Starting phenix.real_space_refine on Fri Jul 3 16:27:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8oi8_16888/07_2026/8oi8_16888.cif" } resolution = 2.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 95 5.16 5 C 9050 2.51 5 N 2390 2.21 5 O 3345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14895 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2834 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 19, 'TRANS': 343} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "A" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 105 Classifications: {'water': 105} Link IDs: {None: 104} Chain: "B" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Classifications: {'water': 129} Link IDs: {None: 128} Chain: "E" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.21, per 1000 atoms: 0.15 Number of scatterers: 14895 At special positions: 0 Unit cell: (92.435, 93.13, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 95 16.00 P 10 15.00 Mg 5 11.99 O 3345 8.00 N 2390 7.00 C 9050 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 496.4 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 30 sheets defined 50.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.945A 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: 3.730A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 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 348 through 353 removed outlier: 6.279A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.946A 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: 3.729A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 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 348 through 353 removed outlier: 6.279A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.946A 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: 3.730A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 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 348 through 353 removed outlier: 6.279A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.945A 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: 3.730A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 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 348 through 353 removed outlier: 6.279A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.946A 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: 3.730A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 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 348 through 353 removed outlier: 6.279A pdb=" N THR E 351 " --> pdb=" O SER E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.274A 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: 4.274A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR 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: 6.380A pdb=" N THR 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: 4.418A 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: 6.589A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL 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: 6.588A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.380A pdb=" N THR 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: 4.499A 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: 6.588A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.589A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.303A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.379A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 733 hydrogen bonds defined for protein. 1863 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.47 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: 4643 1.34 - 1.46: 2873 1.46 - 1.57: 6929 1.57 - 1.69: 15 1.69 - 1.81: 170 Bond restraints: 14630 Sorted by residual: bond pdb=" CG HIC C 73 " pdb=" ND1 HIC C 73 " ideal model delta sigma weight residual 1.370 1.312 0.058 2.00e-02 2.50e+03 8.30e+00 bond pdb=" CG HIC E 73 " pdb=" ND1 HIC E 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" CG HIC B 73 " pdb=" ND1 HIC B 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.14e+00 bond pdb=" CG HIC D 73 " pdb=" ND1 HIC D 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CG HIC A 73 " pdb=" ND1 HIC A 73 " ideal model delta sigma weight residual 1.370 1.313 0.057 2.00e-02 2.50e+03 8.05e+00 ... (remaining 14625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 19444 1.42 - 2.85: 235 2.85 - 4.27: 141 4.27 - 5.69: 20 5.69 - 7.11: 30 Bond angle restraints: 19870 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.47 109.91 3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.47 109.98 3.49 1.01e+00 9.80e-01 1.20e+01 ... (remaining 19865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.25: 8640 32.25 - 64.50: 110 64.50 - 96.76: 10 96.76 - 129.01: 0 129.01 - 161.26: 5 Dihedral angle restraints: 8765 sinusoidal: 3515 harmonic: 5250 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.74 161.26 1 2.00e+01 2.50e-03 4.67e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 138.77 161.22 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 8762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1261 0.031 - 0.062: 626 0.062 - 0.093: 189 0.093 - 0.124: 134 0.124 - 0.155: 5 Chirality restraints: 2215 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2212 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO B 243 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " -0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO C 243 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 243 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.017 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 112 2.42 - 3.04: 8768 3.04 - 3.66: 23764 3.66 - 4.28: 39834 4.28 - 4.90: 61663 Nonbonded interactions: 134141 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 507 " model vdw 1.798 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 512 " model vdw 1.819 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 541 " model vdw 1.824 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 525 " model vdw 1.827 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 530 " model vdw 1.836 2.170 ... (remaining 134136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '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: 3.