Starting phenix.real_space_refine on Sat Aug 23 22:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_16888.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_16888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_16888.map" model { file = "/net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_16888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oi8_16888/08_2025/8oi8_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-2.0-5787/lib/python3.9/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: 2.98, per 1000 atoms: 0.20 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: 1.22 Conformation dependent library (CDL) restraints added in 666.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 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: 2.79 Time building geometry restraints manager: 1.64 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: 0.03 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.650 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 aren 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 covalent geometry : bond 0.00426 (14630) covalent geometry : angle 0.58337 (19870) hydrogen bonds : bond 0.23727 ( 718) hydrogen bonds : angle 8.06822 ( 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 : 0.492 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: 0.6789 (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: 0.7795 time to fit residues: 209.8034 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 : 0.630 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 12 ASN E 121 GLN E 225 GLN E 354 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.108732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087925 restraints weight = 15533.045| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.29 r_work: 0.2855 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2463 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= 0.175 Angle : 0.645 7.895 19870 Z= 0.311 Chirality : 0.046 0.200 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.776 141.587 2026 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.46 % Allowed : 5.82 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.20), residues: 1780 helix: -0.23 (0.18), residues: 740 sheet: 0.14 (0.26), residues: 330 loop : 1.99 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 254 TYR 0.017 0.001 TYR A 143 PHE 0.012 0.002 PHE D 262 TRP 0.014 0.002 TRP C 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00403 (14630) covalent geometry : angle 0.64464 (19870) hydrogen bonds : bond 0.04234 ( 718) hydrogen bonds : angle 5.09487 ( 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 243 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 190 time to evaluate : 0.668 Fit side-chains REVERT: C 57 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: C 72 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: C 123 MET cc_start: 0.9050 (mmt) cc_final: 0.8838 (mmt) REVERT: C 246 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: C 314 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8407 (tt0) REVERT: A 72 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8302 (mp0) REVERT: A 276 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8127 (mt-10) REVERT: A 326 LYS cc_start: 0.8509 (mptp) cc_final: 0.8210 (mmmt) REVERT: D 44 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7177 (mpt) REVERT: D 125 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: D 180 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8899 (tp) REVERT: D 286 ASP cc_start: 0.8215 (m-30) cc_final: 0.7866 (m-30) REVERT: D 360 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7426 (tm130) REVERT: E 44 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.6609 (mpt) REVERT: E 64 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8598 (pp) REVERT: E 328 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8643 (tttt) outliers start: 53 outliers final: 14 residues processed: 216 average time/residue: 0.7438 time to fit residues: 174.8751 Evaluate side-chains 197 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 MET 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 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 B residue 351 THR 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 D residue 360 GLN Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU 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: 0.7980 chunk 162 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085655 restraints weight = 15770.126| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.33 r_work: 0.2821 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.2726 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= 0.154 Angle : 0.594 7.701 19870 Z= 0.285 Chirality : 0.045 0.189 2215 Planarity : 0.004 0.037 2525 Dihedral : 9.763 138.236 2026 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.20 % Allowed : 6.60 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.20), residues: 1780 helix: 0.64 (0.19), residues: 740 sheet: 0.43 (0.26), residues: 330 loop : 2.19 (0.26), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.014 0.001 TYR A 143 PHE 0.010 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 covalent geometry : bond 0.00353 (14630) covalent geometry : angle 0.59412 (19870) hydrogen bonds : bond 0.04396 ( 718) hydrogen bonds : angle 4.88820 ( 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 221 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.662 Fit side-chains REVERT: C 44 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.6745 (mpt) REVERT: C 72 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: C 123 MET cc_start: 0.9108 (mmt) cc_final: 0.8782 (mmt) REVERT: C 246 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: C 314 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8369 (tt0) REVERT: A 72 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8263 (mp0) REVERT: A 95 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7685 (mtm180) REVERT: A 132 MET cc_start: 0.8629 (ttp) cc_final: 0.8261 (ppp) REVERT: A 276 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: A 326 LYS cc_start: 0.8571 (mptp) cc_final: 0.7979 (tttt) REVERT: B 57 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7847 (mt-10) REVERT: B 125 