Starting phenix.real_space_refine on Wed Mar 4 17:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2r_15104/03_2026/8a2r_15104.map" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 100 5.16 5 Be 5 3.05 5 C 9145 2.51 5 N 2445 2.21 5 O 3265 1.98 5 F 15 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14990 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Classifications: {'water': 118} Link IDs: {None: 117} Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "D" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.43, per 1000 atoms: 0.16 Number of scatterers: 14990 At special positions: 0 Unit cell: (95.215, 88.265, 191.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 100 16.00 P 10 15.00 Mg 5 11.99 F 15 9.00 O 3265 8.00 N 2445 7.00 C 9145 6.00 Be 5 4.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 624.8 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 51.9% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.747A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 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 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.958A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.518A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 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 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.747A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.518A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 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 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 351 through 355 removed outlier: 3.905A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.958A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 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 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.959A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.746A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.519A pdb=" N ILE E 208 " --> pdb=" O ALA E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 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 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.904A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.555A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.706A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.706A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.307A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.655A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.554A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.555A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.307A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.746A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.554A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.264A 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: 6.307A 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: 6.554A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.264A 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: 6.306A 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 241 743 hydrogen bonds defined for protein. 1878 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: 2.90 Time building geometry restraints manager: 1.74 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: 4705 1.34 - 1.46: 2936 1.46 - 1.57: 6989 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14820 Sorted by residual: bond pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 ... (remaining 14815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 19869 2.62 - 5.24: 201 5.24 - 7.86: 20 7.86 - 10.47: 5 10.47 - 13.09: 10 Bond angle restraints: 20105 Sorted by residual: angle pdb=" F2 BEF D 403 " pdb="BE BEF D 403 " pdb=" F3 BEF D 403 " ideal model delta sigma weight residual 119.96 106.87 13.09 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF B 403 " pdb="BE BEF B 403 " pdb=" F3 BEF B 403 " ideal model delta sigma weight residual 119.96 106.89 13.07 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF A 403 " pdb="BE BEF A 403 " pdb=" F3 BEF A 403 " ideal model delta sigma weight residual 119.96 106.90 13.06 3.00e+00 1.11e-01 1.90e+01 angle pdb=" F2 BEF E 403 " pdb="BE BEF E 403 " pdb=" F3 BEF E 403 " ideal model delta sigma weight residual 119.96 106.91 13.05 3.00e+00 1.11e-01 1.89e+01 angle pdb=" F2 BEF C 403 " pdb="BE BEF C 403 " pdb=" F3 BEF C 403 " ideal model delta sigma weight residual 119.96 106.93 13.03 3.00e+00 1.11e-01 1.89e+01 ... (remaining 20100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.21: 8725 31.21 - 62.42: 140 62.42 - 93.63: 35 93.63 - 124.84: 0 124.84 - 156.04: 10 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.05 -156.04 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 96.04 -156.04 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 95.98 -155.98 1 2.00e+01 2.50e-03 4.59e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1054 0.027 - 0.054: 758 0.054 - 0.081: 226 0.081 - 0.107: 154 0.107 - 0.134: 38 Chirality restraints: 2230 Sorted by residual: chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.64 0.13 2.00e-01 2.50e+01 4.50e-01 chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 321 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO B 322 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 321 " 0.017 5.00e-02 4.00e+02 2.59e-02 1.07e+00 pdb=" N PRO A 322 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 321 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.06e+00 pdb=" N PRO E 322 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 322 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 322 " 0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 136 2.48 - 3.09: 10379 3.09 - 3.69: 24236 3.69 - 4.30: 39005 4.30 - 4.90: 60736 Nonbonded interactions: 134492 Sorted by model distance: nonbonded pdb="MG MG B 402 " pdb=" O HOH B 526 " model vdw 1.880 2.170 nonbonded pdb="MG MG D 402 " pdb=" F2 BEF D 403 " model vdw 1.898 2.120 nonbonded pdb="MG MG E 402 " pdb=" F2 BEF E 403 " model vdw 1.899 2.120 nonbonded pdb="MG MG B 402 " pdb=" F2 BEF B 403 " model vdw 1.899 2.120 nonbonded pdb="MG MG A 402 " pdb=" F2 BEF A 403 " model vdw 1.899 2.120 ... (remaining 134487 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.200 Find NCS groups from input model: 0.130 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 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 : 0.017 0.900 14825 Z= 1.666 Angle : 0.674 13.092 20105 Z= 0.330 Chirality : 0.044 0.134 2230 Planarity : 0.004 0.027 2565 Dihedral : 13.665 156.045 5510 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.65 % Allowed : 3.55 % Favored : 95.81 % 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: -1.52 (0.18), residues: 1795 helix: -2.41 (0.13), residues: 790 sheet: -0.72 (0.24), residues: 335 loop : 1.17 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 177 TYR 0.007 0.001 TYR A 143 PHE 0.008 0.001 PHE B 262 TRP 0.013 0.002 TRP E 340 HIS 0.005 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00485 (14820) covalent geometry : angle 0.67357 (20105) hydrogen bonds : bond 0.22470 ( 728) hydrogen bonds : angle 7.72740 ( 1878) Misc. bond : bond 0.89894 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 276 time to evaluate : 0.561 Fit side-chains REVERT: C 113 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8335 (mmtt) REVERT: C 286 ASP cc_start: 0.7612 (m-30) cc_final: 0.7386 (m-30) REVERT: C 355 MET cc_start: 0.8157 (mtp) cc_final: 0.7772 (mtt) REVERT: B 113 LYS cc_start: 0.8582 (mtpt) cc_final: 0.8216 (mmtt) REVERT: D 123 MET cc_start: 0.8755 (mmt) cc_final: 0.8413 (mmt) REVERT: E 227 MET cc_start: 0.8889 (mmm) cc_final: 0.8503 (mmm) REVERT: E 311 ASP cc_start: 0.7853 (m-30) cc_final: 0.7653 (m-30) outliers start: 10 outliers final: 3 residues processed: 278 average time/residue: 0.7834 time to fit residues: 234.8058 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 203 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 96 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 173 HIS C 246 GLN C 353 GLN C 360 GLN B 173 HIS B 246 GLN B 360 GLN D 246 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091740 restraints weight = 14819.842| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 1.28 r_work: 0.2898 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14825 Z= 0.273 Angle : 0.713 8.779 20105 Z= 0.361 Chirality : 0.051 0.221 2230 Planarity : 0.005 0.037 2565 Dihedral : 12.824 169.819 2058 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.45 % Favored : 98.44 % Rotamer: Outliers : 2.39 % Allowed : 6.84 % Favored : 90.77 % 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: 0.47 (0.19), residues: 1795 helix: -0.26 (0.17), residues: 790 sheet: -0.26 (0.24), residues: 345 loop : 1.83 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 177 TYR 0.011 0.001 TYR E 143 PHE 0.016 0.002 PHE C 262 TRP 0.023 0.004 TRP B 340 HIS 0.007 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00634 (14820) covalent geometry : angle 0.71331 (20105) hydrogen bonds : bond 0.05533 ( 728) hydrogen bonds : angle 5.35678 ( 1878) Misc. bond : bond 0.00247 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 212 time to evaluate : 0.525 Fit side-chains REVERT: C 355 MET cc_start: 0.8782 (mtp) cc_final: 0.8354 (mtt) REVERT: B 125 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7682 (mt-10) REVERT: B 224 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7758 (mp0) REVERT: B 361 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7595 (mt-10) REVERT: E 51 ASP cc_start: 0.7814 (t0) cc_final: 0.7565 (p0) REVERT: E 311 ASP cc_start: 0.8622 (m-30) cc_final: 0.8247 (m-30) outliers start: 37 outliers final: 14 residues processed: 233 average time/residue: 0.7060 time to fit residues: 178.0295 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 178 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN C 360 GLN A 225 ASN B 225 ASN B 353 GLN B 360 GLN E 353 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093417 restraints weight = 14946.394| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.26 