Starting phenix.real_space_refine on Sat Aug 23 21:25:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.map" model { file = "/net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8p_28932/08_2025/8f8p_28932.cif" } resolution = 2.26 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= 0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9235 2.51 5 N 2470 2.21 5 O 2815 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s 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: 14640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 2.39, per 1000 atoms: 0.16 Number of scatterers: 14640 At special positions: 0 Unit cell: (77.76, 99.36, 195.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2815 8.00 N 2470 7.00 C 9235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Conformation dependent library (CDL) restraints added in 631.0 milliseconds Enol-peptide restraints added in 476.8 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: 110 helices and 30 sheets defined 50.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.722A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) 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 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.839A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.614A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) 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 348 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (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 97 through 101 removed outlier: 3.722A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) 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 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.839A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.614A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) 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 348 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (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 97 through 101 removed outlier: 3.723A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.627A pdb=" N GLY C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) 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 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.838A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.615A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.236A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) 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 348 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (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 97 through 101 removed outlier: 3.723A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.308A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.627A pdb=" N GLY D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) 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 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.838A pdb=" N GLU D 207 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.614A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.236A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) 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 348 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (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 97 through 101 removed outlier: 3.723A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.309A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.628A pdb=" N GLY E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) 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 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.840A pdb=" N GLU E 207 " --> pdb=" O THR E 203 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.614A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 302 through 306 removed outlier: 4.237A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) 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 348 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.598A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.588A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.411A 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: 6.505A 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 removed outlier: 3.549A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.410A 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: 6.505A 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 removed outlier: 3.632A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.410A 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: 6.506A 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 removed outlier: 3.775A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.410A 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: 6.506A 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: 6.588A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.411A 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: 6.506A 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 241 724 hydrogen bonds defined for protein. 