Starting phenix.real_space_refine on Fri Jul 3 15:25:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f8p_28932/07_2026/8f8p_28932.map" } 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-dev-6108/lib/python3.11/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: 2.91, per 1000 atoms: 0.20 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: 1.19 Conformation dependent library (CDL) restraints added in 455.6 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.4% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 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: 2.57 Time building geometry restraints manager: 1.59 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: 1.260 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.880 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 are 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/Z covalent geometry : bond 0.00409 / 0.19 (14960) covalent geometry : angle 0.82549 / 0.42 (20305) hydrogen bonds : bond 0.17660 / 11.97 ( 708) hydrogen bonds : angle 6.71820 / 4.78 ( 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 : 0.553 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: 0.7575 (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: 0.6999 time to fit residues: 295.2215 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 : 0.525 ------------------------------------------------------------------------------- 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... 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 = 0.3627 r_free = 0.3627 target = 0.110257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102572 restraints weight = 19258.080| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.18 r_work: 0.3430 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2324 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= 0.142 Angle : 0.594 6.313 20305 Z= 0.292 Chirality : 0.046 0.144 2255 Planarity : 0.005 0.035 2595 Dihedral : 9.336 148.173 2098 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.51 % Allowed : 19.42 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1830 helix: -0.36 (0.18), residues: 770 sheet: 1.02 (0.30), residues: 345 loop : 0.35 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 95 TYR 0.013 0.001 TYR E 169 PHE 0.012 0.001 PHE E 266 TRP 0.014 0.002 TRP A 356 HIS 0.006 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14960) covalent geometry : angle 0.59394 / 0.29 (20305) hydrogen bonds : bond 0.03538 / 2.42 ( 708) hydrogen bonds : angle 4.51239 / 3.22 ( 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 389 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 334 time to evaluate : 0.445 Fit side-chains REVERT: A 68 LYS cc_start: 0.8420 (mttm) cc_final: 0.8216 (mttm) REVERT: A 176 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7905 (mtp) REVERT: A 368 SER cc_start: 0.8208 (t) cc_final: 0.8007 (t) REVERT: B 47 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.5820 (ppp) REVERT: D 299 MET cc_start: 0.8838 (mtm) cc_final: 0.8627 (mtm) REVERT: E 78 ASN cc_start: 0.8116 (t0) cc_final: 0.7908 (t0) REVERT: E 107 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7657 (tt0) outliers start: 55 outliers final: 16 residues processed: 359 average time/residue: 0.6615 time to fit residues: 256.0830 Evaluate side-chains 321 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 302 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 59 GLN A 297 ASN B 59 GLN B 246 GLN C 162 ASN D 115 ASN D 162 ASN D 297 ASN E 12 ASN E 280 ASN E 297 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.107795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.100031 restraints weight = 19240.668| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.18 r_work: 0.3387 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14960 Z= 0.174 Angle : 0.598 6.592 20305 Z= 0.294 Chirality : 0.047 0.146 2255 Planarity : 0.004 0.039 2595 Dihedral : 7.179 113.344 2085 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.26 % Allowed : 19.81 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.20), residues: 1830 helix: 0.03 (0.18), residues: 800 sheet: 1.08 (0.29), residues: 340 loop : 0.10 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 95 TYR 0.008 0.001 TYR C 188 PHE 0.015 0.001 PHE B 127 TRP 0.010 0.002 TRP A 79 HIS 0.006 0.002 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (14960) covalent geometry : angle 0.59830 / 0.29 (20305) hydrogen bonds : bond 0.03814 / 2.63 ( 708) hydrogen bonds : angle 4.35903 / 3.11 ( 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 378 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 0.470 Fit side-chains REVERT: A 68 LYS cc_start: 0.8458 (mttm) cc_final: 0.8256 (mttm) REVERT: A 176 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: B 12 ASN cc_start: 0.8277 (m-40) cc_final: 0.8061 (m-40) REVERT: B 47 MET cc_start: 0.6700 (OUTLIER) cc_final: 0.5936 (ppp) REVERT: B 82 MET cc_start: 0.8647 (tpt) cc_final: 0.8349 (tpt) REVERT: B 132 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.8033 (ttp) REVERT: B 225 ASN cc_start: 0.8105 (m-40) cc_final: 0.7898 (m110) REVERT: D 119 MET cc_start: 0.8437 (ttp) cc_final: 0.8226 (mtp) REVERT: D 132 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8072 (ttp) REVERT: