Starting phenix.real_space_refine on Thu Aug 6 12:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.map" model { file = "/net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zzi_74998/08_2026/9zzi_74998.cif" } resolution = 2.06 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14845 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.86, per 1000 atoms: 0.19 Number of scatterers: 14845 At special positions: 0 Unit cell: (96.187, 79.275, 192.374, 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 3020 8.00 N 2470 7.00 C 9235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 616.3 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 30 sheets defined 49.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.894A 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 193 Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.571A pdb=" N GLY A 197 " --> pdb=" O THR A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 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 257 Processing helix chain 'A' and resid 258 through 261 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 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 353 removed outlier: 6.406A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.905A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) 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: 3.895A 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 193 Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.570A pdb=" N GLY B 197 " --> pdb=" O THR B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 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 257 Processing helix chain 'B' and resid 258 through 261 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 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.407A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.906A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) 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: 3.894A 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 193 Processing helix chain 'C' and resid 194 through 197 removed outlier: 3.571A pdb=" N GLY C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 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 257 Processing helix chain 'C' and resid 258 through 261 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 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 353 removed outlier: 6.407A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.905A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) 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: 3.895A 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 193 Processing helix chain 'D' and resid 194 through 197 removed outlier: 3.570A pdb=" N GLY D 197 " --> pdb=" O THR D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 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 257 Processing helix chain 'D' and resid 258 through 261 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 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.406A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.905A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) 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: 3.894A 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 193 Processing helix chain 'E' and resid 194 through 197 removed outlier: 3.570A pdb=" N GLY E 197 " --> pdb=" O THR E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 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 257 Processing helix chain 'E' and resid 258 through 261 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 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 353 removed outlier: 6.407A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 3.905A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 6.553A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.553A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.553A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.554A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.554A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.552A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.553A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 752 hydrogen bonds defined for protein. 1923 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: 2.94 Time building geometry restraints manager: 1.56 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: 4194 1.34 - 1.45: 2581 1.45 - 1.57: 7980 1.57 - 1.69: 20 1.69 - 1.81: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CA PHE D 124 " pdb=" CB PHE D 124 " ideal model delta sigma weight residual 1.531 1.504 0.026 1.59e-02 3.96e+03 2.75e+00 bond pdb=" CA PHE A 124 " pdb=" CB PHE A 124 " ideal model delta sigma weight residual 1.531 1.504 0.026 1.59e-02 3.96e+03 2.74e+00 bond pdb=" CA PHE B 124 " pdb=" CB PHE B 124 " ideal model delta sigma weight residual 1.531 1.505 0.026 1.59e-02 3.96e+03 2.71e+00 bond pdb=" CA PHE C 124 " pdb=" CB PHE C 124 " ideal model delta sigma weight residual 1.531 1.505 0.026 1.59e-02 3.96e+03 2.69e+00 bond pdb=" CA PHE E 124 " pdb=" CB PHE E 124 " ideal model delta sigma weight residual 1.531 1.506 0.025 1.59e-02 3.96e+03 2.52e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 19762 3.26 - 6.53: 453 6.53 - 9.79: 65 9.79 - 13.06: 15 13.06 - 16.32: 10 Bond angle restraints: 20305 Sorted by residual: angle pdb=" CB LEU A 180 " pdb=" CG LEU A 180 " pdb=" CD2 LEU A 180 " ideal model delta sigma weight residual 110.70 94.38 16.32 3.00e+00 1.11e-01 2.96e+01 angle pdb=" CB LEU D 180 " pdb=" CG LEU D 180 " pdb=" CD2 