1863 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: 2.83 Time building geometry restraints manager: 1.65 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: 4717 1.34 - 1.46: 3198 1.46 - 1.58: 6845 1.58 - 1.70: 15 1.70 - 1.82: 185 Bond restraints: 14960 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.56e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.36e+00 ... (remaining 14955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 19753 2.10 - 4.20: 391 4.20 - 6.30: 134 6.30 - 8.40: 22 8.40 - 10.50: 5 Bond angle restraints: 20305 Sorted by residual: angle pdb=" C GLY C 46 " pdb=" N MET C 47 " pdb=" CA MET C 47 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY B 46 " pdb=" N MET B 47 " pdb=" CA MET B 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY E 46 " pdb=" N MET E 47 " pdb=" CA MET E 47 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C GLY D 46 " pdb=" N MET D 47 " pdb=" CA MET D 47 " ideal model delta sigma weight residual 121.54 129.40 -7.86 1.91e+00 2.74e-01 1.69e+01 angle pdb=" C GLY A 46 " pdb=" N MET A 47 " pdb=" CA MET A 47 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.69e+01 ... (remaining 20300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 8610 35.73 - 71.46: 355 71.46 - 107.19: 20 107.19 - 142.92: 5 142.92 - 178.65: 5 Dihedral angle restraints: 8995 sinusoidal: 3635 harmonic: 5360 Sorted by residual: 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 300.00 121.35 178.65 1 2.00e+01 2.50e-03 4.80e+01 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 300.00 121.36 178.65 1 2.00e+01 2.50e-03 4.80e+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 300.00 121.37 178.63 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 8992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1287 0.033 - 0.065: 594 0.065 - 0.098: 214 0.098 - 0.131: 135 0.131 - 0.163: 25 Chirality restraints: 2255 Sorted by residual: chirality pdb=" CA CYS E 257 " pdb=" N CYS E 257 " pdb=" C CYS E 257 " pdb=" CB CYS E 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA CYS C 257 " pdb=" N CYS C 257 " pdb=" C CYS C 257 " pdb=" CB CYS C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CB ILE E 309 " pdb=" CA ILE E 309 " pdb=" CG1 ILE E 309 " pdb=" CG2 ILE E 309 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.40e-01 ... (remaining 2252 not shown) Planarity restraints: 2595 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.78e+00 pdb=" N PRO D 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO B 243 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.74e+00 pdb=" N PRO C 243 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.027 5.00e-02 4.00e+02 ... (remaining 2592 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4212 2.82 - 3.34: 11721 3.34 - 3.86: 24582 3.86 - 4.38: 29091 4.38 - 4.90: 50352 Nonbonded interactions: 119958 Sorted by model distance: nonbonded pdb=" O GLN A 314 " pdb=" OG1 THR A 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN D 314 " pdb=" OG1 THR D 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN E 314 " pdb=" OG1 THR E 318 " model vdw 2.301 3.040 nonbonded pdb=" O GLN C 314 " pdb=" OG1 THR C 318 " model vdw 2.302 3.040 nonbonded pdb=" O GLN B 314 " pdb=" OG1 THR B 318 " model vdw 2.302 3.040 ... (remaining 119953 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 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 0.055 14960 Z= 0.189 Angle : 0.825 10.502 20305 Z= 0.421 Chirality : 0.049 0.163 2255 Planarity : 0.006 0.049 2595 Dihedral : 17.731 178.653 5565 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.04 % Allowed : 22.81 % Favored : 75.14 % 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: -1.31 (0.19), residues: 1830 helix: -1.96 (0.14), residues: 745 sheet: 1.04 (0.30), residues: 345 loop : -0.37 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 206 TYR 0.010 0.001 TYR C 143 PHE 0.015 0.001 PHE B 255 TRP 0.005 0.001 TRP B 356 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00409 (14960) covalent geometry : angle 0.82549 (20305) hydrogen bonds : bond 0.17660 ( 708) hydrogen bonds : angle 6.71820 ( 1863) *********************** 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 406 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 374 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 92 ASN cc_start: 0.8356 (m110) cc_final: 0.8152 (m-40) REVERT: A 115 ASN cc_start: 0.8126 (t0) cc_final: 0.7919 (t0) REVERT: A 252 ASN cc_start: 0.8441 (p0) cc_final: 0.8238 (p0) REVERT: B 225 ASN cc_start: 0.7838 (m-40) cc_final: 0.7576 (m-40) REVERT: B 283 MET cc_start: 0.8490 (mmm) cc_final: 0.8254 (mmt) REVERT: D 227 MET cc_start: 0.8628 (mmm) cc_final: 0.8342 (mmm) REVERT: D 288 ASP cc_start: 0.7881 (m-30) cc_final: 0.7665 (m-30) REVERT: D 299 MET cc_start: 0.8900 (mtm) cc_final: 0.8592 (mtm) outliers start: 32 outliers final: 11 residues processed: 391 average time/residue: 0.7890 time to fit residues: 332.0864 Evaluate side-chains 310 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 299 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 260 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 49 GLN A 59 GLN A 78 ASN A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 115 ASN B 128 ASN B 162 ASN B 297 ASN D 78 ASN D 162 ASN D 297 ASN E 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.110382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102717 restraints weight = 19265.634| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.18 r_work: 0.3432 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14960 Z= 0.139 Angle : 0.595 6.364 20305 Z= 0.292 Chirality : 0.045 0.140 2255 