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7258 (mp0) REVERT: B 227 MET cc_start: 0.8747 (mmm) cc_final: 0.8500 (mmm) REVERT: B 314 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8538 (tt0) REVERT: D 44 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7081 (mpt) REVERT: D 57 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: D 180 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8898 (tp) REVERT: D 286 ASP cc_start: 0.8247 (m-30) cc_final: 0.8032 (m-30) REVERT: D 334 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7449 (pp20) REVERT: E 44 MET cc_start: 0.8139 (OUTLIER) cc_final: 0.6603 (mpt) REVERT: E 64 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8582 (pp) REVERT: E 167 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7977 (mp0) REVERT: E 328 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8631 (tttt) outliers start: 49 outliers final: 12 residues processed: 199 average time/residue: 0.7377 time to fit residues: 159.8232 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.634 ------------------------------------------------------------------------------- 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 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 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 370 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 334 GLU 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 167 GLU 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: 2.9990 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 161 HIS E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.106221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.085150 restraints weight = 15732.165| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.32 r_work: 0.2811 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14630 Z= 0.170 Angle : 0.610 7.999 19870 Z= 0.293 Chirality : 0.046 0.196 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.883 138.546 2026 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 3.27 % Allowed : 6.67 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.20), residues: 1780 helix: 0.88 (0.19), residues: 745 sheet: 0.48 (0.26), residues: 330 loop : 2.14 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.014 0.001 TYR A 143 PHE 0.012 0.001 PHE D 262 TRP 0.015 0.002 TRP C 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00396 (14630) covalent geometry : angle 0.61034 (19870) hydrogen bonds : bond 0.04173 ( 718) hydrogen bonds : angle 4.81229 ( 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 225 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.596 Fit side-chains REVERT: C 57 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7707 (pt0) REVERT: C 72 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: C 123 MET cc_start: 0.9106 (mmt) cc_final: 0.8795 (mmt) REVERT: C 246 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8140 (tt0) REVERT: C 314 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8383 (tt0) REVERT: A 57 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: A 72 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8250 (mp0) REVERT: A 132 MET cc_start: 0.8653 (ttp) cc_final: 0.8423 (ptm) REVERT: A 276 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: A 326 LYS cc_start: 0.8617 (mptp) cc_final: 0.8080 (tttt) REVERT: B 95 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7815 (mtp180) REVERT: B 125 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: B 314 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: B 326 LYS cc_start: 0.8456 (mmtm) cc_final: 0.7857 (pttm) REVERT: D 44 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7052 (mpt) REVERT: D 57 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8115 (pt0) REVERT: D 180 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8916 (tp) REVERT: D 286 ASP cc_start: 0.8243 (m-30) cc_final: 0.8030 (m-30) REVERT: D 292 ASP cc_start: 0.8749 (m-30) cc_final: 0.8442 (m-30) REVERT: D 334 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7497 (pp20) REVERT: E 44 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6520 (mpt) REVERT: E 64 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8607 (pp) REVERT: E 167 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: E 328 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8652 (tttt) outliers start: 50 outliers final: 16 residues processed: 203 average time/residue: 0.7283 time to fit residues: 161.3045 Evaluate side-chains 201 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 351 THR Chi-restraints excluded: chain B residue 44 MET 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 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 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 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 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: 1.9990 chunk 34 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 92 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 = 0.3272 r_free = 0.3272 target = 0.106244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085169 restraints weight = 15717.708| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.33 r_work: 0.2811 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2978 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= 0.166 Angle : 0.604 7.942 19870 Z= 0.290 Chirality : 0.046 0.194 2215 Planarity : 0.004 0.036 2525 Dihedral : 9.867 138.603 2026 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 3.27 % Allowed : 7.12 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.20), residues: 1780 helix: 1.01 (0.19), residues: 745 sheet: 0.54 (0.26), residues: 330 loop : 2.14 (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 0.012 0.001 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.004 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00387 (14630) covalent geometry : angle 0.60449 (19870) hydrogen bonds : bond 0.04075 ( 718) hydrogen bonds : angle 4.75709 ( 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: 50 poor density : 175 time to evaluate : 0.663 Fit side-chains REVERT: C 57 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7682 (pt0) REVERT: C 72 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 95 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7919 (mtm-85) REVERT: C 246 