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.280 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14630 Z= 0.188 Angle : 0.583 7.113 19870 Z= 0.280 Chirality : 0.044 0.155 2215 Planarity : 0.004 0.030 2525 Dihedral : 12.070 161.259 5395 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.65 % Allowed : 2.61 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.19), residues: 1780 helix: -2.34 (0.14), residues: 755 sheet: -0.63 (0.26), residues: 325 loop : 0.86 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 116 TYR 0.009 0.001 TYR D 143 PHE 0.009 0.001 PHE D 262 TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS E 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (14630) covalent geometry : angle 0.58337 / 0.28 (19870) hydrogen bonds : bond 0.23727 / 15.77 ( 718) hydrogen bonds : angle 8.06822 / 5.74 ( 1863) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.384 Fit side-chains REVERT: B 121 GLN cc_start: 0.8236 (tt0) cc_final: 0.8015 (tm-30) REVERT: B 211 ASP cc_start: 0.8004 (t70) cc_final: 0.7764 (t70) REVERT: D 44 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6790 (mpt) REVERT: D 276 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7023 (mt-10) REVERT: E 44 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.6044 (mpt) outliers start: 10 outliers final: 0 residues processed: 249 average time/residue: 0.6423 time to fit residues: 173.1177 Evaluate side-chains 177 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain E residue 44 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN C 161 HIS A 12 ASN A 78 ASN A 161 HIS B 12 ASN B 161 HIS D 161 HIS D 225 GLN D 353 GLN E 121 GLN E 225 GLN E 354 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.087702 restraints weight = 15521.678| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.29 r_work: 0.2851 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14630 Z= 0.179 Angle : 0.644 7.962 19870 Z= 0.314 Chirality : 0.047 0.203 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.769 141.618 2026 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.27 % Allowed : 5.95 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.20), residues: 1780 helix: -0.15 (0.18), residues: 740 sheet: 0.16 (0.27), residues: 330 loop : 1.98 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 210 TYR 0.016 0.001 TYR A 143 PHE 0.011 0.001 PHE D 262 TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 (14630) covalent geometry : angle 0.64393 / 0.31 (19870) hydrogen bonds : bond 0.04062 / 2.71 ( 718) hydrogen bonds : angle 5.07682 / 3.64 ( 1863) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.460 Fit side-chains REVERT: C 44 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.6959 (mpt) REVERT: C 72 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: C 123 MET cc_start: 0.9048 (mmt) cc_final: 0.8835 (mmt) REVERT: C 246 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8079 (tt0) REVERT: C 314 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: A 72 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8307 (mp0) REVERT: A 276 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 326 LYS cc_start: 0.8502 (mptp) cc_final: 0.8206 (mmmt) REVERT: D 44 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.7167 (mpt) REVERT: D 125 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7828 (mt-10) REVERT: D 180 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8890 (tp) REVERT: E 44 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.6637 (mpt) REVERT: E 64 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8597 (pp) REVERT: E 328 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8671 (tttt) outliers start: 50 outliers final: 11 residues processed: 215 average time/residue: 0.5662 time to fit residues: 132.9056 Evaluate side-chains 191 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN E 161 HIS E 296 ASN E 354 GLN E 371 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.105707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.084623 restraints weight = 15728.536| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.32 r_work: 0.2800 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2660 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9082 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14630 Z= 0.191 Angle : 0.628 8.138 19870 Z= 0.304 Chirality : 0.047 0.198 2215 Planarity : 0.004 0.038 2525 Dihedral : 9.996 138.398 2026 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.53 % Allowed : 6.01 % Favored : 90.46 % 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: 1.46 (0.20), residues: 1780 helix: 0.60 (0.19), residues: 745 sheet: 0.40 (0.26), residues: 330 loop : 2.07 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 290 TYR 0.014 0.001 TYR A 143 PHE 0.012 0.001 PHE D 262 TRP 0.017 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (14630) covalent geometry : angle 0.62780 / 0.30 (19870) hydrogen bonds : bond 0.04872 / 3.26 ( 718) hydrogen bonds : angle 4.98680 / 3.57 ( 1863) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.599 Fit side-chains REVERT: C 57 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: C 72 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 246 