Starting phenix.real_space_refine on Tue Nov 18 15:10:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.map" model { file = "/net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ooc_3836/11_2025/5ooc_3836.cif" } resolution = 3.6 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= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14885 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 126 Unusual residues: {' MG': 1, '9ZK': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {' MG': 1, '9ZK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.09, per 1000 atoms: 0.21 Number of scatterers: 14885 At special positions: 0 Unit cell: (100.32, 85.5, 190.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 2845 8.00 N 2495 7.00 C 9425 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: 1.29 Conformation dependent library (CDL) restraints added in 688.8 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 25 sheets defined 52.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.135A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 171 through 175 Processing helix chain 'A' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) 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 349 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.134A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 171 through 175 Processing helix chain 'B' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) 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 349 Processing helix chain 'B' and resid 350 through 356 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.134A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 171 through 175 Processing helix chain 'C' and resid 181 through 194 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 230 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 295 removed outlier: 4.484A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) 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 349 Processing helix chain 'C' and resid 350 through 356 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.134A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) 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 349 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.134A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 181 through 194 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 230 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 295 removed outlier: 4.485A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) 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 349 Processing helix chain 'E' and resid 350 through 356 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.780A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.781A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.782A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 765 hydrogen bonds defined for protein. 1920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 2455 1.28 - 1.41: 3835 1.41 - 1.54: 8721 1.54 - 1.68: 24 1.68 - 1.81: 185 Bond restraints: 15220 Sorted by residual: bond pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sigma weight residual 1.610 1.508 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 15215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18866 2.58 - 5.15: 1451 5.15 - 7.73: 253 7.73 - 10.30: 45 10.30 - 12.88: 45 Bond angle restraints: 20660 Sorted by residual: angle pdb=" C PHE A 31 " pdb=" N PRO A 32 " pdb=" CA PRO A 32 " ideal model delta sigma weight residual 119.76 127.17 -7.41 1.00e+00 1.00e+00 5.49e+01 angle pdb=" C PHE E 31 " pdb=" N PRO E 32 " pdb=" CA PRO E 32 " ideal model delta sigma weight residual 119.76 127.15 -7.39 1.00e+00 1.00e+00 5.47e+01 angle pdb=" C PHE C 31 " pdb=" N PRO C 32 " pdb=" CA PRO C 32 " ideal model delta sigma weight residual 119.76 127.14 -7.38 1.00e+00 1.00e+00 5.45e+01 angle pdb=" C PHE B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta sigma weight residual 119.76 127.14 -7.38 1.00e+00 1.00e+00 5.45e+01 angle pdb=" C PHE D 31 " pdb=" N PRO D 32 " pdb=" CA PRO D 32 " ideal