Starting phenix.real_space_refine on Sat Aug 23 23:19:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oid_16889/08_2025/8oid_16889.map" } resolution = 2.3 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= 0.006 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 9210 2.51 5 N 2460 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15206 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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 bond proxies already assigned to first conformer: 2937 Chain: "C" 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} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Classifications: {'water': 159} Link IDs: {None: 158} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.74, per 1000 atoms: 0.18 Number of scatterers: 15206 At special positions: 0 Unit cell: (93.13, 92.435, 193.21, 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 3416 8.00 N 2460 7.00 C 9210 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: 1.00 Conformation dependent library (CDL) restraints added in 834.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 100 helices and 30 sheets defined 48.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) 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 233 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 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) 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 233 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 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) 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 233 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 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.735A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) 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 233 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 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) 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 233 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 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.106A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.562A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.356A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL 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: 6.354A pdb=" N THR 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: 6.563A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL 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: 6.355A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 725 hydrogen bonds defined for protein. 1885 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: 2.12 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4716 1.34 - 1.46: 2340 1.46 - 1.57: 7664 1.57 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 14920 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.76e+00 ... (remaining 14915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 19729 1.50 - 3.00: 358 3.00 - 4.50: 113 4.50 - 6.00: 41 6.00 - 7.49: 9 Bond angle restraints: 20250 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.94 -5.44 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 115.93 -5.43 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 ... (remaining 20245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 8805 32.43 - 64.86: 140 64.86 - 97.28: 20 97.28 - 129.71: 5 129.71 - 162.14: 5 Dihedral angle restraints: 8975 sinusoidal: 3615 harmonic: 5360 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.14 -162.14 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.10 -162.10 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.08 -162.07 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1189 0.029 - 0.058: 693 0.058 - 0.087: 177 0.087 - 0.115: 159 0.115 - 0.144: 27 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2242 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO C 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 164 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO E 164 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 138 2.45 - 3.06: 10189 3.06 - 3.68: 24368 3.68 - 4.29: 40105 4.29 - 4.90: 62710 Nonbonded interactions: 137510 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O HOH C 557 " model vdw 1.840 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 548 " model vdw 1.857 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 514 " model vdw 1.873 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 526 " model vdw 1.877 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 532 " model vdw 