc_start: 0.6073 (tmm) cc_final: 0.5409 (pmm) REVERT: D 9 VAL cc_start: 0.9409 (t) cc_final: 0.9029 (m) REVERT: D 47 MET cc_start: 0.3429 (mmt) cc_final: 0.0535 (mmt) REVERT: D 51 ASP cc_start: 0.8469 (p0) cc_final: 0.7832 (p0) REVERT: D 263 GLN cc_start: 0.8655 (mt0) cc_final: 0.8438 (mt0) REVERT: E 47 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.3364 (tpt) REVERT: E 227 MET cc_start: 0.8521 (tpp) cc_final: 0.8308 (mpp) REVERT: E 246 GLN cc_start: 0.8852 (tt0) cc_final: 0.8205 (mt0) outliers start: 49 outliers final: 38 residues processed: 210 average time/residue: 0.1131 time to fit residues: 36.9539 Evaluate side-chains 201 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 12 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082952 restraints weight = 26186.499| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.19 r_work: 0.2863 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14960 Z= 0.197 Angle : 0.638 10.759 20305 Z= 0.316 Chirality : 0.045 0.152 2255 Planarity : 0.004 0.036 2595 Dihedral : 6.011 50.707 2085 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.55 % Favored : 95.90 % Rotamer: Outliers : 3.32 % Allowed : 13.10 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1830 helix: 0.93 (0.19), residues: 765 sheet: -0.18 (0.32), residues: 255 loop : 0.28 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 372 TYR 0.009 0.001 TYR C 133 PHE 0.019 0.001 PHE C 223 TRP 0.010 0.001 TRP A 86 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00462 (14960) covalent geometry : angle 0.63777 (20305) hydrogen bonds : bond 0.04056 ( 755) hydrogen bonds : angle 4.60125 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8562 (t160) REVERT: A 226 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8778 (tp30) REVERT: B 192 ILE cc_start: 0.9186 (mm) cc_final: 0.8808 (pt) REVERT: C 180 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8871 (tt) REVERT: D 9 VAL cc_start: 0.9391 (t) cc_final: 0.8995 (m) REVERT: D 47 MET cc_start: 0.3405 (mmt) cc_final: 0.0551 (mmt) REVERT: D 51 ASP cc_start: 0.8451 (p0) cc_final: 0.7792 (p0) REVERT: E 47 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.3334 (tpt) outliers start: 52 outliers final: 40 residues processed: 209 average time/residue: 0.1148 time to fit residues: 37.0034 Evaluate side-chains 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 246 GLN Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 172 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS ** D 12 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 = 0.3167 r_free = 0.3167 target = 0.094755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081213 restraints weight = 26475.245| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.19 r_work: 0.2827 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 14960 Z= 0.259 Angle : 0.673 8.908 20305 Z= 0.336 Chirality : 0.047 0.155 2255 Planarity : 0.005 0.044 2595 Dihedral : 6.183 50.081 2085 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.10 % Favored : 95.36 % Rotamer: Outliers : 3.26 % Allowed : 13.55 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 1830 helix: 0.83 (0.19), residues: 760 sheet: -0.35 (0.32), residues: 255 loop : 0.11 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 147 TYR 0.011 0.001 TYR D 294 PHE 0.013 0.001 PHE E 223 TRP 0.010 0.002 TRP B 79 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00609 (14960) covalent geometry : angle 0.67320 (20305) hydrogen bonds : bond 0.04449 ( 755) hydrogen bonds : angle 4.72858 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 226 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8730 (tp30) REVERT: A 294 TYR cc_start: 0.8953 (m-10) cc_final: 0.8631 (m-10) REVERT: B 9 VAL cc_start: 0.9448 (t) cc_final: 0.9211 (m) REVERT: B 192 ILE cc_start: 0.9223 (mm) cc_final: 0.8804 (pt) REVERT: D 9 VAL cc_start: 0.9401 (t) cc_final: 0.8994 (m) REVERT: D 47 MET cc_start: 0.3339 (mmt) cc_final: 0.0439 (mmt) REVERT: D 51 ASP cc_start: 0.8610 (p0) cc_final: 0.8000 (p0) REVERT: D 132 MET cc_start: 0.8967 (tmm) cc_final: 0.8527 (ptm) REVERT: D 176 MET cc_start: 0.8747 (mmm) cc_final: 0.8442 (mtp) REVERT: D 305 MET cc_start: 0.9388 (mmm) cc_final: 0.8995 (tpp) REVERT: E 47 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.3389 (tpt) REVERT: E 354 GLN cc_start: 0.8999 (pt0) cc_final: 0.8697 (pt0) REVERT: E 355 MET cc_start: 0.8418 (tpp) cc_final: 0.8169 (tpp) outliers start: 51 outliers final: 42 residues processed: 199 average time/residue: 0.1165 time to fit residues: 35.5931 Evaluate side-chains 199 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 289 ILE Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 226 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 168 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS D 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.099656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.086000 restraints weight = 25983.964| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.23 r_work: 0.2910 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14960 Z= 0.112 Angle : 0.589 8.486 20305 Z= 0.290 Chirality : 0.043 0.147 2255 Planarity : 0.004 0.041 2595 Dihedral : 5.800 50.001 2085 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.28 % Favored : 96.17 % Rotamer: Outliers : 2.04 % Allowed : 14.38 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1830 helix: 1.00 (0.20), residues: 765 sheet: -0.12 (0.33), residues: 255 loop : 0.33 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 28 TYR 0.013 0.001 TYR C 306 PHE 0.020 0.001 PHE C 223 TRP 0.010 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00254 (14960) covalent geometry : angle 0.58912 (20305) hydrogen bonds : bond 0.03437 ( 755) hydrogen bonds : angle 4.52518 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 0.591 Fit side-chains REVERT: B 192 ILE cc_start: 0.9223 (mm) cc_final: 0.8943 (pt) REVERT: C 28 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8345 (ttm-80) REVERT: C 132 MET cc_start: 0.8648 (ttp) cc_final: 0.8385 (ttp) REVERT: C 227 MET cc_start: 0.8401 (tpp) cc_final: 0.8193 (mmm) REVERT: D 9 VAL cc_start: 0.9337 (t) cc_final: 0.8932 (m) REVERT: D 47 MET cc_start: 0.3097 (mmt) cc_final: 0.0452 (mmt) REVERT: D 51 ASP cc_start: 0.8500 (p0) cc_final: 0.7879 (p0) REVERT: D 176 MET cc_start: 0.8870 (mmm) cc_final: 0.8505 (mtt) REVERT: D 269 MET cc_start: 0.9216 (mmm) cc_final: 0.9014 (mmt) REVERT: D 299 MET cc_start: 0.8833 (mmp) cc_final: 0.8585 (mmm) REVERT: E 16 LEU cc_start: 0.9434 (mt) cc_final: 0.9216 (mp) REVERT: E 34 ILE cc_start: 0.9463 (tp) cc_final: 0.9088 (pt) REVERT: E 41 GLN cc_start: 0.8247 (tp40) cc_final: 0.7698 (mt0) REVERT: E 47 MET cc_start: 0.5036 (OUTLIER) cc_final: 0.3428 (tpt) REVERT: E 120 THR cc_start: 0.9445 (m) cc_final: 0.8989 (p) REVERT: E 151 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8724 (tp) REVERT: E 353 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7920 (mm110) REVERT: E 354 GLN cc_start: 0.8932 (pt0) cc_final: 0.8589 (pt0) REVERT: E 355 MET cc_start: 0.8364 (tpp) cc_final: 0.8095 (tpp) outliers start: 32 outliers final: 26 residues processed: 218 average time/residue: 0.1089 time to fit residues: 36.9720 Evaluate side-chains 204 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 135 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 0.0970 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS ** D 12 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 = 0.3255 r_free = 0.3255 target = 0.100522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.087058 restraints weight = 