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: C 314 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: A 57 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7662 (pt0) REVERT: A 72 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8249 (mp0) REVERT: A 132 MET cc_start: 0.8624 (ttp) cc_final: 0.8340 (ppp) REVERT: A 276 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 326 LYS cc_start: 0.8630 (mptp) cc_final: 0.8121 (tttt) REVERT: B 95 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7828 (mtp180) REVERT: B 125 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: B 314 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8526 (tt0) REVERT: B 326 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7857 (pttm) REVERT: D 44 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7107 (mpt) REVERT: D 51 ASP cc_start: 0.7843 (t0) cc_final: 0.7592 (p0) REVERT: D 57 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8123 (pt0) REVERT: D 180 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8901 (tp) REVERT: D 286 ASP cc_start: 0.8240 (m-30) cc_final: 0.8023 (m-30) REVERT: D 334 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7499 (pp20) REVERT: E 44 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.6480 (mpt) REVERT: E 51 ASP cc_start: 0.8071 (t0) cc_final: 0.7820 (t70) REVERT: E 64 ILE cc_start: 0.9210 (OUTLIER) cc_final: 0.8599 (pp) REVERT: E 167 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: E 314 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8345 (tt0) outliers start: 50 outliers final: 17 residues processed: 202 average time/residue: 0.6893 time to fit residues: 151.9948 Evaluate side-chains 210 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain B residue 44 MET 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 350 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 167 GLU Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 351 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 154 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 161 optimal weight: 0.2980 chunk 137 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 78 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3323 r_free = 0.3323 target = 0.109720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.089045 restraints weight = 15766.418| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.33 r_work: 0.2881 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14630 Z= 0.090 Angle : 0.538 6.842 19870 Z= 0.254 Chirality : 0.043 0.174 2215 Planarity : 0.003 0.035 2525 Dihedral : 9.359 133.931 2026 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.48 % Allowed : 8.17 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.20), residues: 1780 helix: 1.25 (0.20), residues: 740 sheet: 0.60 (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 C 210 TYR 0.012 0.001 TYR A 143 PHE 0.007 0.001 PHE D 262 TRP 0.010 0.001 TRP D 79 HIS 0.005 0.001 HIS A 40 Details of bonding type rmsd covalent geometry : bond 0.00191 (14630) covalent geometry : angle 0.53787 (19870) hydrogen bonds : bond 0.02879 ( 718) hydrogen bonds : angle 4.44769 ( 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 220 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.432 Fit side-chains REVERT: C 57 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7657 (pt0) REVERT: C 72 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: C 171 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8471 (mp) REVERT: C 314 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8399 (tt0) REVERT: A 72 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8224 (mp0) REVERT: A 132 MET cc_start: 0.8594 (ttp) cc_final: 0.8188 (ppp) REVERT: A 276 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: A 326 LYS cc_start: 0.8636 (mptp) cc_final: 0.8155 (tttt) REVERT: B 95 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7853 (mtp180) REVERT: B 125 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 314 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8505 (tt0) REVERT: B 326 LYS cc_start: 0.8431 (mmtm) cc_final: 0.7919 (pttm) REVERT: D 44 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7289 (mpt) REVERT: D 51 ASP cc_start: 0.7825 (t0) cc_final: 0.7524 (p0) REVERT: D 286 ASP cc_start: 0.8202 (m-30) cc_final: 0.7964 (m-30) REVERT: E 44 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.6642 (mpt) REVERT: E 51 ASP cc_start: 0.8045 (t0) cc_final: 0.7809 (t70) REVERT: E 64 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8540 (pp) REVERT: E 167 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7943 (mp0) outliers start: 38 outliers final: 8 residues processed: 204 average time/residue: 0.6449 time to fit residues: 143.4062 Evaluate side-chains 195 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 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 95 ARG 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 171 LEU Chi-restraints excluded: chain D residue 235 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 175 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 136 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 77 optimal weight: 0.0770 chunk 146 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 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 = 0.3282 r_free = 0.3282 target = 0.106950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085954 restraints weight = 15557.989| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.32 r_work: 0.2827 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3061 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= 0.149 Angle : 0.587 7.641 19870 Z= 0.280 Chirality : 0.045 0.187 2215 Planarity : 0.004 0.035 2525 Dihedral : 9.696 134.118 2026 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.48 % Allowed : 8.17 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.20), residues: 1780 helix: 1.26 (0.20), residues: 740 sheet: 0.64 (0.26), residues: 330 loop : 2.34 (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 0.014 0.002 TRP D 340 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00343 (14630) covalent geometry : angle 0.58719 (19870) hydrogen bonds : bond 0.03808 ( 718) hydrogen bonds : angle 4.62487 ( 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 214 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.640 