1.880 2.170 ... (remaining 137505 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 'C' selection = chain 'A' selection = chain 'B' 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=0.50 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: 4.040 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.470 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.004 0.057 14920 Z= 0.185 Angle : 0.608 7.494 20250 Z= 0.303 Chirality : 0.044 0.144 2245 Planarity : 0.004 0.039 2585 Dihedral : 13.008 162.140 5545 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.96 % Allowed : 4.17 % Favored : 94.87 % 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 aren not related in a simple way. whole: -0.64 (0.19), residues: 1830 helix: -1.33 (0.16), residues: 790 sheet: 0.07 (0.26), residues: 335 loop : 0.83 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 210 TYR 0.012 0.001 TYR C 143 PHE 0.006 0.001 PHE B 262 TRP 0.014 0.002 TRP D 340 HIS 0.002 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00413 (14920) covalent geometry : angle 0.60841 (20250) hydrogen bonds : bond 0.13645 ( 715) hydrogen bonds : angle 6.23939 ( 1885) *********************** 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 295 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 0.400 Fit side-chains REVERT: C 47 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5836 (tpt) REVERT: C 180 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8207 (mtt) REVERT: A 180 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8753 (tp) REVERT: D 47 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.5143 (tpt) REVERT: D 121 GLN cc_start: 0.7959 (tt0) cc_final: 0.7674 (tm130) REVERT: D 325 MET cc_start: 0.8917 (mmp) cc_final: 0.8625 (mmp) REVERT: D 351 THR cc_start: 0.8906 (m) cc_final: 0.8674 (m) REVERT: E 47 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.4766 (tpt) outliers start: 15 outliers final: 0 residues processed: 287 average time/residue: 0.6745 time to fit residues: 209.6609 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 128 ASN C 225 GLN C 246 GLN A 128 ASN A 353 GLN B 12 ASN B 41 GLN B 128 ASN B 225 GLN B 353 GLN E 78 ASN E 121 GLN E 353 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.093396 restraints weight = 24083.078| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.58 r_work: 0.2869 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14920 Z= 0.168 Angle : 0.634 8.558 20250 Z= 0.307 Chirality : 0.046 0.190 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.057 167.916 2098 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.67 % Allowed : 8.27 % Favored : 90.06 % 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 aren not related in a simple way. whole: 0.91 (0.20), residues: 1830 helix: 0.21 (0.19), residues: 770 sheet: 0.53 (0.26), residues: 345 loop : 1.44 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.013 0.001 TYR A 143 PHE 0.009 0.001 PHE D 262 TRP 0.016 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00382 (14920) covalent geometry : angle 0.63416 (20250) hydrogen bonds : bond 0.04199 ( 715) hydrogen bonds : angle 4.84058 ( 1885) *********************** 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 234 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.406 Fit side-chains REVERT: C 47 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5692 (tpt) REVERT: C 180 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8553 (tp) REVERT: A 180 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8650 (tt) REVERT: B 64 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9017 (pp) REVERT: B 68 LYS cc_start: 0.9033 (mptt) cc_final: 0.8819 (mmtt) REVERT: D 47 MET cc_start: 0.5648 (OUTLIER) cc_final: 0.5108 (tpt) REVERT: D 121 GLN cc_start: 0.8484 (tt0) cc_final: 0.8246 (tm-30) REVERT: D 325 MET cc_start: 0.9058 (mmp) cc_final: 0.8759 (mmp) REVERT: D 326 LYS cc_start: 0.8395 (tptt) cc_final: 0.7837 (pttm) REVERT: D 351 THR cc_start: 0.9044 (m) cc_final: 0.8781 (m) REVERT: D 353 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8128 (mm-40) REVERT: E 47 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4656 (tpt) outliers start: 26 outliers final: 4 residues processed: 223 average time/residue: 0.6213 time to fit residues: 150.8966 Evaluate side-chains 203 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 0.0000 chunk 42 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 225 GLN C 246 GLN A 354 GLN B 12 ASN B 128 ASN B 225 GLN E 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.120024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.092202 