model delta sigma weight residual 119.76 127.13 -7.37 1.00e+00 1.00e+00 5.44e+01 ... (remaining 20655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.85: 8870 29.85 - 59.69: 190 59.69 - 89.54: 81 89.54 - 119.38: 69 119.38 - 149.23: 30 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: 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 -60.00 89.22 -149.23 1 2.00e+01 2.50e-03 4.46e+01 dihedral pdb=" O1B ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PB ADP E 401 " pdb=" PA ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+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 -60.00 89.20 -149.20 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 1808 0.087 - 0.174: 441 0.174 - 0.261: 26 0.261 - 0.348: 0 0.348 - 0.435: 5 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK A 402 " pdb=" C26 9ZK A 402 " pdb=" C36 9ZK A 402 " pdb=" N23 9ZK A 402 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C25 9ZK A 404 " pdb=" C26 9ZK A 404 " pdb=" C36 9ZK A 404 " pdb=" N23 9ZK A 404 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C25 9ZK B 403 " pdb=" C26 9ZK B 403 " pdb=" C36 9ZK B 403 " pdb=" N23 9ZK B 403 " both_signs ideal model delta sigma weight residual False 2.15 2.58 -0.43 2.00e-01 2.50e+01 4.71e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO A 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 163 " -0.097 5.00e-02 4.00e+02 1.47e-01 3.45e+01 pdb=" N PRO B 164 " 0.254 5.00e-02 4.00e+02 pdb=" CA PRO B 164 " -0.082 5.00e-02 4.00e+02 pdb=" CD PRO B 164 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " 0.097 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C 164 " -0.254 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " 0.082 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " 0.075 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 170 2.62 - 3.19: 14784 3.19 - 3.76: 23000 3.76 - 4.33: 34499 4.33 - 4.90: 53380 Nonbonded interactions: 125833 Sorted by model distance: nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP E 401 " pdb="MG MG E 402 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 403 " model vdw 2.050 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.051 2.170 nonbonded pdb=" O2B ADP D 401 " pdb="MG MG D 402 " model vdw 2.051 2.170 ... (remaining 125828 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 401) selection = (chain 'B' and resid 5 through 401) selection = (chain 'C' and resid 5 through 401) selection = (chain 'D' and resid 5 through 401) selection = (chain 'E' and resid 5 through 401) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.700 Find NCS groups from input model: 0.430 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.016 0.102 15220 Z= 0.957 Angle : 1.665 12.880 20660 Z= 1.009 Chirality : 0.072 0.435 2280 Planarity : 0.018 0.147 2630 Dihedral : 21.045 149.226 5810 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 2.73 % Allowed : 4.37 % Favored : 92.90 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.20), residues: 1830 helix: -1.31 (0.16), residues: 715 sheet: -0.73 (0.26), residues: 310 loop : -0.45 (0.26), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 39 TYR 0.021 0.004 TYR B 198 PHE 0.010 0.003 PHE C 90 TRP 0.021 0.004 TRP C 340 HIS 0.007 0.002 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.01576 (15220) covalent geometry : angle 1.66519 (20660) hydrogen bonds : bond 0.17395 ( 765) hydrogen bonds : angle 7.35694 ( 1920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7640 (mtm) cc_final: 0.7219 (mpp) REVERT: A 103 THR cc_start: 0.9206 (m) cc_final: 0.8898 (p) REVERT: A 154 ASP cc_start: 0.8393 (t70) cc_final: 0.8127 (t70) REVERT: A 269 MET cc_start: 0.7298 (tpp) cc_final: 0.7007 (tpt) REVERT: A 283 MET cc_start: 0.9125 (mmp) cc_final: 0.8735 (mmt) REVERT: A 286 ASP cc_start: 0.7035 (t70) cc_final: 0.6782 (m-30) REVERT: A 355 MET cc_start: 0.7554 (mmm) cc_final: 0.7147 (mmm) REVERT: B 80 ASP cc_start: 0.8525 (m-30) cc_final: 0.8295 (t0) REVERT: B 154 ASP cc_start: 0.7274 (t70) cc_final: 0.6704 (t0) REVERT: C 47 MET cc_start: 0.5942 (mmt) cc_final: 0.5665 (mmt) REVERT: C 78 ASN cc_start: 0.8532 (t0) cc_final: 0.8238 (t0) REVERT: C 82 MET cc_start: 0.9167 (tpt) cc_final: 0.8963 (tpt) REVERT: C 178 LEU cc_start: 0.8698 (mt) cc_final: 0.8479 (mp) REVERT: C 191 LYS cc_start: 0.8573 (mttt) cc_final: 0.8257 (ttmm) REVERT: C 224 GLU cc_start: 0.8133 (tp30) cc_final: 0.7932 (tm-30) REVERT: C 238 LYS cc_start: 0.8849 (tptt) cc_final: 0.8527 (ttmt) REVERT: C 296 ASN cc_start: 0.8426 (m-40) cc_final: 0.8199 (m-40) REVERT: C 336 LYS cc_start: 0.8136 (mttt) cc_final: 0.7368 (ttmt) REVERT: D 44 MET cc_start: 0.7083 (mtm) cc_final: 0.6057 (ttt) REVERT: D 128 ASN cc_start: 0.7985 (m-40) cc_final: 0.7209 (t0) REVERT: D 201 VAL cc_start: 0.9460 (m) cc_final: 0.9046 (p) REVERT: D 211 ASP cc_start: 0.8788 (t70) cc_final: 0.8299 (t0) REVERT: D 222 ASP cc_start: 0.7416 (t0) cc_final: 0.7194 (p0) REVERT: D 249 THR cc_start: 0.9206 (m) cc_final: 0.9005 (p) REVERT: D 296 ASN cc_start: 0.8373 (m-40) cc_final: 0.7826 (m-40) REVERT: E 120 THR cc_start: 0.8371 (m) cc_final: 0.8151 (p) REVERT: E 227 MET cc_start: 0.8305 (mmm) cc_final: 0.8011 (mmm) REVERT: E 244 ASP cc_start: 0.8851 (p0) cc_final: 0.8577 (p0) REVERT: E 249 THR cc_start: 0.8795 (m) cc_final: 0.8563 (p) REVERT: E 353 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8189 (mm-40) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.1436 time to fit residues: 100.6601 Evaluate side-chains 243 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.122041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107931 restraints weight = 23225.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110979 restraints weight = 11949.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113004 restraints weight = 7426.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114324 restraints weight = 5246.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.115259 restraints weight = 4064.782| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15220 Z= 0.152 Angle : 0.759 9.347 20660 Z= 0.376 Chirality : 0.047 0.182 2280 Planarity : 0.008 0.062 2630 Dihedral : 28.859 169.955 2330 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 1.09 % Allowed : 1.69 % Favored : 97.21 % Rotamer: Outliers : 1.53 % Allowed : 8.24 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1830 helix: 1.07 (0.19), residues: 695 sheet: -0.76 (0.26), residues: 290 loop : -0.08 (0.23), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 147 TYR 0.022 0.001 TYR A 166 PHE 0.009 0.001 PHE D 223 TRP 0.016 0.001 TRP A 340 HIS 0.006 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00335 (15220) covalent geometry : angle 0.75853 (20660) hydrogen bonds : bond 0.04238 ( 765) hydrogen bonds : angle 5.01004 ( 1920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 341 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 THR cc_start: 0.8872 (m) cc_final: 0.8476 (p) REVERT: A 123 MET cc_start: 0.8986 (mmm) cc_final: 0.8706 (mmt) REVERT: A 154 ASP cc_start: 0.8266 (t70) cc_final: 0.7818 (t70) REVERT: A 269 MET cc_start: 0.7202 (tpp) cc_final: 0.6704 (tpt) REVERT: A 283 MET cc_start: 0.8823 (mmp) cc_final: 0.8600 (mmp) REVERT: B 78 ASN cc_start: 0.8030 (t0) cc_final: 0.7180 (t0) REVERT: B 269 MET cc_start: 0.7129 (mmm) cc_final: 0.6597 (tpp) REVERT: B 360 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7885 (tm-30) REVERT: C 34 ILE cc_start: 0.9362 (mt) cc_final: 0.9145 (pt) REVERT: C 78 ASN cc_start: 0.8142 (t0) cc_final: 0.7868 (t0) REVERT: C 117 GLU cc_start: 0.7396 (tt0) cc_final: 0.7178 (tt0) REVERT: C 178 LEU cc_start: 0.8609 (mt) cc_final: 0.8394 (mp) REVERT: C 336 LYS cc_start: 0.7960 (mttt) cc_final: 0.7701 (mttt) REVERT: D 161 HIS cc_start: 0.8738 (p90) cc_final: 0.8353 (p-80) REVERT: D 212 ILE cc_start: 0.8938 (mt) cc_final: 0.8656 (mt) REVERT: D 336 LYS cc_start: 0.8337 (mttt) cc_final: 0.7813 (ttmt) REVERT: E 57 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7560 (mm-30) REVERT: E 162 ASN cc_start: 0.8158 (m-40) cc_final: 0.7940 (m-40) REVERT: E 184 ASP cc_start: 0.7903 (m-30) cc_final: 0.7675 (m-30) REVERT: E 192 ILE cc_start: 0.9255 (mm) cc_final: 0.8883 (tp) REVERT: E 206 ARG cc_start: 0.7838 (ttm-80) cc_final: 0.7632 (ttm-80) REVERT: E 246 GLN cc_start: 0.8824 (mt0) cc_final: 0.8490 (mt0) REVERT: E 249 THR cc_start: 0.8706 (m) cc_final: 0.8473 (p) REVERT: E 292 ASP cc_start: 0.7776 (m-30) cc_final: 0.7486 (m-30) REVERT: E 313 MET cc_start: 0.8419 (tpp) cc_final: 0.8208 (ttm) outliers start: 24 outliers final: 16 residues processed: 359 average time/residue: 0.1172 time to fit residues: 64.1679 Evaluate side-chains 266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 250 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 6.9990 chunk 140 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 151 optimal weight: 0.0870 chunk 156 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS E 12 ASN E 115 ASN E 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.112396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097393 restraints weight = 24047.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.100466 restraints weight = 12186.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.102527 restraints weight = 7540.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103928 restraints weight = 5328.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.104866 restraints weight = 4136.140| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15220 Z= 0.226 Angle : 0.753 9.354 20660 Z= 0.376 Chirality : 0.048 0.221 2280 Planarity : 0.007 0.059 2630 Dihedral : 29.420 177.561 2330 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.22 % Favored : 95.68 % Rotamer: Outliers : 3.51 % Allowed : 11.12 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.20), residues: 1830 helix: 0.70 (0.19), residues: 760 sheet: -0.68 (0.29), residues: 280 loop : 0.13 (0.24), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 62 TYR 0.019 0.002 TYR A 166 PHE 0.026 0.002 PHE A 352 TRP 0.018 0.002 TRP A 86 HIS 0.009 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00531 (15220) covalent geometry : angle 0.75302 (20660) hydrogen bonds : bond 0.04575 ( 765) hydrogen bonds : angle 4.87475 ( 1920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 287 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 103 THR cc_start: 0.8975 (m) cc_final: 0.8466 (p) REVERT: A 154 ASP cc_start: 0.8518 (t70) cc_final: 0.8102 (t70) REVERT: A 191 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8769 (ttpp) REVERT: A 269 MET cc_start: 0.7276 (tpp) cc_final: 0.6617 (tpp) REVERT: A 328 LYS cc_start: 0.8591 (tmtt) cc_final: 0.8163 (tmtt) REVERT: B 78 ASN cc_start: 0.8418 (t0) cc_final: 0.7654 (t0) REVERT: B 100 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7287 (tp30) REVERT: B 151 ILE cc_start: 0.8836 (mt) cc_final: 0.8493 (tt) REVERT: B 269 MET cc_start: 0.7247 (mmm) cc_final: 0.6760 (mmt) REVERT: B 294 TYR cc_start: 0.8798 (m-10) cc_final: 0.8510 (m-10) REVERT: C 47 MET cc_start: 0.6900 (tpp) cc_final: 0.6633 (tpp) REVERT: C 78 ASN cc_start: 0.8324 (t0) cc_final: 0.7519 (t0) REVERT: C 81 ASP cc_start: 0.8648 (m-30) cc_final: 0.8335 (m-30) REVERT: C 211 ASP cc_start: 0.8844 (OUTLIER) cc_final: 0.8568 (m-30) REVERT: C 269 MET cc_start: 0.7329 (tpt) cc_final: 0.7035 (tpt) REVERT: C 283 MET cc_start: 0.8347 (mmm) cc_final: 0.7758 (mmm) REVERT: C 336 LYS cc_start: 0.8130 (mttt) cc_final: 0.7567 (ttmt) REVERT: D 120 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8628 (p) REVERT: D 142 LEU cc_start: 0.9065 (tp) cc_final: 0.8840 (tp) REVERT: D 192 ILE cc_start: 0.8999 (tp) cc_final: 0.8793 (tp) REVERT: D 336 LYS cc_start: 0.8573 (mttt) cc_final: 0.7891 (ttmt) REVERT: E 47 MET cc_start: 0.3260 (mtt) cc_final: 0.2984 (mtt) REVERT: E 68 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8025 (mmmt) REVERT: E 82 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8672 (tpt) REVERT: E 162 ASN cc_start: 0.8350 (m-40) cc_final: 0.8139 (m-40) REVERT: E 313 MET cc_start: 0.8695 (tpp) cc_final: 0.8456 (ttm) outliers start: 55 outliers final: 32 residues processed: 324 average time/residue: 0.1077 time to fit residues: 54.7769 Evaluate side-chains 268 