r_work: 0.2938 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14825 Z= 0.153 Angle : 0.613 8.073 20105 Z= 0.302 Chirality : 0.046 0.181 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.446 170.918 2058 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.23 % Favored : 97.66 % Rotamer: Outliers : 1.61 % Allowed : 8.65 % Favored : 89.74 % 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: 1.09 (0.20), residues: 1795 helix: 0.45 (0.19), residues: 790 sheet: -0.18 (0.25), residues: 345 loop : 2.04 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 206 TYR 0.008 0.001 TYR B 143 PHE 0.009 0.001 PHE C 262 TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00344 (14820) covalent geometry : angle 0.61286 (20105) hydrogen bonds : bond 0.04186 ( 728) hydrogen bonds : angle 4.94140 ( 1878) Misc. bond : bond 0.00073 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.585 Fit side-chains REVERT: C 355 MET cc_start: 0.8753 (mtp) cc_final: 0.8312 (mtt) REVERT: A 121 GLN cc_start: 0.8270 (tt0) cc_final: 0.7654 (tm-30) REVERT: A 125 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: A 326 LYS cc_start: 0.8525 (tptp) cc_final: 0.7916 (ptpp) REVERT: B 100 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7586 (mm-30) REVERT: B 125 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: B 224 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7846 (mp0) REVERT: D 121 GLN cc_start: 0.8703 (tt0) cc_final: 0.8409 (tm-30) REVERT: E 51 ASP cc_start: 0.7750 (t0) cc_final: 0.7528 (p0) REVERT: E 311 ASP cc_start: 0.8527 (m-30) cc_final: 0.8165 (m-30) outliers start: 25 outliers final: 12 residues processed: 210 average time/residue: 0.6987 time to fit residues: 159.1964 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 185 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 36 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092394 restraints weight = 14704.933| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.28 r_work: 0.2917 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14825 Z= 0.203 Angle : 0.649 8.413 20105 Z= 0.324 Chirality : 0.048 0.194 2230 Planarity : 0.004 0.035 2565 Dihedral : 12.644 168.018 2057 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.74 % Allowed : 8.90 % Favored : 89.35 % 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: 1.21 (0.20), residues: 1795 helix: 0.56 (0.19), residues: 790 sheet: -0.15 (0.25), residues: 345 loop : 2.09 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 28 TYR 0.008 0.001 TYR E 143 PHE 0.012 0.002 PHE C 262 TRP 0.018 0.003 TRP B 340 HIS 0.005 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00466 (14820) covalent geometry : angle 0.64942 (20105) hydrogen bonds : bond 0.04597 ( 728) hydrogen bonds : angle 4.96912 ( 1878) Misc. bond : bond 0.00108 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.484 Fit side-chains REVERT: C 284 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8371 (mttp) REVERT: C 354 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: C 355 MET cc_start: 0.8780 (mtp) cc_final: 0.8324 (mtt) REVERT: A 28 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8515 (ttm170) REVERT: A 121 GLN cc_start: 0.8294 (tt0) cc_final: 0.7653 (tm-30) REVERT: A 125 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7267 (mp0) REVERT: A 234 SER cc_start: 0.8430 (p) cc_final: 0.8208 (t) REVERT: A 326 LYS cc_start: 0.8532 (tptp) cc_final: 0.7899 (ptpp) REVERT: B 100 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7611 (mm-30) REVERT: B 125 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7687 (mt-10) REVERT: B 224 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7915 (mp0) REVERT: B 361 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7601 (mt-10) REVERT: D 121 GLN cc_start: 0.8703 (tt0) cc_final: 0.8397 (tm-30) REVERT: D 328 LYS cc_start: 0.8794 (tptm) cc_final: 0.8550 (tppt) REVERT: E 311 ASP cc_start: 0.8563 (m-30) cc_final: 0.8214 (m-30) REVERT: E 314 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8156 (tt0) outliers start: 27 outliers final: 17 residues processed: 204 average time/residue: 0.7324 time to fit residues: 161.8160 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 284 LYS Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 171 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN B 360 GLN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.094439 restraints weight = 14902.109| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.26 r_work: 0.2955 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14825 Z= 0.126 Angle : 0.585 7.756 20105 Z= 0.285 Chirality : 0.045 0.173 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.290 170.782 2057 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.68 % Allowed : 9.16 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.20), residues: 1795 helix: 0.89 (0.19), residues: 775 sheet: -0.10 (0.25), residues: 345 loop : 2.32 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 28 TYR 0.006 0.001 TYR E 91 PHE 0.007 0.001 PHE C 31 TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00276 (14820) covalent geometry : angle 0.58515 (20105) hydrogen bonds : bond 0.03656 ( 728) hydrogen bonds : angle 4.73194 ( 1878) Misc. bond : bond 0.00035 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.560 Fit side-chains REVERT: C 355 MET cc_start: 0.8745 (mtp) cc_final: 0.8292 (mtt) REVERT: A 28 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8497 (ttm170) REVERT: A 227 MET cc_start: 0.8528 (mmm) cc_final: 0.8057 (mmm) REVERT: A 234 SER cc_start: 0.8343 (p) cc_final: 0.8140 (t) REVERT: A 326 LYS cc_start: 0.8507 (tptp) cc_final: 0.7901 (ptpp) REVERT: B 92 ASN cc_start: 0.8637 (m110) cc_final: 0.8295 (m110) REVERT: B 100 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7547 (mm-30) REVERT: B 125 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: B 224 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7937 (mp0) REVERT: B 361 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 121 GLN cc_start: 0.8694 (tt0) cc_final: 0.8370 (tm-30) REVERT: D 225 ASN cc_start: 0.8218 (t0) cc_final: 0.7887 (m-40) REVERT: D 328 LYS cc_start: 0.8799 (tptm) cc_final: 0.8563 (tppt) REVERT: E 41 GLN cc_start: 0.6880 (tt0) cc_final: 0.6596 (mm-40) REVERT: E 77 THR cc_start: 0.9072 (m) cc_final: 0.8799 (p) REVERT: E 311 ASP cc_start: 0.8530 (m-30) cc_final: 0.8209 (m-30) REVERT: E 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8205 (tt0) outliers start: 26 outliers final: 12 residues processed: 206 average time/residue: 0.7274 time to fit residues: 162.2588 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 0.6980 chunk 3 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 118 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092621 restraints weight = 14727.946| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.25 r_work: 0.2925 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14825 Z= 0.196 Angle : 0.640 8.319 20105 Z= 0.317 Chirality : 0.048 0.192 2230 Planarity : 0.004 0.040 2565 Dihedral : 12.582 169.156 2056 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.42 % Allowed : 9.68 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.20), residues: 1795 helix: 0.76 (0.19), residues: 790 sheet: -0.12 (0.25), residues: 345 loop : 2.17 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 206 TYR 0.007 0.001 TYR E 143 PHE 0.012 0.002 PHE C 262 TRP 0.018 0.003 TRP B 340 HIS 0.006 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00451 (14820) covalent geometry : angle 0.64043 (20105) hydrogen bonds : bond 0.04424 ( 728) hydrogen bonds : angle 4.89620 ( 1878) Misc. bond : bond 0.00098 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.589 Fit side-chains REVERT: C 95 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7164 (mmp80) REVERT: C 354 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8196 (pt0) REVERT: C 355 MET cc_start: 0.8760 (mtp) cc_final: 0.8286 (mtt) REVERT: A 28 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8530 (ttm170) REVERT: A 326 LYS cc_start: 0.8524 (tptp) cc_final: 0.7918 (ptpp) REVERT: B 100 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7579 (mm-30) REVERT: B 125 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: B 224 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7936 (mp0) REVERT: B 361 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 121 GLN cc_start: 0.8690 (tt0) cc_final: 0.8380 (tm-30) REVERT: D 225 ASN cc_start: 0.8270 (t0) cc_final: 0.7883 (m-40) REVERT: D 328 LYS cc_start: 0.8791 (tptm) cc_final: 0.8554 (tppt) REVERT: E 41 GLN cc_start: 0.6775 (tt0) cc_final: 0.6525 (mp10) REVERT: E 77 THR cc_start: 0.9082 (m) cc_final: 0.8813 (p) REVERT: E 311 ASP cc_start: 0.8569 (m-30) cc_final: 0.8231 (m-30) REVERT: E 314 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8160 (tt0) outliers start: 22 outliers final: 14 residues processed: 196 average time/residue: 0.7192 time to fit residues: 152.8541 Evaluate side-chains 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 77 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093543 restraints weight = 14651.501| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.27 r_work: 0.2937 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14825 Z= 0.160 Angle : 0.613 8.100 20105 Z= 0.301 Chirality : 0.046 0.183 2230 Planarity : 0.004 0.037 2565 Dihedral : 12.433 170.046 2056 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 9.48 % Favored : 88.90 % 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: 1.48 (0.20), residues: 1795 helix: 0.85 (0.19), residues: 790 sheet: -0.13 (0.25), residues: 345 loop : 2.21 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 206 TYR 0.006 0.001 TYR E 91 PHE 0.009 0.001 PHE C 262 TRP 0.016 0.002 TRP C 340 HIS 0.005 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00363 (14820) covalent geometry : angle 0.61337 (20105) hydrogen bonds : bond 0.04033 ( 728) hydrogen bonds : angle 4.81593 ( 1878) Misc. bond : bond 0.00077 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.625 Fit side-chains REVERT: C 95 