restraints weight = 19970.186| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.51 r_work: 0.2864 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2717 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2717 r_free = 0.2717 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2717 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14920 Z= 0.232 Angle : 0.678 8.894 20250 Z= 0.332 Chirality : 0.049 0.185 2245 Planarity : 0.005 0.042 2585 Dihedral : 12.285 171.662 2098 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.05 % Allowed : 8.78 % Favored : 89.17 % 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 aren not related in a simple way. whole: 1.36 (0.20), residues: 1830 helix: 0.59 (0.19), residues: 770 sheet: 0.77 (0.26), residues: 345 loop : 1.68 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 28 TYR 0.013 0.001 TYR A 143 PHE 0.013 0.002 PHE D 262 TRP 0.021 0.003 TRP B 340 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00538 (14920) covalent geometry : angle 0.67817 (20250) hydrogen bonds : bond 0.04870 ( 715) hydrogen bonds : angle 4.81883 ( 1885) *********************** 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 232 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.482 Fit side-chains REVERT: C 47 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5861 (tpt) REVERT: C 180 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8657 (tp) REVERT: A 180 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8624 (tt) REVERT: A 276 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: B 47 MET cc_start: 0.4581 (mmt) cc_final: 0.4195 (tpt) REVERT: B 64 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.9061 (pp) REVERT: B 68 LYS cc_start: 0.9017 (mptt) cc_final: 0.8787 (mmtt) REVERT: B 72 GLU cc_start: 0.7937 (mp0) cc_final: 0.7724 (mp0) REVERT: B 153 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8748 (ttp) REVERT: B 314 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8094 (tp40) REVERT: D 47 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5201 (tpt) REVERT: D 121 GLN cc_start: 0.8525 (tt0) cc_final: 0.8268 (tm-30) REVERT: D 292 ASP cc_start: 0.8718 (m-30) cc_final: 0.8512 (m-30) REVERT: D 326 LYS cc_start: 0.8416 (tptt) cc_final: 0.7960 (pttm) REVERT: D 351 THR cc_start: 0.9056 (m) cc_final: 0.8740 (m) REVERT: D 353 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8278 (mm110) REVERT: E 47 MET cc_start: 0.5472 (OUTLIER) cc_final: 0.4672 (tpt) REVERT: E 95 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.7643 (mtt-85) REVERT: E 132 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8114 (ttp) outliers start: 32 outliers final: 8 residues processed: 219 average time/residue: 0.5825 time to fit residues: 139.1118 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 181 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 148 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN E 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095030 restraints weight = 29553.551| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.91 r_work: 0.2881 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14920 Z= 0.119 Angle : 0.591 8.095 20250 Z= 0.279 Chirality : 0.044 0.180 2245 Planarity : 0.004 0.037 2585 Dihedral : 11.946 173.969 2098 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.35 % Allowed : 10.51 % Favored : 88.14 % 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 aren not related in a simple way. whole: 1.70 (0.20), residues: 1830 helix: 0.89 (0.19), residues: 775 sheet: 0.87 (0.26), residues: 345 loop : 1.89 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.012 0.001 TYR A 143 PHE 0.008 0.001 PHE B 262 TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00263 (14920) covalent geometry : angle 0.59056 (20250) hydrogen bonds : bond 0.03366 ( 715) hydrogen bonds : angle 4.48120 ( 1885) *********************** 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 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.511 Fit side-chains REVERT: C 47 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5849 (tpt) REVERT: C 180 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8427 (tp) REVERT: A 180 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8654 (tt) REVERT: A 276 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (mm-30) REVERT: B 47 MET cc_start: 0.4670 (mmt) cc_final: 0.4269 (tpt) REVERT: B 68 LYS cc_start: 0.9048 (mptt) cc_final: 0.8809 (mmtt) REVERT: B 72 GLU cc_start: 0.8010 (mp0) cc_final: 0.7791 (mp0) REVERT: D 47 MET cc_start: 0.5745 (OUTLIER) cc_final: 0.5210 (tpt) REVERT: D 64 