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: C 314 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: A 72 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8266 (mp0) REVERT: A 95 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7689 (mtm180) REVERT: A 276 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8105 (mt-10) REVERT: A 326 LYS cc_start: 0.8581 (mptp) cc_final: 0.7995 (tttt) REVERT: B 57 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: B 95 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: B 125 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: B 314 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8537 (tt0) REVERT: D 44 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.6972 (mpt) REVERT: D 57 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (pt0) REVERT: D 125 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: D 180 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8921 (tp) REVERT: D 334 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7457 (pp20) REVERT: E 44 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.6485 (mpt) REVERT: E 64 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8606 (pp) REVERT: E 167 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: E 328 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8620 (tttt) outliers start: 54 outliers final: 17 residues processed: 199 average time/residue: 0.6170 time to fit residues: 134.1139 Evaluate side-chains 202 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 95 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 225 GLN B 12 ASN B 128 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN E 371 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.104903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.083902 restraints weight = 15683.635| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.32 r_work: 0.2789 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 14630 Z= 0.239 Angle : 0.663 8.672 19870 Z= 0.323 Chirality : 0.049 0.214 2215 Planarity : 0.004 0.037 2525 Dihedral : 10.207 139.927 2026 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.66 % Allowed : 5.95 % Favored : 90.39 % 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: 1.56 (0.20), residues: 1780 helix: 0.78 (0.19), residues: 745 sheet: 0.45 (0.26), residues: 330 loop : 2.00 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.014 0.001 TYR A 143 PHE 0.016 0.002 PHE D 262 TRP 0.019 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.24 (14630) covalent geometry : angle 0.66302 / 0.32 (19870) hydrogen bonds : bond 0.04832 / 3.23 ( 718) hydrogen bonds : angle 4.97761 / 3.56 ( 1863) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 0.576 Fit side-chains REVERT: C 57 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: C 72 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7636 (mp0) REVERT: C 95 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7941 (mtm-85) REVERT: C 123 MET cc_start: 0.9132 (mmt) cc_final: 0.8856 (mmt) REVERT: C 246 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 314 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: A 57 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: A 72 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8290 (mp0) REVERT: A 132 MET cc_start: 0.8704 (ttp) cc_final: 0.8456 (ptm) REVERT: A 276 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: A 326 LYS cc_start: 0.8614 (mptp) cc_final: 0.8121 (tttt) REVERT: B 57 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: B 95 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7844 (mtp180) REVERT: B 125 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: B 314 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8566 (tt0) REVERT: B 326 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7853 (pttm) REVERT: D 44 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.6998 (mpt) REVERT: D 51 ASP cc_start: 0.7879 (t0) cc_final: 0.7632 (p0) REVERT: D 57 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8128 (pt0) REVERT: D 125 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7854 (mt-10) REVERT: D 292 ASP cc_start: 0.8797 (m-30) cc_final: 0.8486 (m-30) REVERT: D 334 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: E 41 GLN cc_start: 0.6727 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: E 44 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.6414 (mpt) REVERT: E 64 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8644 (pp) REVERT: E 132 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8430 (ttp) REVERT: E 167 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: E 314 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.8334 (tt0) REVERT: E 328 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8673 (tttt) REVERT: E 355 MET cc_start: 0.8477 (mmt) cc_final: 0.8218 (mmm) outliers start: 56 outliers final: 18 residues processed: 201 average time/residue: 0.6027 time to fit residues: 132.1954 Evaluate side-chains 207 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 328 LYS Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 77 optimal weight: 0.0060 chunk 102 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.086596 restraints weight = 15686.899| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.32 r_work: 0.2836 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14630 Z= 0.117 Angle : 0.570 7.442 19870 Z= 0.271 Chirality : 0.044 0.191 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.659 135.815 2026 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.01 % Allowed : 7.19 % Favored : 89.80 % 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: 1.92 (0.20), residues: 1780 helix: 1.12 (0.20), residues: 740 sheet: 0.54 (0.26), residues: 330 