Planarity : 0.005 0.035 2595 Dihedral : 9.489 150.757 2098 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.64 % Allowed : 19.17 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.20), residues: 1830 helix: -0.38 (0.18), residues: 770 sheet: 1.04 (0.30), residues: 345 loop : 0.35 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 95 TYR 0.012 0.001 TYR E 169 PHE 0.013 0.002 PHE B 31 TRP 0.014 0.002 TRP A 356 HIS 0.005 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00324 (14960) covalent geometry : angle 0.59453 (20305) hydrogen bonds : bond 0.03472 ( 708) hydrogen bonds : angle 4.52345 ( 1863) *********************** 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 391 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 334 time to evaluate : 0.567 Fit side-chains REVERT: A 68 LYS cc_start: 0.8416 (mttm) cc_final: 0.8211 (mttm) REVERT: A 176 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7895 (mtp) REVERT: B 47 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.5809 (ppp) REVERT: D 299 MET cc_start: 0.8839 (mtm) cc_final: 0.8625 (mtm) REVERT: E 107 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 364 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6904 (tm-30) outliers start: 57 outliers final: 19 residues processed: 360 average time/residue: 0.7755 time to fit residues: 300.0293 Evaluate side-chains 325 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 277 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 79 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 0.0370 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 59 GLN B 12 ASN B 59 GLN B 246 GLN C 162 ASN D 115 ASN D 162 ASN D 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.102160 restraints weight = 19375.580| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.19 r_work: 0.3421 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14960 Z= 0.109 Angle : 0.548 6.003 20305 Z= 0.266 Chirality : 0.044 0.137 2255 Planarity : 0.004 0.035 2595 Dihedral : 6.781 106.225 2085 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.88 % Allowed : 20.89 % Favored : 76.23 % 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: 0.42 (0.20), residues: 1830 helix: 0.12 (0.19), residues: 800 sheet: 1.17 (0.29), residues: 340 loop : 0.24 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 28 TYR 0.006 0.001 TYR C 188 PHE 0.015 0.001 PHE B 31 TRP 0.010 0.001 TRP A 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00251 (14960) covalent geometry : angle 0.54842 (20305) hydrogen bonds : bond 0.03082 ( 708) hydrogen bonds : angle 4.24894 ( 1863) *********************** 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 368 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 0.604 Fit side-chains REVERT: A 68 LYS cc_start: 0.8457 (mttm) cc_final: 0.8254 (mttm) REVERT: B 47 MET cc_start: 0.6647 (OUTLIER) cc_final: 0.5870 (ppp) REVERT: B 225 ASN cc_start: 0.8093 (m-40) cc_final: 0.7883 (m110) REVERT: D 6 THR cc_start: 0.7957 (m) cc_final: 0.7705 (t) REVERT: D 95 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7662 (mtm110) REVERT: D 299 MET cc_start: 0.8831 (mtm) cc_final: 0.8583 (mtm) REVERT: E 107 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7576 (tt0) REVERT: E 364 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6968 (tm-30) outliers start: 45 outliers final: 17 residues processed: 342 average time/residue: 0.8599 time to fit residues: 314.8018 Evaluate side-chains 327 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 307 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 162 ASN A 297 ASN B 59 GLN B 78 ASN B 162 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 297 ASN D 353 GLN E 296 ASN E 297 ASN E 371 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.099872 restraints weight = 19210.032| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.17 r_work: 0.3385 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14960 Z= 0.172 Angle : 0.590 6.705 20305 Z= 0.289 Chirality : 0.047 0.146 2255 Planarity : 0.004 0.041 2595 Dihedral : 6.529 95.255 2085 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.32 % Allowed : 20.00 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.20), residues: 1830 helix: 0.32 (0.19), residues: 800 sheet: 1.11 (0.29), residues: 340 loop : 0.15 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.008 0.001 TYR C 188 PHE 0.015 0.001 PHE B 31 TRP 0.010 0.002 TRP D 340 HIS 0.006 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00418 (14960) covalent geometry : angle 0.58964 (20305) hydrogen bonds : bond 0.03623 ( 708) hydrogen bonds : angle 4.24930 ( 1863) *********************** 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 381 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.422 Fit side-chains REVERT: A 68 LYS cc_start: 0.8460 (mttm) cc_final: 0.8257 (mttm) REVERT: A 176 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7942 (mtp) REVERT: B 47 MET cc_start: 0.6714 (OUTLIER) cc_final: 0.5931 (ppp) REVERT: B 225 ASN cc_start: 0.8095 (m-40) cc_final: 0.7865 (m110) REVERT: D 6 THR cc_start: 0.8074 (m) cc_final: 0.7804 (t) REVERT: D 95 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7654 (mtm110) REVERT: D 132 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8156 (ttp) REVERT: D 176 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7863 (mtp) REVERT: D 299 MET cc_start: 0.8899 (mtm) cc_final: 0.8606 (mtm) REVERT: E 107 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7495 (tt0) REVERT: E 364 GLU cc_start: 0.7424 (tm-30) cc_final: 0.7173 (tm-30) outliers start: 52 outliers final: 21 residues processed: 353 average time/residue: 0.8200 time to fit residues: 309.6160 Evaluate side-chains 333 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 306 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 10 optimal weight: 0.0470 chunk 90 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 59 GLN B 78 ASN B 162 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 297 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.108672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.100991 restraints weight = 19150.470| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.17 r_work: 0.3405 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14960 Z= 0.114 Angle : 0.548 6.149 20305 Z= 0.265 Chirality : 0.045 0.133 2255 Planarity : 0.003 0.038 2595 Dihedral : 6.119 91.811 2085 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.13 % Allowed : 20.70 % Favored : 76.17 % 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: 0.78 (0.20), residues: 1830 helix: 0.63 (0.19), residues: 800 sheet: 1.13 (0.29), residues: 340 loop : 0.28 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 95 TYR 0.005 0.001 TYR C 188 PHE 0.013 0.001 PHE B 31 TRP 0.010 0.001 TRP A 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00268 (14960) covalent geometry : angle 0.54784 (20305) hydrogen bonds : bond 0.03000 ( 708) hydrogen bonds : angle 4.11090 ( 1863) *********************** 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 357 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 0.566 Fit side-chains REVERT: A 68 LYS cc_start: 0.8444 (mttm) cc_final: 0.8232 (mttm) REVERT: B 47 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.5913 (ppp) REVERT: B 225 ASN cc_start: 0.8140 (m-40) cc_final: 0.7896 (m110) REVERT: C 314 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7203 (tt0) REVERT: C 363 ASP cc_start: 0.8146 (m-30) cc_final: 0.7844 (m-30) REVERT: D 6 THR cc_start: 0.8111 (m) cc_final: 0.7869 (t) REVERT: D 95 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7658 (mtm110) REVERT: D 119 MET cc_start: 0.8428 (ttp) cc_final: 0.8193 (mtp) REVERT: D 132 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8159 (ttp) REVERT: D 299 MET cc_start: 0.8900 (mtm) cc_final: 0.8616 (mtm) REVERT: E 107 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7390 (tt0) REVERT: E 113 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7853 (mmtm) REVERT: E 364 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7148 (tm-30) outliers start: 49 outliers final: 24 residues processed: 333 average time/residue: 0.8480 time to fit residues: 302.5989 Evaluate side-chains 333 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 303 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 162 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 115 ASN D 297 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.108001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.100447 restraints weight = 19145.362| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.17 r_work: 0.3392 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14960 Z= 0.136 Angle : 0.564 7.650 20305 Z= 0.273 Chirality : 0.045 0.132 2255 Planarity : 0.004 0.067 2595 Dihedral : 6.090 91.724 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.13 % Allowed : 20.58 % Favored : 76.29 % 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: 0.83 (0.20), residues: 1830 helix: 0.71 (0.19), residues: 800 sheet: 1.10 (0.28), residues: 340 loop : 0.26 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 95 TYR 0.007 0.001 TYR C 188 PHE 0.014 0.001 PHE B 31 TRP 0.009 0.002 TRP A 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00327 (14960) covalent geometry : angle 0.56421 (20305) hydrogen bonds : bond 0.03207 ( 708) hydrogen bonds : angle 4.10321 ( 1863) *********************** 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 361 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 0.577 Fit side-chains REVERT: A 68 LYS cc_start: 0.8444 (mttm) cc_final: 0.8238 (mttm) REVERT: B 225 ASN cc_start: 0.8131 (m-40) cc_final: 0.7880 (m110) REVERT: C 6 THR cc_start: 0.8497 (p) cc_final: 0.8260 (t) REVERT: D 6 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7906 (t) REVERT: D 95 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7672 (mtm110) REVERT: D 119 MET cc_start: 0.8412 (ttp) cc_final: 0.8182 (mtp) REVERT: D 132 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8138 (ttp) REVERT: D 176 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.7838 (mtp) REVERT: D 299 MET cc_start: 0.8889 (mtm) cc_final: 0.8552 (mtm) REVERT: E 107 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: E 113 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7897 (mmtm) REVERT: E 364 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7106 (tm-30) outliers start: 49 outliers final: 26 residues processed: 334 average time/residue: 0.8767 time to fit residues: 313.4547 Evaluate side-chains 349 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 317 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 232 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 