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7194 (mmp80) REVERT: C 354 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8207 (pt0) REVERT: C 355 MET cc_start: 0.8757 (mtp) cc_final: 0.8288 (mtt) REVERT: A 28 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8506 (ttm170) REVERT: A 125 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7330 (mp0) REVERT: A 326 LYS cc_start: 0.8537 (tptp) cc_final: 0.7939 (ptpp) REVERT: B 100 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 125 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7647 (mt-10) REVERT: B 224 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7926 (mp0) REVERT: B 361 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 121 GLN cc_start: 0.8693 (tt0) cc_final: 0.8384 (tm-30) REVERT: D 225 ASN cc_start: 0.8246 (t0) cc_final: 0.7878 (m-40) REVERT: D 314 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8310 (tp40) REVERT: D 328 LYS cc_start: 0.8809 (tptm) cc_final: 0.8559 (tppt) REVERT: E 41 GLN cc_start: 0.6764 (tt0) cc_final: 0.6351 (mp10) REVERT: E 77 THR cc_start: 0.9088 (m) cc_final: 0.8844 (p) REVERT: E 311 ASP cc_start: 0.8548 (m-30) cc_final: 0.8211 (m-30) REVERT: E 314 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8184 (tt0) outliers start: 25 outliers final: 14 residues processed: 199 average time/residue: 0.7624 time to fit residues: 164.3008 Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 77 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 161 HIS E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.116248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.094039 restraints weight = 14716.870| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.27 r_work: 0.2943 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14825 Z= 0.143 Angle : 0.601 7.957 20105 Z= 0.293 Chirality : 0.045 0.179 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.358 171.314 2056 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.42 % Allowed : 9.61 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.20), residues: 1795 helix: 1.01 (0.19), residues: 775 sheet: -0.11 (0.25), residues: 345 loop : 2.36 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 206 TYR 0.007 0.001 TYR A 143 PHE 0.008 0.001 PHE C 262 TRP 0.015 0.002 TRP C 340 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00321 (14820) covalent geometry : angle 0.60070 (20105) hydrogen bonds : bond 0.03838 ( 728) hydrogen bonds : angle 4.76340 ( 1878) Misc. bond : bond 0.00060 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.575 Fit side-chains REVERT: C 354 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8195 (pt0) REVERT: C 355 MET cc_start: 0.8746 (mtp) cc_final: 0.8277 (mtt) REVERT: A 28 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8514 (ttm170) REVERT: A 125 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 326 LYS cc_start: 0.8512 (tptp) cc_final: 0.7921 (ptpp) REVERT: B 100 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7556 (mm-30) REVERT: B 125 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: B 224 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7936 (mp0) REVERT: B 361 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7572 (mt-10) REVERT: D 225 ASN cc_start: 0.8230 (t0) cc_final: 0.7867 (m-40) REVERT: D 314 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: D 328 LYS cc_start: 0.8812 (tptm) cc_final: 0.8572 (tppt) REVERT: E 41 GLN cc_start: 0.6726 (tt0) cc_final: 0.6394 (mp10) REVERT: E 77 THR cc_start: 0.9082 (m) cc_final: 0.8844 (p) REVERT: E 311 ASP cc_start: 0.8552 (m-30) cc_final: 0.8223 (m-30) REVERT: E 314 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8192 (tt0) outliers start: 22 outliers final: 14 residues processed: 191 average time/residue: 0.7493 time to fit residues: 155.3495 Evaluate side-chains 190 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 124 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 18 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 104 optimal weight: 0.0060 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.116465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.094373 restraints weight = 14771.753| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.28 r_work: 0.2952 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14825 Z= 0.128 Angle : 0.590 7.768 20105 Z= 0.285 Chirality : 0.045 0.173 2230 Planarity : 0.003 0.034 2565 Dihedral : 12.261 172.478 2056 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.42 % Allowed : 9.81 % Favored : 88.77 % 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: 1.75 (0.20), residues: 1795 helix: 1.08 (0.19), residues: 775 sheet: -0.09 (0.25), residues: 345 loop : 2.37 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 206 TYR 0.006 0.001 TYR E 91 PHE 0.008 0.001 PHE C 31 TRP 0.015 0.002 TRP D 340 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00283 (14820) covalent geometry : angle 0.58982 (20105) hydrogen bonds : bond 0.03627 ( 728) hydrogen bonds : angle 4.70325 ( 1878) Misc. bond : bond 0.00050 