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 232 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 289 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 64 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 175 optimal weight: 0.3980 chunk 172 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 39 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 49 GLN A 297 ASN B 49 GLN C 12 ASN C 41 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN C 296 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.118062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.103135 restraints weight = 23573.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106321 restraints weight = 11856.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108449 restraints weight = 7284.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109875 restraints weight = 5104.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110898 restraints weight = 3935.918| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15220 Z= 0.112 Angle : 0.644 9.804 20660 Z= 0.316 Chirality : 0.044 0.186 2280 Planarity : 0.005 0.053 2630 Dihedral : 28.833 177.274 2330 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 1.09 % Allowed : 2.57 % Favored : 96.34 % Rotamer: Outliers : 2.49 % Allowed : 14.82 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.20), residues: 1830 helix: 1.08 (0.19), residues: 765 sheet: -0.73 (0.28), residues: 305 loop : 0.33 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 206 TYR 0.014 0.001 TYR A 166 PHE 0.012 0.001 PHE D 375 TRP 0.019 0.001 TRP A 86 HIS 0.004 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00237 (15220) covalent geometry : angle 0.64369 (20660) hydrogen bonds : bond 0.03232 ( 765) hydrogen bonds : angle 4.44770 ( 1920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 278 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8852 (mt) cc_final: 0.8606 (mt) REVERT: A 103 THR cc_start: 0.8826 (m) cc_final: 0.8277 (p) REVERT: A 154 ASP cc_start: 0.8322 (t70) cc_final: 0.7834 (t70) REVERT: A 269 MET cc_start: 0.7259 (tpp) cc_final: 0.6689 (tpp) REVERT: B 100 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7132 (tp30) REVERT: B 161 HIS cc_start: 0.8774 (p-80) cc_final: 0.8519 (p-80) REVERT: B 269 MET cc_start: 0.7089 (mmm) cc_final: 0.6801 (mmt) REVERT: B 294 TYR cc_start: 0.8591 (m-10) cc_final: 0.8283 (m-10) REVERT: C 78 ASN cc_start: 0.8207 (t0) cc_final: 0.7342 (t0) REVERT: C 81 ASP cc_start: 0.8626 (m-30) cc_final: 0.8359 (m-30) REVERT: C 269 MET cc_start: 0.7333 (tpt) cc_final: 0.6974 (tpt) REVERT: C 283 MET cc_start: 0.8145 (mmm) cc_final: 0.7642 (mmm) REVERT: C 336 LYS cc_start: 0.7929 (mttt) cc_final: 0.7480 (ttpt) REVERT: C 337 TYR cc_start: 0.8736 (m-80) cc_final: 0.8084 (m-80) REVERT: D 72 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7527 (pp20) REVERT: D 161 HIS cc_start: 0.8963 (p90) cc_final: 0.8623 (p90) REVERT: D 212 ILE cc_start: 0.8917 (mt) cc_final: 0.8696 (mt) REVERT: E 68 LYS cc_start: 0.8240 (mmtt) cc_final: 0.7972 (mmmt) REVERT: E 246 GLN cc_start: 0.8800 (mt0) cc_final: 0.8472 (mt0) REVERT: E 292 ASP cc_start: 0.7846 (m-30) cc_final: 0.7621 (m-30) outliers start: 39 outliers final: 23 residues processed: 301 average time/residue: 0.1027 time to fit residues: 49.0153 Evaluate side-chains 260 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 252 ASN E 87 HIS ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.110039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.094888 restraints weight = 24353.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.097885 restraints weight = 12468.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.099909 restraints weight = 7785.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101250 restraints weight = 5546.