loop : 2.19 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.013 0.001 TYR A 143 PHE 0.010 0.001 PHE D 262 TRP 0.013 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14630) covalent geometry : angle 0.56953 / 0.27 (19870) hydrogen bonds : bond 0.03493 / 2.33 ( 718) hydrogen bonds : angle 4.63917 / 3.34 ( 1863) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 179 time to evaluate : 0.398 Fit side-chains REVERT: C 57 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: C 72 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: C 246 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8096 (tt0) REVERT: C 314 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 72 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 132 MET cc_start: 0.8634 (ttp) cc_final: 0.8382 (ptm) REVERT: A 211 ASP cc_start: 0.8663 (t70) cc_final: 0.8313 (t70) REVERT: A 276 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: A 326 LYS cc_start: 0.8633 (mptp) cc_final: 0.8146 (tttt) REVERT: B 57 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7835 (mt-10) REVERT: B 125 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: B 171 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8635 (mp) REVERT: B 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: B 326 LYS cc_start: 0.8449 (mmtm) cc_final: 0.7896 (pttm) REVERT: D 44 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7160 (mpt) REVERT: D 51 ASP cc_start: 0.7850 (t0) cc_final: 0.7599 (p0) REVERT: D 57 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8104 (pt0) REVERT: E 41 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: E 44 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.6528 (mpt) REVERT: E 51 ASP cc_start: 0.8046 (t0) cc_final: 0.7794 (t70) REVERT: E 64 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8610 (pp) REVERT: E 167 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7974 (mp0) outliers start: 46 outliers final: 8 residues processed: 205 average time/residue: 0.5759 time to fit residues: 128.8885 Evaluate side-chains 192 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 161 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN E 92 ASN E 246 GLN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.106264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085257 restraints weight = 15598.504| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.32 r_work: 0.2813 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9071 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14630 Z= 0.163 Angle : 0.603 7.880 19870 Z= 0.289 Chirality : 0.046 0.194 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.858 137.385 2026 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 3.27 % Allowed : 7.25 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.20), residues: 1780 helix: 1.11 (0.19), residues: 745 sheet: 0.57 (0.26), residues: 330 loop : 2.15 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.012 0.001 TYR A 143 PHE 0.011 0.001 PHE D 262 TRP 0.016 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (14630) covalent geometry : angle 0.60293 / 0.29 (19870) hydrogen bonds : bond 0.04008 / 2.67 ( 718) hydrogen bonds : angle 4.72193 / 3.39 ( 1863) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 0.493 Fit side-chains REVERT: C 57 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: C 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 95 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7936 (mtm-85) REVERT: C 246 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: C 314 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: A 72 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8265 (mp0) REVERT: A 132 MET cc_start: 0.8663 (ttp) cc_final: 0.8408 (ptm) REVERT: A 276 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 326 LYS cc_start: 0.8621 (mptp) cc_final: 0.8122 (tttt) REVERT: B 125 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: B 314 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: B 326 LYS cc_start: 0.8453 (mmtm) cc_final: 0.7941 (pttm) REVERT: D 44 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7082 (mpt) REVERT: D 51 ASP cc_start: 0.7861 (t0) cc_final: 0.7622 (p0) REVERT: D 57 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: D 334 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: E 41 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.6465 (pm20) REVERT: E 44 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.6473 (mpt) REVERT: E 51 ASP cc_start: 0.8076 (t0) cc_final: 0.7834 (t70) REVERT: E 64 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8608 (pp) REVERT: E 167 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7959 (mp0) outliers start: 50 outliers final: 17 residues processed: 203 average time/residue: 0.5652 time to fit residues: 125.4656 Evaluate side-chains 203 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 77 optimal weight: 0.0070 chunk 146 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087966 restraints weight = 15532.165| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.32 r_work: 0.2861 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9034 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14630 Z= 0.101 Angle : 0.547 7.025 19870 Z= 0.259 Chirality : 0.043 0.178 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.465 133.435 2026 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.48 % Allowed : 8.30 % Favored : 89.22 % 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: 2.13 (0.20), residues: 1780 helix: 1.31 (0.20), residues: 740 sheet: 0.62 (0.26), residues: 330 loop : 2.31 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.012 0.001 TYR A 143 PHE 0.008 0.001 PHE D 262 TRP 0.011 