25765.346| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.21 r_work: 0.2936 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14960 Z= 0.107 Angle : 0.589 8.091 20305 Z= 0.289 Chirality : 0.043 0.182 2255 Planarity : 0.004 0.040 2595 Dihedral : 5.607 48.502 2085 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.06 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 14.82 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1830 helix: 1.29 (0.20), residues: 735 sheet: -0.01 (0.33), residues: 255 loop : 0.39 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 372 TYR 0.011 0.001 TYR C 306 PHE 0.026 0.001 PHE C 223 TRP 0.009 0.001 TRP C 79 HIS 0.008 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00240 (14960) covalent geometry : angle 0.58901 (20305) hydrogen bonds : bond 0.03347 ( 755) hydrogen bonds : angle 4.44357 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.592 Fit side-chains REVERT: B 65 LEU cc_start: 0.8928 (mt) cc_final: 0.8717 (mt) REVERT: B 192 ILE cc_start: 0.9221 (mm) cc_final: 0.8884 (pt) REVERT: C 28 ARG cc_start: 0.8588 (ttm-80) cc_final: 0.8317 (ttm-80) REVERT: C 72 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 132 MET cc_start: 0.8663 (ttp) cc_final: 0.8386 (ttp) REVERT: D 9 VAL cc_start: 0.9299 (t) cc_final: 0.8930 (m) REVERT: D 47 MET cc_start: 0.2990 (mmt) cc_final: 0.0337 (mmt) REVERT: D 51 ASP cc_start: 0.8478 (p0) cc_final: 0.7865 (p0) REVERT: D 176 MET cc_start: 0.8873 (mmm) cc_final: 0.8508 (mtt) REVERT: D 269 MET cc_start: 0.9209 (mmm) cc_final: 0.8987 (mmt) REVERT: D 299 MET cc_start: 0.8840 (mmp) cc_final: 0.8624 (mmm) REVERT: E 16 LEU cc_start: 0.9424 (mt) cc_final: 0.9210 (mp) REVERT: E 34 ILE cc_start: 0.9449 (tp) cc_final: 0.9122 (pt) REVERT: E 41 GLN cc_start: 0.8206 (tp40) cc_final: 0.7697 (mt0) REVERT: E 47 MET cc_start: 0.4914 (OUTLIER) cc_final: 0.3462 (tpt) REVERT: E 120 THR cc_start: 0.9463 (m) cc_final: 0.9037 (p) REVERT: E 151 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8721 (tp) REVERT: E 353 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7829 (mm110) REVERT: E 354 GLN cc_start: 0.8879 (pt0) cc_final: 0.8518 (pt0) REVERT: E 355 MET cc_start: 0.8161 (tpp) cc_final: 0.7710 (tpp) outliers start: 29 outliers final: 22 residues processed: 210 average time/residue: 0.1137 time to fit residues: 36.7757 Evaluate side-chains 200 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 40 HIS Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 298 VAL Chi-restraints excluded: chain D residue 349 LEU Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 199 SER Chi-restraints excluded: chain E residue 360 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 175 optimal weight: 0.0570 chunk 63 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.099328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.085839 restraints weight = 25978.774| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.22 r_work: 0.2915 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14960 Z= 0.132 Angle : 0.596 8.788 20305 Z= 0.292 Chirality : 0.043 0.184 2255 Planarity : 0.004 0.040 2595 Dihedral : 5.595 46.564 2085 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.22 % Favored : 96.23 % Rotamer: Outliers : 1.98 % Allowed : 15.34 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.20), residues: 1830 helix: 1.10 (0.20), residues: 765 sheet: 0.00 (0.33), residues: 255 loop : 0.38 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 147 TYR 0.009 0.001 TYR C 306 PHE 0.009 0.001 PHE E 223 TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00305 (14960) covalent geometry : angle 0.59645 (20305) hydrogen bonds : bond 0.03492 ( 755) hydrogen bonds : angle 4.43601 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3395.65 seconds wall clock time: 59 minutes 7.99 seconds (3547.99 seconds total)