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.102191 restraints weight = 4350.829| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15220 Z= 0.246 Angle : 0.742 9.358 20660 Z= 0.365 Chirality : 0.048 0.235 2280 Planarity : 0.006 0.052 2630 Dihedral : 28.354 178.653 2330 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 1.09 % Allowed : 3.66 % Favored : 95.25 % Rotamer: Outliers : 3.96 % Allowed : 14.50 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1830 helix: 0.73 (0.19), residues: 765 sheet: -0.71 (0.29), residues: 305 loop : 0.21 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 116 TYR 0.015 0.002 TYR E 294 PHE 0.027 0.002 PHE A 352 TRP 0.018 0.002 TRP D 79 HIS 0.007 0.001 HIS B 40 Details of bonding type rmsd covalent geometry : bond 0.00585 (15220) covalent geometry : angle 0.74155 (20660) hydrogen bonds : bond 0.04412 ( 765) hydrogen bonds : angle 4.71376 ( 1920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 245 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 103 THR cc_start: 0.8948 (m) cc_final: 0.8394 (p) REVERT: A 107 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: A 269 MET cc_start: 0.7298 (tpp) cc_final: 0.6833 (tpp) REVERT: A 313 MET cc_start: 0.8477 (mmm) cc_final: 0.8240 (tpt) REVERT: B 78 ASN cc_start: 0.8562 (t0) cc_final: 0.7690 (t0) REVERT: B 136 ILE cc_start: 0.8919 (mp) cc_final: 0.8617 (mt) REVERT: C 78 ASN cc_start: 0.8270 (t0) cc_final: 0.7403 (t0) REVERT: C 81 ASP cc_start: 0.8648 (m-30) cc_final: 0.8177 (m-30) REVERT: C 132 MET cc_start: 0.8090 (ppp) cc_final: 0.7740 (ptt) REVERT: C 148 THR cc_start: 0.8605 (p) cc_final: 0.8383 (t) REVERT: C 269 MET cc_start: 0.7408 (tpt) cc_final: 0.7062 (tpt) REVERT: C 283 MET cc_start: 0.8289 (mmm) cc_final: 0.7873 (mmm) REVERT: C 336 LYS cc_start: 0.8172 (mttt) cc_final: 0.7725 (ttpt) REVERT: C 337 TYR cc_start: 0.8760 (m-80) cc_final: 0.8265 (m-80) REVERT: D 336 LYS cc_start: 0.8029 (mttp) cc_final: 0.7711 (mttp) REVERT: D 353 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: E 68 LYS cc_start: 0.8411 (mmtt) cc_final: 0.8081 (mmmt) REVERT: E 115 ASN cc_start: 0.8492 (m-40) cc_final: 0.8216 (t0) REVERT: E 206 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7816 (ttm-80) outliers start: 62 outliers final: 38 residues processed: 284 average time/residue: 0.1057 time to fit residues: 47.4265 Evaluate side-chains 273 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 162 ASN Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 299 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 184 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 chunk 43 optimal weight: 0.0030 chunk 42 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.4980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 41 GLN C 49 GLN C 115 ASN C 161 HIS C 162 ASN ** D 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.115536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100334 restraints weight = 23562.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103442 restraints weight = 11991.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105498 restraints weight = 7429.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.106899 restraints weight = 5281.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.107875 restraints weight = 4106.298| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15220 Z= 0.114 Angle : 0.643 8.989 20660 Z= 0.313 Chirality : 0.044 0.209 2280 Planarity : 0.005 0.049 2630 Dihedral : 27.827 178.290 2330 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.11 % Favored : 95.90 % Rotamer: Outliers : 2.56 % Allowed : 16.42 % Favored : 81.02 % 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 are not related in a simple way. whole: 0.51 (0.20), residues: 1830 helix: 1.03 (0.19), residues: 765 sheet: -0.61 (0.29), residues: 300 loop : 0.22 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 206 TYR 0.014 0.001 TYR C 166 PHE 0.030 0.001 PHE A 352 TRP 0.019 0.001 TRP A 86 HIS 0.005 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00248 (15220) covalent geometry : angle 0.64298 (20660) hydrogen bonds : bond 0.03153 ( 765) hydrogen bonds : angle 4.42404 ( 1920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 250 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8852 (mt) cc_final: 0.8625 (mt) REVERT: A 103 THR cc_start: 0.8775 (m) cc_final: 