LEU D 180 " ideal model delta sigma weight residual 110.70 94.38 16.32 3.00e+00 1.11e-01 2.96e+01 angle pdb=" CB LEU B 180 " pdb=" CG LEU B 180 " pdb=" CD2 LEU B 180 " ideal model delta sigma weight residual 110.70 94.39 16.31 3.00e+00 1.11e-01 2.96e+01 angle pdb=" CB LEU C 180 " pdb=" CG LEU C 180 " pdb=" CD2 LEU C 180 " ideal model delta sigma weight residual 110.70 94.41 16.29 3.00e+00 1.11e-01 2.95e+01 angle pdb=" CB LEU E 180 " pdb=" CG LEU E 180 " pdb=" CD2 LEU E 180 " ideal model delta sigma weight residual 110.70 94.44 16.26 3.00e+00 1.11e-01 2.94e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 8394 22.31 - 44.62: 496 44.62 - 66.92: 75 66.92 - 89.23: 25 89.23 - 111.54: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.54 -111.54 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.54 -111.54 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 51.53 -111.53 1 2.00e+01 2.50e-03 3.28e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1911 0.088 - 0.175: 294 0.175 - 0.263: 20 0.263 - 0.350: 20 0.350 - 0.438: 10 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CG LEU E 171 " pdb=" CB LEU E 171 " pdb=" CD1 LEU E 171 " pdb=" CD2 LEU E 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CG LEU D 171 " pdb=" CB LEU D 171 " pdb=" CD1 LEU D 171 " pdb=" CD2 LEU D 171 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 95 " -0.577 9.50e-02 1.11e+02 2.59e-01 4.10e+01 pdb=" NE ARG B 95 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 95 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG B 95 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 95 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 95 " 0.577 9.50e-02 1.11e+02 2.59e-01 4.10e+01 pdb=" NE ARG E 95 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG E 95 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG E 95 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 95 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 95 " 0.577 9.50e-02 1.11e+02 2.58e-01 4.09e+01 pdb=" NE ARG A 95 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 95 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 95 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 95 " 0.018 2.00e-02 2.50e+03 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 30 2.55 - 3.14: 11310 3.14 - 3.72: 24955 3.72 - 4.31: 36481 4.31 - 4.90: 57931 Nonbonded interactions: 130707 Sorted by model distance: nonbonded pdb="MG MG B 402 " pdb=" O HOH B 521 " model vdw 1.959 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 516 " model vdw 1.992 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 514 " model vdw 1.992 2.170 nonbonded pdb="MG MG E 402 " pdb=" O HOH E 514 " model vdw 1.994 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 514 " model vdw 1.994 2.170 ... (remaining 130702 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.150 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:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9028 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 : 0.007 0.055 14960 Z= 0.317 Angle : 1.286 16.322 20305 Z= 0.658 Chirality : 0.073 0.438 2255 Planarity : 0.020 0.259 2595 Dihedral : 15.634 111.537 5565 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.17), residues: 1830 helix: -1.96 (0.15), residues: 740 sheet: -1.09 (0.24), residues: 325 loop : 0.01 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.005 ARG B 196 TYR 0.075 0.010 TYR D 133 PHE 0.045 0.010 PHE E 255 TRP 0.046 0.013 TRP B 79 HIS 0.019 0.007 HIS E 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.32 (14960) covalent geometry : angle 1.28615 / 0.66 (20305) hydrogen bonds : bond 0.15218 / 10.56 ( 736) hydrogen bonds : angle 7.41725 / 5.17 ( 1923) *********************** 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 214 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.596 Fit side-chains REVERT: A 41 GLN cc_start: 0.7667 (tt0) cc_final: 0.7425 (tp40) REVERT: B 44 MET cc_start: 0.8358 (mtp) cc_final: 0.8125 (mtp) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.8875 time to fit residues: 203.3519 Evaluate side-chains 154 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 246 GLN C 246 GLN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.087477 restraints weight = 13662.776| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 0.91 r_work: 0.2881 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9225 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14960 Z= 0.144 Angle : 0.648 8.344 20305 Z= 0.318 Chirality : 0.045 0.184 2255 Planarity : 0.006 0.041 2595 Dihedral : 8.647 117.521 2085 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.83 % Allowed : 7.67 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.19), residues: 1830 helix: 0.24 (0.19), residues: 785 sheet: -0.30 (0.23), residues: 350 loop : 1.19 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 95 TYR 0.010 0.001 TYR D 188 PHE 0.011 0.002 PHE C 262 TRP 0.016 0.002 TRP A 340 HIS 0.007 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (14960) covalent geometry : angle 0.64813 / 0.32 (20305) hydrogen bonds : bond 0.04663 / 3.19 ( 736) hydrogen bonds : angle 5.51227 / 3.89 ( 1923) *********************** 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 185 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.611 Fit side-chains REVERT: A 41 GLN cc_start: 0.7526 (tt0) cc_final: 0.7115 (tp40) REVERT: A 47 MET cc_start: 0.5308 (ttp) cc_final: 0.4992 (ttm) REVERT: C 224 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: E 237 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: E 354 