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8733 (pp) REVERT: D 121 GLN cc_start: 0.8619 (tt0) cc_final: 0.8332 (tm-30) REVERT: D 292 ASP cc_start: 0.8765 (m-30) cc_final: 0.8561 (m-30) REVERT: D 314 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8422 (tt0) REVERT: D 326 LYS cc_start: 0.8450 (tptt) cc_final: 0.7902 (pttm) REVERT: D 351 THR cc_start: 0.9039 (m) cc_final: 0.8721 (m) REVERT: E 47 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.4686 (tpt) REVERT: E 64 ILE cc_start: 0.9402 (OUTLIER) cc_final: 0.8875 (pp) REVERT: E 95 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7705 (mtt-85) outliers start: 21 outliers final: 3 residues processed: 214 average time/residue: 0.6518 time to fit residues: 152.3222 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 183 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095171 restraints weight = 19492.901| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.54 r_work: 0.2925 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14920 Z= 0.126 Angle : 0.590 8.018 20250 Z= 0.279 Chirality : 0.044 0.178 2245 Planarity : 0.004 0.037 2585 Dihedral : 11.931 173.658 2098 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.60 % Allowed : 10.45 % Favored : 87.95 % 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 aren not related in a simple way. whole: 1.88 (0.20), residues: 1830 helix: 1.03 (0.19), residues: 775 sheet: 0.96 (0.27), residues: 345 loop : 2.00 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.012 0.001 TYR A 143 PHE 0.008 0.001 PHE D 262 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00281 (14920) covalent geometry : angle 0.58961 (20250) hydrogen bonds : bond 0.03504 ( 715) hydrogen bonds : angle 4.43551 ( 1885) *********************** 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 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.589 Fit side-chains REVERT: C 47 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5888 (tpt) REVERT: C 64 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8573 (pp) REVERT: C 180 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8400 (tp) REVERT: A 180 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 276 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8159 (mm-30) REVERT: B 47 MET cc_start: 0.4662 (mmt) cc_final: 0.4279 (tpt) REVERT: B 64 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 68 LYS cc_start: 0.9008 (mptt) cc_final: 0.8757 (mmtt) REVERT: B 72 GLU cc_start: 0.7894 (mp0) cc_final: 0.7628 (mp0) REVERT: D 47 MET cc_start: 0.5672 (OUTLIER) cc_final: 0.5176 (tpt) REVERT: D 64 ILE cc_start: 0.9118 (OUTLIER) cc_final: 0.8706 (pp) REVERT: D 121 GLN cc_start: 0.8538 (tt0) cc_final: 0.8265 (tm-30) REVERT: D 222 ASP cc_start: 0.8534 (t70) cc_final: 0.8238 (t70) REVERT: D 241 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8321 (tt0) REVERT: D 292 ASP cc_start: 0.8681 (m-30) cc_final: 0.8469 (m-30) REVERT: D 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: D 326 LYS cc_start: 0.8404 (tptt) cc_final: 0.7914 (pttm) REVERT: D 351 THR cc_start: 0.9037 (m) cc_final: 0.8723 (m) REVERT: E 64 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8862 (pp) REVERT: E 95 ARG cc_start: 0.7896 (mtt-85) cc_final: 0.7663 (mtt-85) REVERT: E 326 LYS cc_start: 0.8191 (tptt) cc_final: 0.7843 (tttm) REVERT: E 351 THR cc_start: 0.9136 (p) cc_final: 0.8928 (t) outliers start: 25 outliers final: 6 residues processed: 214 average time/residue: 0.6234 time to fit residues: 145.6133 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 187 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 181 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.093394 restraints weight = 25972.140| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.83 r_work: 0.2861 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14920 Z= 0.174 Angle : 0.629 8.504 20250 Z= 0.303 Chirality : 0.046 0.183 2245 Planarity : 0.004 0.038 2585 Dihedral : 12.105 173.031 2098 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.92 % Allowed : 10.51 % Favored : 87.56 % 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 aren not related in a simple way. whole: 1.87 (0.20), residues: 1830 helix: 1.00 (0.19), residues: 770 sheet: 1.00 (0.27), residues: 345 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.011 0.001 TYR A 143 PHE 0.010 0.001 PHE B 262 TRP 0.017 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00398 (14920) covalent geometry : angle 0.62936 (20250) hydrogen bonds : bond 0.04089 ( 715) hydrogen bonds : angle 4.55810 ( 1885) *********************** 