Fit side-chains REVERT: C 57 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7695 (pt0) REVERT: C 72 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: C 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7930 (mtm-85) REVERT: C 314 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 72 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8254 (mp0) REVERT: A 132 MET cc_start: 0.8623 (ttp) cc_final: 0.8383 (ptm) REVERT: A 276 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 326 LYS cc_start: 0.8622 (mptp) cc_final: 0.8145 (tttt) REVERT: B 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7847 (mtp180) REVERT: B 125 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: B 314 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8535 (tt0) REVERT: B 326 LYS cc_start: 0.8463 (mmtm) cc_final: 0.7991 (pttm) REVERT: D 44 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7160 (mpt) REVERT: D 51 ASP cc_start: 0.7836 (t0) cc_final: 0.7550 (p0) REVERT: D 180 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8793 (tp) REVERT: D 286 ASP cc_start: 0.8247 (m-30) cc_final: 0.8006 (m-30) REVERT: E 44 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.6544 (mpt) REVERT: E 51 ASP cc_start: 0.8073 (t0) cc_final: 0.7814 (t70) REVERT: E 57 GLU cc_start: 0.8327 (tp30) cc_final: 0.8100 (pt0) REVERT: E 64 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8596 (pp) REVERT: E 167 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.7968 (mp0) outliers start: 38 outliers final: 13 residues processed: 198 average time/residue: 0.6305 time to fit residues: 136.7181 Evaluate side-chains 200 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 314 GLN 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 95 ARG 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 350 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 111 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 92 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 = 0.3313 r_free = 0.3313 target = 0.108994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.088218 restraints weight = 15766.445| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.33 r_work: 0.2865 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14630 Z= 0.101 Angle : 0.545 6.940 19870 Z= 0.258 Chirality : 0.043 0.174 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.387 132.406 2026 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.22 % Allowed : 8.76 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.22 (0.20), residues: 1780 helix: 1.34 (0.20), residues: 740 sheet: 0.65 (0.26), residues: 330 loop : 2.40 (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 0.007 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 covalent geometry : bond 0.00225 (14630) covalent geometry : angle 0.54538 (19870) hydrogen bonds : bond 0.03060 ( 718) hydrogen bonds : angle 4.44275 ( 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 209 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.588 Fit side-chains REVERT: C 57 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7661 (pt0) REVERT: C 72 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: C 171 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 314 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: A 64 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.8799 (pp) REVERT: A 72 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8219 (mp0) REVERT: A 132 MET cc_start: 0.8604 (ttp) cc_final: 0.8355 (ptm) REVERT: A 276 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 326 LYS cc_start: 0.8609 (mptp) cc_final: 0.8158 (tttm) REVERT: B 57 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7839 (pt0) REVERT: B 95 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7842 (mtp180) REVERT: B 125 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: B 314 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: B 326 LYS cc_start: 0.8454 (mmtm) cc_final: 0.8003 (pttm) REVERT: D 44 MET cc_start: 0.8294 (OUTLIER) cc_final: 0.7269 (mpt) REVERT: D 51 ASP cc_start: 0.7796 (t0) cc_final: 0.7507 (p0) REVERT: D 180 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8795 (tp) REVERT: E 44 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.6627 (mpt) REVERT: E 51 ASP cc_start: 0.8023 (t0) cc_final: 0.7779 (t70) REVERT: E 64 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8554 (pp) REVERT: E 167 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: E 355 MET cc_start: 0.8427 (mmt) cc_final: 0.8131 (mmm) outliers start: 34 outliers final: 9 residues processed: 195 average time/residue: 0.7036 time to fit residues: 149.7344 Evaluate side-chains 195 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 64 ILE 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 95 ARG 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN E 92 ASN E 296 ASN E 354 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.085027 restraints weight = 15725.740| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.32 r_work: 0.2809 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14630 Z= 0.194 Angle : 0.623 8.151 19870 Z= 0.300 Chirality : 0.047 0.193 2215 Planarity : 0.004 0.034 2525 Dihedral : 9.928 137.485 2026 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.35 % Allowed : 8.63 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.20), residues: 1780 helix: 1.18 (0.20), residues: 745 sheet: 0.65 (0.26), residues: 330 loop : 2.25 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.009 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 covalent geometry : bond 0.00455 (14630) covalent geometry : angle 0.62278 (19870) hydrogen bonds : bond 0.04240 ( 718) hydrogen bonds : angle 4.71575 ( 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: 36 poor density : 173 time to evaluate : 0.636 Fit side-chains REVERT: C 57 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7715 (pt0) REVERT: C 72 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: C 95 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7921 (mtm-85) REVERT: C 314 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: A 64 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 72 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8268 (mp0) REVERT: A 125 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: A 132 MET cc_start: 0.8649 (ttp) cc_final: 0.8420 (ptm) REVERT: A 276 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: A 326 LYS cc_start: 0.8617 (mptp) cc_final: 0.8125 (tttm) REVERT: B 95 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7882 (mtp180) REVERT: B 125 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7139 (mp0) REVERT: B 314 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8552 (tt0) REVERT: B 326 LYS cc_start: 0.8478 (mmtm) cc_final: 0.8006 (pttm) REVERT: D 44 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7067 (mpt) REVERT: D 180 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8810 (tp) REVERT: D 286 ASP cc_start: 0.8248 (m-30) cc_final: 0.8020 (m-30) REVERT: D 334 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7549 (pp20) REVERT: E 44 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6418 (mpt) REVERT: E 64 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8626 (pp) REVERT: E 167 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7966 (mp0) REVERT: E 355 MET cc_start: 0.8482 (mmt) cc_final: 0.8205 (mmm) outliers start: 36 outliers final: 12 residues processed: 194 average time/residue: 0.7063 time to fit residues: 149.5764 Evaluate side-chains 199 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 125 GLU 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 95 ARG 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU 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 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 144 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 152 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 130 optimal weight: 0.0980 chunk 77 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 225 GLN B 12 ASN B 128 ASN D 92 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 = 0.3278 r_free = 0.3278 target = 0.106721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085707 restraints weight = 15582.877| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.32 r_work: 0.2822 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14630 Z= 0.158 Angle : 0.599 7.786 19870 Z= 0.287 Chirality : 0.046 0.191 2215 Planarity : 0.004 0.035 2525 Dihedral : 9.793 137.136 2026 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.03 % Allowed : 9.08 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.20), residues: 1780 helix: 1.18 (0.20), residues: 745 sheet: 0.63 (0.26), residues: 330 loop : 2.23 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 290 TYR 0.010 0.001 TYR A 143 PHE 0.011 0.001 PHE D 262 TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00367 (14630) covalent geometry : angle 0.59875 (19870) hydrogen bonds : bond 0.03865 ( 718) hydrogen bonds : angle 4.64818 ( 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 204 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 0.624 Fit side-chains REVERT: C 57 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: C 72 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: C 95 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7948 (mtm-85) REVERT: C 314 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: A 64 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.8801 (pp) REVERT: A 72 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8257 (mp0) REVERT: A 125 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: A 132 MET cc_start: 0.8624 (ttp) cc_final: 0.8387 (ptm) REVERT: A 276 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: A 326 LYS cc_start: 0.8625 (mptp) cc_final: 0.8158 (tttt) REVERT: B 95 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7847 (mtp180) REVERT: B 125 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: B 314 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: B 326 LYS cc_start: 0.8483 (mmtm) cc_final: 0.8004 (pttm) REVERT: D 44 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7103 (mpt) REVERT: D 180 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8810 (tp) REVERT: D 286 ASP cc_start: 0.8240 (m-30) cc_final: 0.8017 (m-30) REVERT: D 334 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7555 (pp20) REVERT: E 44 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6436 (mpt) REVERT: E 64 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8605 (pp) REVERT: E 167 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: E 355 MET cc_start: 0.8471 (mmt) cc_final: 0.8200 (mmm) outliers start: 31 outliers final: 11 residues processed: 191 average time/residue: 0.7280 time to fit residues: 151.6290 Evaluate side-chains 198 residues out of total 1530 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 171 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 314 GLN Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 125 GLU 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 95 ARG 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 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 334 GLU 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: 7.9990 chunk 132 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.0370 chunk 98 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN A 12 ASN A 225 GLN B 12 ASN D 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 = 0.3308 r_free = 0.3308 target = 0.108707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.087987 restraints weight = 15687.793| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.32 r_work: 0.2863 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14630 Z= 0.101 Angle : 0.555 6.991 19870 Z= 0.262 Chirality : 0.043 0.175 2215 Planarity : 0.003 0.036 2525 Dihedral : 9.422 132.985 2026 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.09 % Allowed : 8.95 % 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 aren not related in a simple way. whole: 2.19 (0.20), residues: 1780 helix: 1.35 (0.20), residues: 740 sheet: 0.64 (0.25), residues: 330 loop : 2.35 (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 C 143 PHE 0.007 0.001 PHE D 262 TRP 0.011 0.002 TRP D 79 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00224 (14630) covalent geometry : angle 0.55475 (19870) hydrogen bonds : bond 0.03072 ( 718) hydrogen bonds : angle 4.44273 ( 1863) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6191.07 seconds wall clock time: 106 minutes 25.16 seconds (6385.16 seconds total)