D 176 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7873 (mtp) REVERT: D 299 MET cc_start: 0.8880 (mtm) cc_final: 0.8582 (mtm) REVERT: E 78 ASN cc_start: 0.8262 (t0) cc_final: 0.7938 (t0) REVERT: E 107 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: E 132 MET cc_start: 0.8539 (ttp) cc_final: 0.8337 (ttp) outliers start: 51 outliers final: 20 residues processed: 345 average time/residue: 0.7672 time to fit residues: 284.3442 Evaluate side-chains 327 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 LYS 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 47 MET Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET 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 149 THR Chi-restraints excluded: chain D residue 5 THR 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 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 269 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 12 ASN B 59 GLN B 78 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN D 115 ASN D 162 ASN D 297 ASN D 353 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.106612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099103 restraints weight = 19187.423| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.14 r_work: 0.3370 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14960 Z= 0.219 Angle : 0.618 7.409 20305 Z= 0.305 Chirality : 0.049 0.155 2255 Planarity : 0.004 0.044 2595 Dihedral : 6.948 103.876 2085 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.83 % Allowed : 19.23 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.20), residues: 1830 helix: 0.21 (0.19), residues: 800 sheet: 1.12 (0.29), residues: 330 loop : 0.07 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.008 0.001 TYR C 188 PHE 0.016 0.001 PHE B 127 TRP 0.012 0.002 TRP D 79 HIS 0.007 0.002 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (14960) covalent geometry : angle 0.61809 / 0.31 (20305) hydrogen bonds : bond 0.04014 / 2.77 ( 708) hydrogen bonds : angle 4.34487 / 3.10 ( 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 380 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 320 time to evaluate : 0.635 Fit side-chains REVERT: A 176 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7889 (mtp) REVERT: A 349 LEU cc_start: 0.8813 (mt) cc_final: 0.8491 (mp) REVERT: B 47 MET cc_start: 0.6702 (OUTLIER) cc_final: 0.5901 (ppp) REVERT: B 225 ASN cc_start: 0.8122 (m-40) cc_final: 0.7898 (m110) REVERT: D 176 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7886 (mtp) REVERT: D 299 MET cc_start: 0.8874 (mtm) cc_final: 0.8581 (mtm) REVERT: E 107 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: E 113 LYS cc_start: 0.8412 (mmmm) cc_final: 0.7911 (mmtm) outliers start: 60 outliers final: 31 residues processed: 346 average time/residue: 0.7942 time to fit residues: 294.9667 Evaluate side-chains 342 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 307 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 178 LEU 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 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 6 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 159 VAL Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 350 SER 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 269 MET 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: 0.9980 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN 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 D 371 HIS E 296 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 = 0.3573 r_free = 0.3573 target = 0.106781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.099154 restraints weight = 19087.405| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.18 r_work: 0.3371 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14960 Z= 0.192 Angle : 0.596 6.864 20305 Z= 0.293 Chirality : 0.048 0.158 2255 Planarity : 0.004 0.066 2595 Dihedral : 6.758 101.978 2085 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.45 % Allowed : 20.00 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.20), residues: 1830 helix: 0.42 (0.19), residues: 800 sheet: 1.07 (0.29), residues: 330 loop : 0.11 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 28 TYR 0.007 0.001 TYR C 240 PHE 0.015 0.001 PHE B 127 TRP 0.012 0.002 TRP D 79 HIS 0.005 0.002 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 (14960) covalent geometry : angle 0.59597 / 0.29 (20305) hydrogen bonds : bond 0.03739 / 2.59 ( 708) hydrogen bonds : angle 4.29132 / 3.05 ( 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 377 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 323 time to evaluate : 0.546 Fit side-chains REVERT: A 28 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8155 (ttp-170) REVERT: A 176 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: A 314 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7777 (tt0) REVERT: B 47 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5958 (ppp) REVERT: B 132 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: B 225 ASN cc_start: 0.8147 (m-40) cc_final: 0.7890 (m110) REVERT: C 314 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: C 363 ASP cc_start: 0.8166 (m-30) cc_final: 0.7856 (m-30) REVERT: D 6 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7919 (t) REVERT: D 299 MET cc_start: 0.8877 (mtm) cc_final: 0.8564 (mtm) REVERT: E 78 ASN cc_start: 0.8386 (t0) cc_final: 0.8043 (t0) REVERT: E 107 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: E 113 LYS cc_start: 0.8438 (mmmm) cc_final: 0.7896 (mmtm) outliers start: 54 outliers final: 29 residues processed: 344 average time/residue: 0.7291 time to fit residues: 269.7350 Evaluate side-chains 350 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 313 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG 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 276 GLU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 47 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 215 LYS 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 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 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 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 232 SER Chi-restraints excluded: chain E residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 168 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 169 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 154 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN B 78 ASN B 162 ASN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 162 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.107407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099824 restraints weight = 19095.259| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.18 r_work: 0.3380 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14960 Z= 0.149 Angle : 0.572 6.486 20305 Z= 0.279 Chirality : 0.046 0.137 2255 Planarity : 0.004 0.065 2595 Dihedral : 6.494 96.998 2085 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.51 % Allowed : 20.13 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.20), residues: 1830 helix: 0.57 (0.19), residues: 800 sheet: 0.99 (0.28), residues: 340 loop : 0.15 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 95 TYR 0.006 0.001 TYR C 188 PHE 0.013 0.001 PHE B 127 TRP 0.012 0.002 TRP A 79 HIS 0.004 0.001 HIS E 173 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (14960) covalent geometry : angle 0.57189 / 0.28 (20305) hydrogen bonds : bond 0.03381 / 2.33 ( 708) hydrogen bonds : angle 4.20635 / 2.99 ( 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 388 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 333 time to evaluate : 0.471 Fit side-chains REVERT: B 132 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: B 225 ASN cc_start: 0.8150 (m-40) cc_final: 0.7881 (m110) REVERT: C 6 THR cc_start: 0.8461 (p) cc_final: 0.8218 (t) REVERT: C 314 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: C 363 ASP cc_start: 0.8154 (m-30) cc_final: 0.7849 (m-30) REVERT: D 6 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7960 (t) REVERT: D 119 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: D 132 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8011 (ttp) REVERT: D 176 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7915 (mtp) REVERT: D 299 MET cc_start: 0.8856 (mtm) cc_final: 0.8536 (mtm) REVERT: E 59 GLN cc_start: 0.8524 (tp-100) cc_final: 0.8300 (tp40) REVERT: E 107 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: E 113 LYS cc_start: 0.8451 (mmmm) cc_final: 0.7917 (mmtm) outliers start: 55 outliers final: 27 residues processed: 354 average time/residue: 0.7163 time to fit residues: 272.1521 Evaluate side-chains 360 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 326 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 132 MET 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 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET 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 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 119 MET 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 232 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 96 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 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 ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.098807 restraints weight = 19006.572| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.13 r_work: 0.3365 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14960 Z= 0.250 Angle : 0.631 7.143 20305 Z= 0.311 Chirality : 0.050 0.172 2255 Planarity : 0.005 0.065 2595 Dihedral : 6.859 100.701 2085 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.71 % Allowed : 19.94 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1830 helix: 0.47 (0.19), residues: 800 sheet: 0.99 (0.28), residues: 330 loop : 0.06 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.008 0.001 TYR C 240 PHE 0.016 0.002 PHE C 127 TRP 0.012 0.002 TRP D 79 HIS 0.005 0.002 HIS A 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (14960) covalent geometry : angle 0.63071 / 0.31 (20305) hydrogen bonds : bond 0.04180 / 2.89 ( 708) hydrogen bonds : angle 4.35396 / 3.10 ( 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 387 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 329 time to evaluate : 0.468 Fit side-chains REVERT: A 28 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8132 (ttp-170) REVERT: A 314 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7728 (tt0) REVERT: B 47 MET cc_start: 0.6799 (ppp) cc_final: 