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 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.549 Fit side-chains REVERT: C 47 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5811 (tpt) REVERT: C 51 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7849 (p0) REVERT: C 180 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 180 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8653 (tt) REVERT: A 276 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8246 (mm-30) REVERT: B 47 MET cc_start: 0.4689 (mmt) cc_final: 0.4359 (tpt) REVERT: B 64 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.8989 (pp) REVERT: B 68 LYS cc_start: 0.9079 (mptt) cc_final: 0.8822 (mmtt) REVERT: B 72 GLU cc_start: 0.7968 (mp0) cc_final: 0.7757 (mp0) REVERT: B 286 ASP cc_start: 0.8089 (m-30) cc_final: 0.7707 (m-30) REVERT: D 47 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5245 (tpt) REVERT: D 64 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8748 (pp) REVERT: D 121 GLN cc_start: 0.8583 (tt0) cc_final: 0.8321 (tm-30) REVERT: D 292 ASP cc_start: 0.8773 (m-30) cc_final: 0.8558 (m-30) REVERT: D 314 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: D 326 LYS cc_start: 0.8447 (tptt) cc_final: 0.7958 (pttm) REVERT: D 351 THR cc_start: 0.9020 (m) cc_final: 0.8761 (m) REVERT: E 95 ARG cc_start: 0.7910 (mtt-85) cc_final: 0.7678 (mtt-85) REVERT: E 326 LYS cc_start: 0.8229 (tptt) cc_final: 0.7884 (tttm) REVERT: E 351 THR cc_start: 0.9140 (p) cc_final: 0.8932 (t) outliers start: 30 outliers final: 10 residues processed: 217 average time/residue: 0.6113 time to fit residues: 144.5324 Evaluate side-chains 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 177 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.092739 restraints weight = 22522.168| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.57 r_work: 0.2860 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2711 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2711 r_free = 0.2711 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2711 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14920 Z= 0.215 Angle : 0.662 8.754 20250 Z= 0.321 Chirality : 0.048 0.186 2245 Planarity : 0.004 0.038 2585 Dihedral : 12.223 171.709 2098 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.92 % Allowed : 10.71 % Favored : 87.37 % 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 aren not related in a simple way. whole: 1.82 (0.20), residues: 1830 helix: 0.95 (0.19), residues: 770 sheet: 0.94 (0.27), residues: 345 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.010 0.001 TYR A 143 PHE 0.012 0.002 PHE B 262 TRP 0.020 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00497 (14920) covalent geometry : angle 0.66193 (20250) hydrogen bonds : bond 0.04485 ( 715) hydrogen bonds : angle 4.65318 ( 1885) *********************** 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 226 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.489 Fit side-chains REVERT: C 47 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5903 (tpt) REVERT: C 51 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7811 (p0) REVERT: C 64 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8671 (pp) REVERT: C 180 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8552 (tp) REVERT: A 180 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 205 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8373 (mt-10) REVERT: A 276 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8177 (mm-30) REVERT: B 47 MET cc_start: 0.4704 (mmt) cc_final: 0.4394 (tpt) REVERT: B 64 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9038 (pp) REVERT: B 68 LYS cc_start: 0.9060 (mptt) cc_final: 0.8804 (mmtt) REVERT: B 153 MET cc_start: 0.9046 (OUTLIER) cc_final: 0.8747 (ttp) REVERT: B 286 ASP cc_start: 0.8074 (m-30) cc_final: 0.7698 (m-30) REVERT: D 47 MET cc_start: 0.5706 (OUTLIER) cc_final: 0.5305 (tpt) REVERT: D 64 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8741 (pp) REVERT: D 121 GLN cc_start: 0.8513 (tt0) cc_final: 0.8271 (tm-30) REVERT: D 292 ASP cc_start: 0.8742 (m-30) cc_final: 0.8529 (m-30) REVERT: D 314 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: D 326 LYS cc_start: 0.8416 (tptt) cc_final: 0.7955 (pttm) REVERT: E 64 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.8886 (pp) REVERT: E 95 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7663 (mtt-85) REVERT: E 326 LYS cc_start: 0.8222 (tptt) cc_final: 0.7895 (tttm) REVERT: E 351 THR cc_start: 0.9161 (p) cc_final: 0.8949 (t) outliers start: 30 outliers final: 12 residues processed: 213 average time/residue: 