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7642 (mp-120) outliers start: 13 outliers final: 0 residues processed: 182 average time/residue: 0.8351 time to fit residues: 163.6174 Evaluate side-chains 160 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 158 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 GLN D 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.087753 restraints weight = 13914.546| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 0.92 r_work: 0.2885 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14960 Z= 0.119 Angle : 0.594 7.810 20305 Z= 0.289 Chirality : 0.044 0.179 2255 Planarity : 0.004 0.037 2595 Dihedral : 8.202 110.782 2085 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.58 % Allowed : 7.99 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.20), residues: 1830 helix: 1.00 (0.20), residues: 770 sheet: -0.10 (0.24), residues: 350 loop : 1.69 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 95 TYR 0.007 0.001 TYR C 143 PHE 0.010 0.001 PHE D 255 TRP 0.013 0.002 TRP A 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (14960) covalent geometry : angle 0.59378 / 0.29 (20305) hydrogen bonds : bond 0.04057 / 2.77 ( 736) hydrogen bonds : angle 5.18271 / 3.66 ( 1923) *********************** 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 179 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 170 time to evaluate : 0.674 Fit side-chains REVERT: A 41 GLN cc_start: 0.7512 (tt0) cc_final: 0.7078 (tp40) REVERT: A 47 MET cc_start: 0.5277 (ttp) cc_final: 0.5011 (ttm) REVERT: B 41 GLN cc_start: 0.7903 (tt0) cc_final: 0.7471 (tp40) REVERT: B 360 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 47 MET cc_start: 0.5234 (ttp) cc_final: 0.5022 (ttp) REVERT: C 224 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7987 (mp0) outliers start: 9 outliers final: 1 residues processed: 178 average time/residue: 0.8338 time to fit residues: 159.7906 Evaluate side-chains 162 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 224 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN B 162 ASN C 49 GLN C 162 ASN D 49 GLN D 162 ASN E 49 GLN E 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.105004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.085663 restraints weight = 13817.717| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 0.91 r_work: 0.2849 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9246 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14960 Z= 0.156 Angle : 0.639 8.540 20305 Z= 0.315 Chirality : 0.046 0.185 2255 Planarity : 0.005 0.036 2595 Dihedral : 8.637 119.248 2085 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.70 % Allowed : 7.60 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.20), residues: 1830 helix: 1.08 (0.20), residues: 785 sheet: -0.03 (0.25), residues: 350 loop : 1.75 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.006 0.001 TYR D 188 PHE 0.012 0.002 PHE D 255 TRP 0.014 0.003 TRP A 340 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (14960) covalent geometry : angle 0.63908 / 0.31 (20305) hydrogen bonds : bond 0.04685 / 3.22 ( 736) hydrogen bonds : angle 5.29044 / 3.73 ( 1923) *********************** 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 178 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.624 Fit side-chains REVERT: A 41 GLN cc_start: 0.7490 (tt0) cc_final: 0.7070 (tp40) REVERT: A 237 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7977 (mt-10) REVERT: C 224 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: C 237 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: D 237 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8301 (mt-10) REVERT: E 47 MET cc_start: 0.5150 (OUTLIER) cc_final: 0.4923 (ttp) REVERT: E 237 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 354 GLN cc_start: 0.8177 (mm110) cc_final: 0.7853 (mp-120) outliers start: 11 outliers final: 2 residues processed: 177 average time/residue: 0.8351 time to fit residues: 159.2469 Evaluate side-chains 170 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 8 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 chunk 143 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.084869 restraints weight = 13865.206| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 0.91 r_work: 0.2836 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9255 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14960 Z= 0.177 Angle : 0.662 8.725 20305 Z= 0.328 Chirality : 0.047 0.187 2255 Planarity : 0.005 0.039 2595 Dihedral : 8.818 121.961 2085 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.89 % Allowed : 7.54 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.20), residues: 1830 helix: 1.11 (0.20), residues: 785 sheet: -0.02 (0.25), residues: 340 loop : 1.73 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 210 TYR 0.006 0.001 TYR D 188 PHE 0.013 0.002 PHE C 262 TRP 0.015 0.003 TRP C 79 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (14960) covalent geometry : angle 0.66226 / 0.33 (20305) hydrogen bonds : bond 0.04969 / 3.42 ( 736) hydrogen bonds : angle 5.35564 / 3.78 ( 1923) *********************** 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 183 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.763 Fit side-chains REVERT: A 41 GLN cc_start: 0.7499 (tt0) cc_final: 0.7059 (tp40) REVERT: A 237 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7987 (mt-10) REVERT: C 237 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: D 237 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: E 47 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4960 (ttp) REVERT: E 237 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: E 354 GLN cc_start: 0.8234 (mm110) cc_final: 0.7910 (mp-120) outliers start: 14 outliers final: 2 residues processed: 179 average time/residue: 0.8199 time to fit residues: 158.2110 Evaluate side-chains 169 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 162 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 chunk 77 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.104072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.084697 restraints weight = 13799.163| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 0.91 r_work: 0.2833 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9259 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14960 Z= 0.181 Angle : 0.667 8.730 20305 Z= 0.331 Chirality : 0.048 0.190 2255 Planarity : 0.005 0.040 2595 Dihedral : 8.843 122.163 2085 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.70 % Allowed : 7.73 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.20), residues: 1830 helix: 1.12 (0.20), residues: 785 sheet: -0.05 (0.25), residues: 340 loop : 1.74 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 210 TYR 0.006 0.001 TYR C 279 PHE 0.013 0.002 PHE C 262 TRP 0.016 0.003 TRP C 79 HIS 0.006 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (14960) covalent geometry : angle 0.66714 / 0.33 (20305) hydrogen bonds : bond 0.05017 / 3.46 ( 736) hydrogen bonds : angle 5.36761 / 3.78 ( 1923) *********************** 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 176 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.609 Fit side-chains REVERT: A 41 GLN cc_start: 0.7486 (tt0) cc_final: 0.7039 (tp40) REVERT: A 237 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: C 237 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8358 (mt-10) REVERT: D 237 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: E 237 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: E 354 GLN cc_start: 0.8255 (mm110) cc_final: 0.7900 (mp-120) outliers start: 11 outliers final: 2 residues processed: 174 average time/residue: 0.8356 time to fit residues: 156.4567 Evaluate side-chains 167 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 89 optimal weight: 9.9990 chunk 34 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 137 optimal weight: 0.0970 chunk 176 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.107222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.088052 restraints weight = 13833.819| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 0.91 r_work: 0.2892 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9217 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14960 Z= 0.106 Angle : 0.576 7.539 20305 Z= 0.280 Chirality : 0.044 0.177 2255 Planarity : 0.003 0.034 2595 Dihedral : 7.969 108.463 2085 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.77 % Allowed : 7.73 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.20), residues: 1830 helix: 1.34 (0.20), residues: 770 sheet: 0.11 (0.26), residues: 340 loop : 1.94 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 95 TYR 0.008 0.001 TYR B 294 PHE 0.011 0.001 PHE A 255 TRP 0.014 0.002 TRP C 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (14960) covalent geometry : angle 0.57639 / 0.28 (20305) hydrogen bonds : bond 0.03632 / 2.47 ( 736) hydrogen bonds : angle 4.97688 / 3.52 ( 1923) *********************** 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 176 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.604 Fit side-chains REVERT: A 41 GLN cc_start: 0.7452 (tt0) cc_final: 0.6992 (tp40) REVERT: A 314 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8496 (tt0) REVERT: C 237 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: D 237 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8272 (mt-10) REVERT: E 237 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: E 354 GLN cc_start: 0.8191 (mm110) cc_final: 0.7882 (mp-120) outliers start: 12 outliers final: 2 residues processed: 174 average time/residue: 0.8346 time to fit residues: 156.2779 Evaluate side-chains 163 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 125 optimal weight: 9.9990 chunk 34 optimal weight: 0.7980 chunk 117 optimal weight: 4.9990 chunk 147 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 166 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 246 GLN E 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089288 restraints weight = 13812.591| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 0.92 r_work: 0.2918 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9183 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14960 Z= 0.098 Angle : 0.558 6.917 20305 Z= 0.270 Chirality : 0.043 0.162 2255 Planarity : 0.003 0.036 2595 Dihedral : 7.421 100.650 2085 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.64 % Allowed : 7.86 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1830 helix: 1.40 (0.20), residues: 770 sheet: 0.24 (0.26), residues: 340 loop : 1.97 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 95 TYR 0.008 0.001 TYR B 294 PHE 0.011 0.001 PHE A 255 TRP 0.012 0.002 TRP C 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (14960) covalent geometry : angle 0.55790 / 0.27 (20305) hydrogen bonds : bond 0.03403 / 2.32 ( 736) hydrogen bonds : angle 4.84149 / 3.43 ( 1923) *********************** 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 174 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.658 Fit side-chains REVERT: A 41 GLN cc_start: 0.7383 (tt0) cc_final: 0.6896 (tp40) REVERT: A 314 