0.8234 (p) REVERT: A 166 TYR cc_start: 0.8457 (t80) cc_final: 0.8251 (t80) REVERT: A 269 MET cc_start: 0.7271 (tpp) cc_final: 0.6840 (tpp) REVERT: B 132 MET cc_start: 0.7956 (ptm) cc_final: 0.7669 (ttm) REVERT: B 136 ILE cc_start: 0.8850 (mp) cc_final: 0.8586 (mt) REVERT: C 78 ASN cc_start: 0.8219 (t0) cc_final: 0.7371 (t0) REVERT: C 81 ASP cc_start: 0.8601 (m-30) cc_final: 0.8255 (m-30) REVERT: C 132 MET cc_start: 0.8067 (ppp) cc_final: 0.7676 (ptt) REVERT: C 217 CYS cc_start: 0.8657 (m) cc_final: 0.7854 (m) REVERT: C 269 MET cc_start: 0.7340 (tpt) cc_final: 0.7041 (tpt) REVERT: C 283 MET cc_start: 0.8214 (mmm) cc_final: 0.7742 (mmm) REVERT: C 336 LYS cc_start: 0.8052 (mttt) cc_final: 0.7457 (ttpt) REVERT: C 337 TYR cc_start: 0.8614 (m-80) cc_final: 0.8085 (m-80) REVERT: D 72 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7352 (pt0) REVERT: D 212 ILE cc_start: 0.8872 (mt) cc_final: 0.8667 (mt) REVERT: D 353 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: E 47 MET cc_start: 0.3850 (mtt) cc_final: 0.3092 (mtt) REVERT: E 68 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8033 (mmmt) REVERT: E 162 ASN cc_start: 0.8215 (m110) cc_final: 0.7957 (m-40) REVERT: E 246 GLN cc_start: 0.8770 (mt0) cc_final: 0.8360 (mt0) REVERT: E 325 MET cc_start: 0.8065 (mmp) cc_final: 0.7348 (mmm) outliers start: 40 outliers final: 29 residues processed: 276 average time/residue: 0.1014 time to fit residues: 44.9577 Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 117 optimal weight: 5.9990 chunk 76 optimal weight: 0.0030 chunk 55 optimal weight: 0.5980 chunk 111 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 HIS E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097138 restraints weight = 23708.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100169 restraints weight = 12333.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.102215 restraints weight = 7781.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.103554 restraints weight = 5587.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104500 restraints weight = 4413.033| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15220 Z= 0.154 Angle : 0.666 8.829 20660 Z= 0.324 Chirality : 0.045 0.177 2280 Planarity : 0.005 0.047 2630 Dihedral : 27.569 179.711 2330 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.98 % Allowed : 3.83 % Favored : 95.19 % Rotamer: Outliers : 3.45 % Allowed : 16.49 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1830 helix: 1.14 (0.19), residues: 735 sheet: -0.66 (0.29), residues: 305 loop : 0.18 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 206 TYR 0.011 0.001 TYR C 166 PHE 0.019 0.001 PHE A 223 TRP 0.018 0.002 TRP A 86 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00361 (15220) covalent geometry : angle 0.66572 (20660) hydrogen bonds : bond 0.03551 ( 765) hydrogen bonds : angle 4.45237 ( 1920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8906 (mt) cc_final: 0.8659 (mt) REVERT: A 269 MET cc_start: 0.7177 (tpp) cc_final: 0.6876 (tpp) REVERT: B 136 ILE cc_start: 0.8919 (mp) cc_final: 0.8678 (mt) REVERT: B 313 MET cc_start: 0.8610 (tpp) cc_final: 0.8393 (ttm) REVERT: C 40 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7987 (m-70) REVERT: C 78 ASN cc_start: 0.8274 (t0) cc_final: 0.7295 (t0) REVERT: C 81 ASP cc_start: 0.8644 (m-30) cc_final: 0.8289 (m-30) REVERT: C 132 MET cc_start: 0.8166 (ppp) cc_final: 0.7771 (ptt) REVERT: C 269 MET cc_start: 0.7338 (tpt) cc_final: 0.7047 (tpt) REVERT: C 283 MET cc_start: 0.8222 (mmm) cc_final: 0.7842 (mmm) REVERT: C 336 LYS cc_start: 0.8248 (mttt) cc_final: 0.7686 (ttpt) REVERT: C 337 TYR cc_start: 0.8682 (m-80) cc_final: 0.8076 (m-80) REVERT: D 72 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7310 (pt0) REVERT: D 128 ASN cc_start: 0.8133 (m-40) cc_final: 0.7867 (p0) REVERT: D 353 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7071 (mp10) REVERT: E 47 MET cc_start: 0.4115 (mtt) cc_final: 0.3616 (mtt) REVERT: E 82 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8724 (tpt) REVERT: E 162 ASN cc_start: 0.8265 (m110) cc_final: 