0.6116 time to fit residues: 141.9905 Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 123 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094931 restraints weight = 29396.814| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.85 r_work: 0.2876 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14920 Z= 0.112 Angle : 0.583 8.031 20250 Z= 0.276 Chirality : 0.044 0.181 2245 Planarity : 0.003 0.037 2585 Dihedral : 11.946 173.565 2098 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.67 % Allowed : 11.15 % Favored : 87.18 % 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 aren not related in a simple way. whole: 1.99 (0.20), residues: 1830 helix: 1.12 (0.19), residues: 775 sheet: 0.92 (0.27), residues: 345 loop : 2.12 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.012 0.001 TYR A 143 PHE 0.006 0.001 PHE D 255 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00244 (14920) covalent geometry : angle 0.58292 (20250) hydrogen bonds : bond 0.03233 ( 715) hydrogen bonds : angle 4.39799 ( 1885) *********************** 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 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.430 Fit side-chains REVERT: C 47 MET cc_start: 0.6317 (OUTLIER) cc_final: 0.5843 (tpt) REVERT: C 132 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8330 (tmt) REVERT: C 180 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8395 (tp) REVERT: A 180 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8665 (tt) REVERT: A 205 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: A 276 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8265 (mm-30) REVERT: B 47 MET cc_start: 0.4702 (mmt) cc_final: 0.4396 (tpt) REVERT: B 64 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 68 LYS cc_start: 0.9043 (mptt) cc_final: 0.8798 (mmtt) REVERT: D 47 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5314 (tpt) REVERT: D 64 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8721 (pp) REVERT: D 121 GLN cc_start: 0.8585 (tt0) cc_final: 0.8327 (tm-30) REVERT: D 222 ASP cc_start: 0.8559 (t70) cc_final: 0.8273 (t70) REVERT: D 292 ASP cc_start: 0.8770 (m-30) cc_final: 0.8539 (m-30) REVERT: D 314 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8419 (tt0) REVERT: D 326 LYS cc_start: 0.8436 (tptt) cc_final: 0.7934 (pttm) REVERT: D 351 THR cc_start: 0.9019 (m) cc_final: 0.8739 (m) REVERT: E 95 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7677 (mtt-85) REVERT: E 326 LYS cc_start: 0.8246 (tptt) cc_final: 0.7875 (tttm) outliers start: 26 outliers final: 8 residues processed: 208 average time/residue: 0.5975 time to fit residues: 135.5848 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 47 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 158 optimal weight: 0.4980 chunk 147 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 79 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.097079 restraints weight = 21986.949| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.63 r_work: 0.2951 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14920 Z= 0.101 Angle : 0.567 7.520 20250 Z= 0.265 Chirality : 0.043 0.175 2245 Planarity : 0.003 0.038 2585 Dihedral : 11.722 174.844 2098 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.47 % Allowed : 11.41 % Favored : 87.12 % 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 aren not related in a simple way. whole: 2.11 (0.20), residues: 1830 helix: 1.23 (0.19), residues: 775 sheet: 0.96 (0.26), residues: 345 loop : 2.19 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 28 TYR 0.012 0.001 TYR A 143 PHE 0.006 0.001 PHE D 31 TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00220 (14920) covalent geometry : angle 0.56672 (20250) hydrogen bonds : bond 0.02967 ( 715) hydrogen bonds : angle 4.27317 ( 1885) *********************** 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 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.462 Fit side-chains REVERT: C 47 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5826 (tpt) REVERT: C 132 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8295 (tmt) REVERT: C 180 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 205 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: B 47 MET cc_start: 0.4701 (mmt) cc_final: 0.4448 (tpt) REVERT: B 64 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.8897 (pp) REVERT: B 68 LYS cc_start: 0.8992 (mptt) cc_final: 0.8745 (mmtt) REVERT: D 47 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5339 (tpt) REVERT: D 64 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8690 (pp) REVERT: D 121 