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: C 224 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8172 (mp0) REVERT: C 237 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: D 237 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8274 (mt-10) REVERT: E 237 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: E 354 GLN cc_start: 0.8101 (mm110) cc_final: 0.7768 (mp-120) outliers start: 10 outliers final: 0 residues processed: 171 average time/residue: 0.8433 time to fit residues: 155.2876 Evaluate side-chains 160 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 121 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 106 optimal weight: 0.0070 chunk 171 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084473 restraints weight = 13852.200| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 0.91 r_work: 0.2829 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9261 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14960 Z= 0.195 Angle : 0.682 8.850 20305 Z= 0.339 Chirality : 0.049 0.189 2255 Planarity : 0.005 0.042 2595 Dihedral : 8.724 123.507 2085 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.51 % Allowed : 7.67 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.21), residues: 1830 helix: 1.19 (0.20), residues: 785 sheet: 0.04 (0.26), residues: 340 loop : 1.86 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 95 TYR 0.006 0.001 TYR C 279 PHE 0.014 0.002 PHE C 262 TRP 0.015 0.003 TRP A 340 HIS 0.007 0.002 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (14960) covalent geometry : angle 0.68151 / 0.34 (20305) hydrogen bonds : bond 0.05099 / 3.52 ( 736) hydrogen bonds : angle 5.33502 / 3.76 ( 1923) *********************** 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 162 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.649 Fit side-chains REVERT: A 41 GLN cc_start: 0.7473 (tt0) cc_final: 0.6986 (tp40) REVERT: A 237 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: C 237 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8362 (mt-10) REVERT: D 237 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: E 47 MET cc_start: 0.5325 (ttt) cc_final: 0.5059 (ttt) REVERT: E 237 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: E 354 GLN cc_start: 0.8164 (mm110) cc_final: 0.7867 (mp-120) outliers start: 8 outliers final: 1 residues processed: 162 average time/residue: 0.8363 time to fit residues: 146.1058 Evaluate side-chains 164 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 20 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084690 restraints weight = 13675.560| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 0.91 r_work: 0.2828 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9260 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14960 Z= 0.194 Angle : 0.683 8.785 20305 Z= 0.340 Chirality : 0.048 0.189 2255 Planarity : 0.005 0.042 2595 Dihedral : 8.773 123.251 2085 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.45 % Allowed : 8.12 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1830 helix: 1.13 (0.20), residues: 785 sheet: -0.02 (0.26), residues: 340 loop : 1.82 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 95 TYR 0.006 0.001 TYR C 279 PHE 0.014 0.002 PHE C 262 TRP 0.015 0.003 TRP A 340 HIS 0.007 0.002 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (14960) covalent geometry : angle 0.68347 / 0.34 (20305) hydrogen bonds : bond 0.05131 / 3.54 ( 736) hydrogen bonds : angle 5.38377 / 3.79 ( 1923) ********************** 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 166 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.623 Fit side-chains REVERT: A 41 GLN cc_start: 0.7454 (tt0) cc_final: 0.6972 (tp40) REVERT: A 237 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: C 237 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: D 237 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: E 237 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8226 (mt-10) REVERT: E 354 GLN cc_start: 0.8152 (mm110) cc_final: 0.7819 (mp-120) outliers start: 7 outliers final: 1 residues processed: 166 average time/residue: 0.8559 time to fit residues: 152.8717 Evaluate side-chains 161 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 GLU Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain C residue 237 GLU Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain E residue 237 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 141 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 159 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085290 restraints weight = 13731.774| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 0.91 r_work: 0.2844 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9249 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14960 Z= 0.156 Angle : 0.645 8.969 20305 Z= 0.318 Chirality : 0.047 0.186 2255 Planarity : 0.004 0.037 2595 Dihedral : 8.506 119.457 2085 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.45 % Allowed : 8.05 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.21), residues: 1830 helix: 1.18 (0.20), residues: 785 sheet: 0.00 (0.26), residues: 340 loop : 1.81 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 95 TYR 0.006 0.001 TYR B 294 PHE 0.012 0.002 PHE D 255 TRP 0.014 0.002 TRP C 79 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (14960) covalent geometry : angle 0.64462 / 0.32 (20305) hydrogen bonds : bond 0.04623 / 3.18 ( 736) hydrogen bonds : angle 5.25184 / 3.71 ( 1923) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7251.84 seconds wall clock time: 124 minutes 25.23 seconds (7465.23 seconds total)