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.608 Fit side-chains REVERT: C 354 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: C 355 MET cc_start: 0.8745 (mtp) cc_final: 0.8275 (mtt) REVERT: A 28 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8522 (ttm170) REVERT: A 125 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 326 LYS cc_start: 0.8534 (tptp) cc_final: 0.7950 (ptpp) REVERT: B 100 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7543 (mm-30) REVERT: B 125 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: D 225 ASN cc_start: 0.8232 (t0) cc_final: 0.7882 (m-40) REVERT: D 314 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8291 (tp40) REVERT: D 328 LYS cc_start: 0.8801 (tptm) cc_final: 0.8564 (tppt) REVERT: E 41 GLN cc_start: 0.6686 (tt0) cc_final: 0.6427 (mp10) REVERT: E 77 THR cc_start: 0.9076 (m) cc_final: 0.8842 (p) REVERT: E 100 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: E 311 ASP cc_start: 0.8520 (m-30) cc_final: 0.8197 (m-30) REVERT: E 314 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8212 (tt0) outliers start: 22 outliers final: 15 residues processed: 191 average time/residue: 0.7750 time to fit residues: 160.5835 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 65 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.092735 restraints weight = 14801.084| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.28 r_work: 0.2924 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14825 Z= 0.181 Angle : 0.634 8.245 20105 Z= 0.311 Chirality : 0.047 0.186 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.505 170.305 2056 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.55 % Allowed : 9.74 % Favored : 88.71 % 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: 1.52 (0.20), residues: 1795 helix: 0.90 (0.19), residues: 790 sheet: -0.11 (0.25), residues: 345 loop : 2.21 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 28 TYR 0.007 0.001 TYR A 69 PHE 0.010 0.002 PHE C 262 TRP 0.016 0.003 TRP C 79 HIS 0.005 0.002 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00414 (14820) covalent geometry : angle 0.63413 (20105) hydrogen bonds : bond 0.04248 ( 728) hydrogen bonds : angle 4.85570 ( 1878) Misc. bond : bond 0.00091 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.599 Fit side-chains REVERT: C 95 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7105 (mmp80) REVERT: C 354 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8197 (pt0) REVERT: C 355 MET cc_start: 0.8761 (mtp) cc_final: 0.8286 (mtt) REVERT: A 28 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8530 (ttm170) REVERT: A 125 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 326 LYS cc_start: 0.8529 (tptp) cc_final: 0.7952 (ptpp) REVERT: B 100 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 125 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7667 (mt-10) REVERT: B 361 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7595 (mt-10) REVERT: D 225 ASN cc_start: 0.8280 (t0) cc_final: 0.7893 (m-40) REVERT: D 314 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8294 (tp40) REVERT: D 328 LYS cc_start: 0.8786 (tptm) cc_final: 0.8554 (tppt) REVERT: E 41 GLN cc_start: 0.6737 (tt0) cc_final: 0.6435 (mp10) REVERT: E 77 THR cc_start: 0.9093 (m) cc_final: 0.8844 (p) REVERT: E 100 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: E 311 ASP cc_start: 0.8556 (m-30) cc_final: 0.8218 (m-30) REVERT: E 314 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8174 (tt0) outliers start: 24 outliers final: 15 residues processed: 190 average time/residue: 0.7863 time to fit residues: 161.7851 Evaluate side-chains 196 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 374 CYS Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 106 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 129 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN B 225 ASN B 353 GLN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.115635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093472 restraints weight = 14755.143| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.28 r_work: 0.2935 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14825 Z= 0.153 Angle : 0.613 8.044 20105 Z= 0.299 Chirality : 0.046 0.181 2230 Planarity : 0.004 0.033 2565 Dihedral : 12.393 170.695 2056 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.48 % Allowed : 10.06 % Favored : 88.45 % 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: 1.69 (0.20), residues: 1795 helix: 1.04 (0.19), residues: 775 sheet: -0.10 (0.25), residues: 345 loop : 2.33 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 28 TYR 0.006 0.001 TYR E 91 PHE 0.009 0.001 PHE C 262 TRP 0.016 0.002 TRP C 340 HIS 0.006 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00344 (14820) covalent geometry : angle 0.61322 (20105) hydrogen bonds : bond 0.03930 ( 728) hydrogen bonds : angle 4.79158 ( 1878) Misc. bond : bond 0.00070 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6853.70 seconds wall clock time: 117 minutes 12.70 seconds (7032.70 seconds total)