GLN cc_start: 0.8539 (tt0) cc_final: 0.8278 (tm-30) REVERT: D 222 ASP cc_start: 0.8494 (t70) cc_final: 0.8224 (t70) REVERT: D 292 ASP cc_start: 0.8699 (m-30) cc_final: 0.8468 (m-30) REVERT: D 314 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: D 326 LYS cc_start: 0.8394 (tptt) cc_final: 0.7928 (pttm) REVERT: D 351 THR cc_start: 0.9027 (m) cc_final: 0.8707 (m) REVERT: E 95 ARG cc_start: 0.7842 (mtt-85) cc_final: 0.7627 (mtt-85) REVERT: E 326 LYS cc_start: 0.8241 (tptt) cc_final: 0.7938 (tttm) outliers start: 23 outliers final: 9 residues processed: 204 average time/residue: 0.6144 time to fit residues: 136.9203 Evaluate side-chains 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 129 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.121318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.093525 restraints weight = 20839.135| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.60 r_work: 0.2885 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14920 Z= 0.242 Angle : 0.681 8.798 20250 Z= 0.331 Chirality : 0.049 0.186 2245 Planarity : 0.005 0.038 2585 Dihedral : 12.226 170.987 2096 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.41 % Allowed : 11.28 % Favored : 87.31 % 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 aren not related in a simple way. whole: 1.89 (0.20), residues: 1830 helix: 1.03 (0.19), residues: 770 sheet: 0.88 (0.27), residues: 345 loop : 2.07 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 95 TYR 0.009 0.001 TYR D 143 PHE 0.012 0.002 PHE D 262 TRP 0.021 0.003 TRP B 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00558 (14920) covalent geometry : angle 0.68091 (20250) hydrogen bonds : bond 0.04665 ( 715) hydrogen bonds : angle 4.63366 ( 1885) ********************** 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 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.573 Fit side-chains REVERT: C 47 MET cc_start: 0.6292 (OUTLIER) cc_final: 0.5844 (tpt) REVERT: C 51 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (p0) REVERT: C 132 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8264 (tmt) REVERT: C 180 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8535 (tp) REVERT: A 205 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: B 47 MET cc_start: 0.4715 (mmt) cc_final: 0.4451 (tpt) REVERT: B 64 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8993 (pp) REVERT: B 68 LYS cc_start: 0.9061 (mptt) cc_final: 0.8806 (mmtt) REVERT: D 47 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5431 (tpt) REVERT: D 64 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8765 (pp) REVERT: D 121 GLN cc_start: 0.8494 (tt0) cc_final: 0.8222 (tm-30) REVERT: D 292 ASP cc_start: 0.8739 (m-30) cc_final: 0.8513 (m-30) REVERT: D 314 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8341 (tt0) REVERT: D 326 LYS cc_start: 0.8409 (tptt) cc_final: 0.7968 (pttm) REVERT: E 95 ARG cc_start: 0.7841 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: E 326 LYS cc_start: 0.8234 (tptt) cc_final: 0.7866 (tttm) outliers start: 22 outliers final: 8 residues processed: 202 average time/residue: 0.5924 time to fit residues: 130.6667 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 35 optimal weight: 10.0000 chunk 106 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 174 optimal weight: 0.0970 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.095202 restraints weight = 22603.306| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.70 r_work: 0.2915 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2771 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2771 r_free = 0.2771 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2771 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14920 Z= 0.127 Angle : 0.601 8.257 20250 Z= 0.285 Chirality : 0.045 0.181 2245 Planarity : 0.004 0.038 2585 Dihedral : 11.981 173.291 2096 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.28 % Allowed : 11.86 % Favored : 86.86 % 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 aren not related in a simple way. whole: 1.97 (0.20), residues: 1830 helix: 1.10 (0.19), residues: 775 sheet: 0.87 (0.27), residues: 345 loop : 2.13 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 95 TYR 0.011 0.001 TYR A 143 PHE 0.008 0.001 PHE B 262 TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00286 (14920) covalent geometry : angle 0.60067 (20250) hydrogen bonds : bond 0.03459 ( 715) hydrogen bonds : angle 4.41322 ( 1885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6549.15 seconds wall clock time: 111 minutes 55.14 seconds (6715.14 seconds total)