0.8980 chunk 173 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 116 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS B 12 ASN B 59 GLN B 78 ASN B 162 ASN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 115 ASN D 162 ASN D 297 ASN E 297 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.108676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101215 restraints weight = 19199.223| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.16 r_work: 0.3411 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14960 Z= 0.099 Angle : 0.538 7.166 20305 Z= 0.259 Chirality : 0.044 0.132 2255 Planarity : 0.004 0.073 2595 Dihedral : 5.688 82.641 2085 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.07 % Allowed : 21.21 % Favored : 75.72 % 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: 0.99 (0.21), residues: 1830 helix: 0.89 (0.19), residues: 800 sheet: 1.03 (0.29), residues: 345 loop : 0.36 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.005 0.001 TYR C 143 PHE 0.012 0.001 PHE B 31 TRP 0.010 0.001 TRP E 79 HIS 0.004 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00232 (14960) covalent geometry : angle 0.53810 (20305) hydrogen bonds : bond 0.02752 ( 708) hydrogen bonds : angle 4.01377 ( 1863) *********************** 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 363 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 315 time to evaluate : 0.611 Fit side-chains REVERT: A 68 LYS cc_start: 0.8432 (mttm) cc_final: 0.8221 (mttm) REVERT: B 225 ASN cc_start: 0.8123 (m-40) cc_final: 0.7871 (m110) REVERT: C 6 THR cc_start: 0.8482 (p) cc_final: 0.8258 (t) REVERT: C 44 MET cc_start: 0.8444 (mmm) cc_final: 0.7465 (mtm) REVERT: C 314 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: C 363 ASP cc_start: 0.8125 (m-30) cc_final: 0.7847 (m-30) REVERT: D 95 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7688 (mtm110) REVERT: D 119 MET cc_start: 0.8377 (ttp) cc_final: 0.8165 (mtp) REVERT: D 132 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7991 (ttp) REVERT: D 299 MET cc_start: 0.8881 (mtm) cc_final: 0.8544 (mtm) REVERT: E 84 LYS cc_start: 0.8751 (mtmm) cc_final: 0.8545 (mttm) REVERT: E 107 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: E 113 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7902 (mmtm) REVERT: E 364 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7013 (tm-30) outliers start: 48 outliers final: 25 residues processed: 336 average time/residue: 0.8702 time to fit residues: 313.1354 Evaluate side-chains 337 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 284 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 162 ASN B 12 ASN B 78 ASN B 246 GLN B 297 ASN C 246 GLN C 353 GLN E 297 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.106232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.098763 restraints weight = 19148.029| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.14 r_work: 0.3365 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 14960 Z= 0.254 Angle : 0.633 7.621 20305 Z= 0.312 Chirality : 0.050 0.200 2255 Planarity : 0.005 0.068 2595 Dihedral : 6.512 93.552 2085 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.00 % Allowed : 20.96 % Favored : 76.04 % 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: 0.70 (0.20), residues: 1830 helix: 0.62 (0.19), residues: 800 sheet: 1.10 (0.29), residues: 330 loop : 0.16 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 95 TYR 0.008 0.001 TYR C 188 PHE 0.017 0.002 PHE C 127 TRP 0.014 0.002 TRP D 340 HIS 0.006 0.002 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00630 (14960) covalent geometry : angle 0.63337 (20305) hydrogen bonds : bond 0.04105 ( 708) hydrogen bonds : angle 4.27758 ( 1863) *********************** 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 360 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.602 Fit side-chains REVERT: A 314 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: B 225 ASN cc_start: 0.8121 (m-40) cc_final: 0.7851 (m110) REVERT: C 6 THR cc_start: 0.8467 (p) cc_final: 0.8241 (t) REVERT: C 314 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: D 95 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7650 (mtm110) REVERT: D 119 MET cc_start: 0.8425 (ttp) cc_final: 0.8184 (mtp) REVERT: D 132 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8089 (ttp) REVERT: D 176 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7902 (mtp) REVERT: D 299 MET cc_start: 0.8899 (mtm) cc_final: 0.8555 (mtm) REVERT: E 107 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: E 113 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8116 (mptt) outliers start: 47 outliers final: 28 residues processed: 329 average time/residue: 0.8811 time to fit residues: 310.4770 Evaluate side-chains 347 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 284 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 136 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN B 12 ASN B 59 GLN B 78 ASN B 92 ASN B 162 ASN B 297 ASN C 246 GLN C 353 GLN D 115 ASN D 162 ASN D 296 ASN D 297 ASN E 297 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.108164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.100688 restraints weight = 19104.317| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.15 r_work: 0.3395 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3263 