0.6071 (ppp) REVERT: B 225 ASN cc_start: 0.8121 (m-40) cc_final: 0.7857 (m110) REVERT: C 6 THR cc_start: 0.8430 (p) cc_final: 0.8224 (t) REVERT: C 314 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: C 363 ASP cc_start: 0.8178 (m-30) cc_final: 0.7909 (m-30) REVERT: D 119 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8202 (mtp) REVERT: D 176 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.7919 (mtp) REVERT: D 299 MET cc_start: 0.8886 (mtm) cc_final: 0.8560 (mtm) REVERT: E 59 GLN cc_start: 0.8494 (tp-100) cc_final: 0.8271 (tp40) REVERT: E 107 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: E 113 LYS cc_start: 0.8440 (mmmm) cc_final: 0.7941 (mmtm) outliers start: 58 outliers final: 39 residues processed: 350 average time/residue: 0.7613 time to fit residues: 285.9236 Evaluate side-chains 361 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 28 ARG 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 A residue 354 GLN Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 136 ILE Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 336 LYS 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 136 ILE Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 336 LYS Chi-restraints excluded: chain C residue 368 SER 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 119 MET 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 D residue 344 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 128 ASN Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 336 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 52 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 172 optimal weight: 0.0870 chunk 136 optimal weight: 0.6980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 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 296 ASN D 297 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN E 246 GLN E 297 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100988 restraints weight = 19233.808| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.15 r_work: 0.3407 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14960 Z= 0.096 Angle : 0.543 6.169 20305 Z= 0.263 Chirality : 0.044 0.132 2255 Planarity : 0.004 0.067 2595 Dihedral : 6.007 86.084 2085 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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 are not related in a simple way. whole: 0.84 (0.20), residues: 1830 helix: 0.83 (0.19), residues: 800 sheet: 0.85 (0.28), residues: 345 loop : 0.27 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.006 0.001 TYR C 143 PHE 0.009 0.001 PHE A 255 TRP 0.013 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (14960) covalent geometry : angle 0.54336 / 0.26 (20305) hydrogen bonds : bond 0.02804 / 1.94 ( 708) hydrogen bonds : angle 4.10795 / 2.91 ( 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 363 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 327 time to evaluate : 0.607 Fit side-chains REVERT: B 47 MET cc_start: 0.6816 (ppp) cc_final: 0.6106 (ppp) REVERT: B 113 LYS cc_start: 0.8539 (mmtp) cc_final: 0.8275 (mttm) REVERT: B 225 ASN cc_start: 0.8126 (m-40) cc_final: 0.7866 (m-40) REVERT: C 314 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7044 (tt0) REVERT: C 363 ASP cc_start: 0.8132 (m-30) cc_final: 0.7845 (m-30) REVERT: D 119 MET cc_start: 0.8401 (ttp) cc_final: 0.8191 (mtp) REVERT: D 299 MET cc_start: 0.8831 (mtm) cc_final: 0.8510 (mtm) REVERT: D 326 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8011 (mptp) REVERT: E 107 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7273 (tt0) REVERT: E 113 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8152 (mptt) outliers start: 36 outliers final: 19 residues processed: 342 average time/residue: 0.7914 time to fit residues: 290.4448 Evaluate side-chains 346 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 324 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain B residue 99 GLU 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 85 ILE Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 313 MET 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 149 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 326 LYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 336 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 49 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 137 GLN A 162 ASN B 59 GLN B 78 ASN B 128 ASN B 162 ASN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 12 ASN D 115 ASN D 162 ASN D 296 ASN D 297 ASN E 297 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.101532 restraints weight = 19056.570| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.17 r_work: 0.3412 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14960 Z= 0.105 Angle : 0.546 6.813 20305 Z= 0.264 Chirality : 0.044 0.132 2255 Planarity : 0.004 0.067 2595 Dihedral : 5.740 80.998 2085 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.04 % Allowed : 22.17 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1830 helix: 0.94 (0.19), residues: 800 sheet: 0.87 (0.28), residues: 345 loop : 0.29 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 95 TYR 0.006 0.001 TYR C 143 PHE 0.009 0.001 PHE B 127 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (14960) covalent geometry : angle 0.54589 / 0.26 (20305) hydrogen bonds : bond 0.02885 / 1.99 ( 708) hydrogen bonds : angle 4.06411 / 2.88 ( 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 354 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 322 time to evaluate : 0.581 Fit side-chains REVERT: B 47 MET cc_start: 0.6780 (ppp) cc_final: 0.6082 (ppp) REVERT: C 314 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: C 363 ASP cc_start: 0.8105 (m-30) cc_final: 0.7847 (m-30) REVERT: D 119 MET cc_start: 0.8400 (ttp) cc_final: 0.8162 (mtp) REVERT: D 299 MET cc_start: 0.8857 (mtm) cc_final: 0.8532 (mtm) REVERT: E 47 MET cc_start: 0.6342 (ptm) cc_final: 0.6051 (ptm) REVERT: E 78 ASN cc_start: 0.8280 (t0) cc_final: 0.7971 (t0) REVERT: E 107 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7308 (tt0) REVERT: E 113 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8165 (mptt) outliers start: 32 outliers final: 17 residues processed: 336 average time/residue: 0.7621 time to fit residues: 274.7276 Evaluate side-chains 330 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 311 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 128 ASN 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 313 MET 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 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 336 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.0670 chunk 92 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 135 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN A 297 ASN B 59 GLN B 78 ASN B 128 ASN B 162 ASN B 225 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN C 353 GLN D 162 ASN D 296 ASN D 371 HIS E 297 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.109187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.101581 restraints weight = 18938.119| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.17 r_work: 0.3413 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 14960 Z= 0.150 Angle : 0.924 59.191 20305 Z= 0.534 Chirality : 0.048 0.658 2255 Planarity : 0.004 0.069 2595 Dihedral : 5.726 80.961 2085 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 1.47 % Allowed : 23.13 % Favored : 75.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1830 helix: 0.95 (0.19), residues: 800 sheet: 0.87 (0.28), residues: 345 loop : 0.29 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.006 0.001 TYR C 143 PHE 0.008 0.001 PHE E 31 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14960) covalent geometry : angle 0.92436 / 0.53 (20305) hydrogen bonds : bond 0.02887 / 1.99 ( 708) hydrogen bonds : angle 4.06642 / 2.88 ( 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 333 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.437 Fit side-chains REVERT: B 47 MET cc_start: 0.6780 (ppp) cc_final: 0.6082 (ppp) REVERT: C 314 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7096 (tt0) REVERT: C 363 ASP cc_start: 0.8100 (m-30) cc_final: 0.7843 (m-30) REVERT: D 119 MET cc_start: 0.8411 (ttp) cc_final: 0.8176 (mtp) REVERT: D 299 MET cc_start: 0.8846 (mtm) cc_final: 0.8514 (mtm) REVERT: E 47 MET cc_start: 0.6347 (ptm) cc_final: 0.6051 (ptm) REVERT: E 78 ASN cc_start: 0.8279 (t0) cc_final: 0.7968 (t0) REVERT: E 107 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7316 (tt0) REVERT: E 113 LYS cc_start: 0.8444 (mmmm) cc_final: 0.8156 (mptt) outliers start: 23 outliers final: 15 residues processed: 320 average time/residue: 0.7672 time to fit residues: 263.3256 Evaluate side-chains 327 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 310 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 349 LEU 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 100 GLU Chi-restraints excluded: chain C residue 313 MET 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 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 336 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: 3.9990 chunk 3 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 108 optimal weight: 3.9990 chunk 126 optimal weight: 8.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 59 GLN B 78 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 246 GLN B 297 ASN C 246 GLN C 263 GLN D 162 ASN D 296 ASN E 297 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.101595 restraints weight = 18999.145| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.17 r_work: 0.3413 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.174 14960 Z= 0.150 Angle : 0.924 59.191 20305 Z= 0.534 Chirality : 0.048 0.658 2255 Planarity : 0.004 0.071 2595 Dihedral : 5.726 80.961 2085 Min Nonbonded Distance : 1.317 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.95 % Favored : 96.99 % Rotamer: Outliers : 1.15 % Allowed : 23.45 % Favored : 75.40 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1830 helix: 0.95 (0.19), residues: 800 sheet: 0.87 (0.28), residues: 345 loop : 0.29 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 95 TYR 0.006 0.001 TYR C 143 PHE 0.008 0.001 PHE E 31 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (14960) covalent geometry : angle 0.92436 / 0.53 (20305) hydrogen bonds : bond 0.02887 / 1.99 ( 708) hydrogen bonds : angle 4.06642 / 2.88 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6339.97 seconds wall clock time: 108 minutes 25.51 seconds (6505.51 seconds total)