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (14630) covalent geometry : angle 0.54739 / 0.26 (19870) hydrogen bonds : bond 0.03091 / 2.06 ( 718) hydrogen bonds : angle 4.48987 / 3.24 ( 1863) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 0.428 Fit side-chains REVERT: C 57 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: C 72 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7648 (mp0) REVERT: C 246 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: C 314 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: A 72 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8247 (mp0) REVERT: A 132 MET cc_start: 0.8631 (ttp) cc_final: 0.8363 (ptm) REVERT: A 211 ASP cc_start: 0.8628 (t70) cc_final: 0.8296 (t70) REVERT: A 276 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: A 326 LYS cc_start: 0.8593 (mptp) cc_final: 0.8139 (tttm) REVERT: B 125 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: B 314 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: B 326 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7967 (pttm) REVERT: D 44 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7201 (mpt) REVERT: D 51 ASP cc_start: 0.7845 (t0) cc_final: 0.7587 (p0) REVERT: E 41 GLN cc_start: 0.6788 (OUTLIER) cc_final: 0.6560 (pm20) REVERT: E 44 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.6535 (mpt) REVERT: E 51 ASP cc_start: 0.8046 (t0) cc_final: 0.7818 (t70) REVERT: E 64 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8562 (pp) REVERT: E 167 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7950 (mp0) outliers start: 38 outliers final: 8 residues processed: 201 average time/residue: 0.6003 time to fit residues: 132.0494 Evaluate side-chains 193 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 151 optimal weight: 0.4980 chunk 127 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN D 128 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086374 restraints weight = 15686.646| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.32 r_work: 0.2836 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14630 Z= 0.132 Angle : 0.573 7.424 19870 Z= 0.273 Chirality : 0.045 0.182 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.603 132.831 2026 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.55 % Allowed : 8.37 % Favored : 89.08 % 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: 2.16 (0.20), residues: 1780 helix: 1.33 (0.20), residues: 740 sheet: 0.64 (0.26), residues: 330 loop : 2.32 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.011 0.001 TYR A 143 PHE 0.009 0.001 PHE D 262 TRP 0.013 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (14630) covalent geometry : angle 0.57322 / 0.27 (19870) hydrogen bonds : bond 0.03552 / 2.36 ( 718) hydrogen bonds : angle 4.56152 / 3.28 ( 1863) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 173 time to evaluate : 0.410 Fit side-chains REVERT: C 57 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7710 (pt0) REVERT: C 72 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: C 95 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7928 (mtm-85) REVERT: C 246 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 314 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 72 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8273 (mp0) REVERT: A 132 MET cc_start: 0.8636 (ttp) cc_final: 0.8389 (ptm) REVERT: A 211 ASP cc_start: 0.8673 (t70) cc_final: 0.8337 (t70) REVERT: A 276 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 326 LYS cc_start: 0.8624 (mptp) cc_final: 0.8143 (tttm) REVERT: B 125 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 314 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: B 326 LYS cc_start: 0.8459 (mmtm) cc_final: 0.7987 (pttm) REVERT: D 44 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7166 (mpt) REVERT: D 51 ASP cc_start: 0.7859 (t0) cc_final: 0.7581 (p0) REVERT: D 180 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8806 (tp) REVERT: E 41 GLN cc_start: 0.6762 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: E 44 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6479 (mpt) REVERT: E 64 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8586 (pp) REVERT: E 167 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: E 355 MET cc_start: 0.8496 (mmt) cc_final: 0.8221 (mmm) outliers start: 39 outliers final: 13 residues processed: 191 average time/residue: 0.5591 time to fit residues: 116.9319 Evaluate side-chains 196 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 169 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 GLN B 12 ASN D 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.083445 restraints weight = 15693.295| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.32 r_work: 0.2782 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 14630 Z= 0.296 Angle : 0.694 8.749 19870 Z= 0.340 Chirality : 0.052 0.203 2215 Planarity : 0.005 0.045 2525 Dihedral : 10.337 141.449 2026 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 2.42 % Allowed : 8.37 % Favored : 89.22 % 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: 1.84 (0.20), residues: 1780 helix: 1.02 (0.19), residues: 745 sheet: 0.62 (0.26), residues: 330 loop : 2.11 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 290 TYR 0.010 0.001 TYR B 166 PHE 0.017 0.002 PHE D 262 TRP 0.022 0.003 TRP C 340 HIS 0.006 0.002 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.30 (14630) covalent geometry : angle 0.69352 / 0.34 (19870) hydrogen bonds : bond 0.05074 / 3.39 ( 718) hydrogen bonds : angle 4.93125 / 3.52 ( 1863) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 0.510 Fit side-chains REVERT: C 57 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: C 72 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: C 95 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7883 (mtm-85) REVERT: C 246 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: C 314 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: A 72 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8305 (mp0) REVERT: A 132 MET cc_start: 0.8713 (ttp) cc_final: 0.8441 (ptm) REVERT: A 276 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8111 (mt-10) REVERT: A 326 LYS cc_start: 0.8617 (mptp) cc_final: 0.8134 (tttm) REVERT: A 360 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: B 125 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: B 314 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: B 326 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7981 (pttm) REVERT: D 44 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.6944 (mpt) REVERT: D 180 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8851 (tp) REVERT: E 41 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6353 (pm20) REVERT: E 44 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.6374 (mpt) REVERT: E 64 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8663 (pp) REVERT: E 167 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: E 355 MET cc_start: 0.8509 (mmt) cc_final: 0.8251 (mmm) outliers start: 37 outliers final: 15 residues processed: 191 average time/residue: 0.5878 time to fit residues: 122.5238 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 360 GLN Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 130 optimal weight: 0.0470 chunk 77 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.8680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087015 restraints weight = 15586.625| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.32 r_work: 0.2846 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14630 Z= 0.113 Angle : 0.570 7.367 19870 Z= 0.272 Chirality : 0.044 0.187 2215 Planarity : 0.003 0.035 2525 Dihedral : 9.596 135.657 2026 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 2.03 % Allowed : 9.02 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.20), residues: 1780 helix: 1.26 (0.20), residues: 740 sheet: 0.62 (0.26), residues: 330 loop : 2.26 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.011 0.001 TYR A 143 PHE 0.009 0.001 PHE D 262 TRP 0.013 0.002 TRP B 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14630) covalent geometry : angle 0.56988 / 0.27 (19870) hydrogen bonds : bond 0.03318 / 2.21 ( 718) hydrogen bonds : angle 4.56409 / 3.29 ( 1863) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.581 Fit side-chains REVERT: C 57 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: C 72 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: C 246 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: C 314 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: A 72 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8282 (mp0) REVERT: A 132 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8371 (ptm) REVERT: A 211 ASP cc_start: 0.8665 (t70) cc_final: 0.8328 (t70) REVERT: A 276 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8143 (mt-10) REVERT: A 326 LYS cc_start: 0.8639 (mptp) cc_final: 0.8169 (tttt) REVERT: A 360 GLN cc_start: 0.8208 (pt0) cc_final: 0.7994 (tm-30) REVERT: B 125 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7069 (mp0) REVERT: B 314 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8548 (tt0) REVERT: B 326 LYS cc_start: 0.8450 (mmtm) cc_final: 0.7990 (pttm) REVERT: D 44 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7142 (mpt) REVERT: D 51 ASP cc_start: 0.7851 (t0) cc_final: 0.7541 (p0) REVERT: D 180 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8806 (tp) REVERT: D 314 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: E 41 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6456 (pm20) REVERT: E 44 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.6518 (mpt) REVERT: E 64 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8578 (pp) REVERT: E 167 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: E 355 MET cc_start: 0.8477 (mmt) cc_final: 0.8216 (mmm) outliers start: 31 outliers final: 10 residues processed: 192 average time/residue: 0.5865 time to fit residues: 123.1314 Evaluate side-chains 197 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain E residue 41 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 167 GLU Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 116 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 161 optimal weight: 0.5980 chunk 150 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 12 ASN D 92 ASN D 128 ASN E 92 ASN E 354 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.109240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.088598 restraints weight = 15647.163| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.32 r_work: 0.2873 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14630 Z= 0.099 Angle : 0.549 6.903 19870 Z= 0.260 Chirality : 0.043 0.171 2215 Planarity : 0.003 0.037 2525 Dihedral : 9.352 131.369 2026 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.16 % Allowed : 9.28 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.20), residues: 1780 helix: 1.41 (0.20), residues: 740 sheet: 0.67 (0.25), residues: 330 loop : 2.37 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 28 TYR 0.011 0.001 TYR A 143 PHE 0.007 0.001 PHE D 262 TRP 0.011 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (14630) covalent geometry : angle 0.54857 / 0.26 (19870) hydrogen bonds : bond 0.03014 / 2.01 ( 718) hydrogen bonds : angle 4.39980 / 3.18 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5113.58 seconds wall clock time: 87 minutes 50.60 seconds (5270.60 seconds total)