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= 0.117 Angle : 0.555 6.377 20305 Z= 0.269 Chirality : 0.045 0.131 2255 Planarity : 0.004 0.068 2595 Dihedral : 5.918 83.227 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.81 % Allowed : 21.28 % Favored : 75.91 % 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: 0.89 (0.20), residues: 1830 helix: 0.86 (0.19), residues: 800 sheet: 0.92 (0.28), residues: 345 loop : 0.28 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.005 0.001 TYR A 69 PHE 0.013 0.001 PHE B 31 TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00279 (14960) covalent geometry : angle 0.55518 (20305) hydrogen bonds : bond 0.02985 ( 708) hydrogen bonds : angle 4.10151 ( 1863) *********************** 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 361 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 317 time to evaluate : 0.614 Fit side-chains REVERT: B 225 ASN cc_start: 0.8131 (m-40) cc_final: 0.7868 (m110) REVERT: C 363 ASP cc_start: 0.8124 (m-30) cc_final: 0.7855 (m-30) REVERT: D 95 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7666 (mtm110) REVERT: D 119 MET cc_start: 0.8401 (ttp) cc_final: 0.8178 (mtp) REVERT: D 132 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7961 (ttp) REVERT: D 299 MET cc_start: 0.8882 (mtm) cc_final: 0.8524 (mtm) REVERT: E 107 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: E 113 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8122 (mptt) outliers start: 44 outliers final: 24 residues processed: 333 average time/residue: 0.8239 time to fit residues: 293.6920 Evaluate side-chains 344 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 316 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.1980 chunk 92 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 92 ASN B 162 ASN B 297 ASN C 246 GLN C 353 GLN D 115 ASN D 296 ASN D 297 ASN E 297 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.107668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100183 restraints weight = 18959.351| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.15 r_work: 0.3387 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14960 Z= 0.150 Angle : 0.576 6.369 20305 Z= 0.281 Chirality : 0.046 0.131 2255 Planarity : 0.004 0.070 2595 Dihedral : 6.001 83.897 2085 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.30 % Allowed : 21.66 % Favored : 76.04 % 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: 0.85 (0.20), residues: 1830 helix: 0.83 (0.19), residues: 800 sheet: 1.00 (0.28), residues: 340 loop : 0.21 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 95 TYR 0.007 0.001 TYR C 188 PHE 0.014 0.001 PHE B 31 TRP 0.010 0.002 TRP D 79 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00364 (14960) covalent geometry : angle 0.57609 (20305) hydrogen bonds : bond 0.03318 ( 708) hydrogen bonds : angle 4.12303 ( 1863) ********************** 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 353 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 0.497 Fit side-chains REVERT: A 314 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: B 47 MET cc_start: 0.6746 (ppp) cc_final: 0.6035 (ppp) REVERT: B 225 ASN cc_start: 0.8144 (m-40) cc_final: 0.7888 (m110) REVERT: C 363 ASP cc_start: 0.8130 (m-30) cc_final: 0.7852 (m-30) REVERT: D 95 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7661 (mtm110) REVERT: D 119 MET cc_start: 0.8398 (ttp) cc_final: 0.8162 (mtp) REVERT: D 132 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7995 (ttp) REVERT: D 299 MET cc_start: 0.8900 (mtm) cc_final: 0.8564 (mtm) REVERT: E 47 MET cc_start: 0.6360 (ptm) cc_final: 0.6062 (ptm) REVERT: E 107 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: E 113 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (mptt) outliers start: 36 outliers final: 25 residues processed: 329 average time/residue: 0.7712 time to fit residues: 271.7634 Evaluate side-chains 344 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 LYS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 122 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 113 LYS Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 GLN A 162 ASN B 12 ASN B 59 GLN B 78 ASN B 92 ASN B 162 ASN B 246 GLN B 297 ASN C 246 GLN C 353 GLN D 115 ASN D 162 ASN D 297 ASN E 297 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099832 restraints weight = 19024.031| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.17 r_work: 0.3380 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14960 Z= 0.233 Angle : 0.808 59.200 20305 Z= 0.449 Chirality : 0.050 0.340 2255 Planarity : 0.004 0.070 2595 Dihedral : 6.018 84.080 2085 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.04 % Allowed : 21.98 % Favored : 75.97 % 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: 0.82 (0.20), residues: 1830 helix: 0.79 (0.19), residues: 800 sheet: 0.99 (0.28), residues: 340 loop : 0.20 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.007 0.001 TYR C 188 PHE 0.014 0.001 PHE B 31 TRP 0.010 0.002 TRP D 79 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00545 (14960) covalent geometry : angle 0.80793 (20305) hydrogen bonds : bond 0.03491 ( 708) hydrogen bonds : angle 4.12607 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6893.29 seconds wall clock time: 117 minutes 51.26 seconds (7071.26 seconds total)