0.7972 (m-40) REVERT: E 246 GLN cc_start: 0.8784 (mt0) cc_final: 0.8462 (mt0) outliers start: 54 outliers final: 38 residues processed: 276 average time/residue: 0.1034 time to fit residues: 45.4234 Evaluate side-chains 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 86 optimal weight: 0.7980 chunk 162 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 149 optimal weight: 0.4980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 104 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN D 296 ASN E 12 ASN E 353 GLN E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100727 restraints weight = 23696.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.103821 restraints weight = 12129.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.105927 restraints weight = 7575.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107292 restraints weight = 5392.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.108271 restraints weight = 4231.983| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15220 Z= 0.113 Angle : 0.640 8.853 20660 Z= 0.310 Chirality : 0.044 0.172 2280 Planarity : 0.005 0.047 2630 Dihedral : 27.148 178.794 2330 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.93 % Allowed : 3.22 % Favored : 95.85 % Rotamer: Outliers : 2.75 % Allowed : 17.32 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.20), residues: 1830 helix: 1.27 (0.20), residues: 735 sheet: -0.58 (0.30), residues: 305 loop : 0.24 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 206 TYR 0.033 0.001 TYR A 166 PHE 0.018 0.001 PHE A 223 TRP 0.021 0.001 TRP A 86 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00252 (15220) covalent geometry : angle 0.63978 (20660) hydrogen bonds : bond 0.03026 ( 765) hydrogen bonds : angle 4.34028 ( 1920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8802 (mt) cc_final: 0.8573 (mt) REVERT: A 103 THR cc_start: 0.8741 (m) cc_final: 0.8400 (p) REVERT: A 269 MET cc_start: 0.7185 (tpp) cc_final: 0.6897 (tpp) REVERT: A 285 CYS cc_start: 0.8358 (m) cc_final: 0.8083 (m) REVERT: B 136 ILE cc_start: 0.8884 (mp) cc_final: 0.8637 (mt) REVERT: C 40 HIS cc_start: 0.8168 (OUTLIER) cc_final: 0.7790 (m-70) REVERT: C 78 ASN cc_start: 0.8245 (t0) cc_final: 0.7282 (t0) REVERT: C 81 ASP cc_start: 0.8618 (m-30) cc_final: 0.8278 (m-30) REVERT: C 132 MET cc_start: 0.8106 (ppp) cc_final: 0.7749 (ptt) REVERT: C 217 CYS cc_start: 0.8640 (m) cc_final: 0.7839 (m) REVERT: C 269 MET cc_start: 0.7260 (tpt) cc_final: 0.6969 (tpt) REVERT: C 283 MET cc_start: 0.8120 (mmm) cc_final: 0.7762 (mmm) REVERT: C 336 LYS cc_start: 0.8233 (mttt) cc_final: 0.7635 (ttpt) REVERT: C 337 TYR cc_start: 0.8569 (m-80) cc_final: 0.7981 (m-80) REVERT: D 72 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7317 (pt0) REVERT: D 353 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7148 (mp10) REVERT: E 246 GLN cc_start: 0.8727 (mt0) cc_final: 0.8254 (mt0) outliers start: 43 outliers final: 32 residues processed: 269 average time/residue: 0.0999 time to fit residues: 43.0963 Evaluate side-chains 259 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 GLN E 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.112365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096941 restraints weight = 24023.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.099933 restraints weight = 12410.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.101940 restraints weight = 7823.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103248 restraints weight = 5641.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104182 restraints weight = 4472.498| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15220 Z= 0.159 Angle : 0.679 8.712 20660 Z= 0.330 Chirality : 0.046 0.216 2280 Planarity : 0.005 0.045 2630 Dihedral : 26.940 179.658 2330 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.93 % Favored : 95.19 % Rotamer: Outliers : 2.94 % Allowed : 17.83 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.20), residues: 1830 helix: 1.20 (0.20), residues: 735 sheet: -0.57 (0.30), residues: 305 loop : 0.23 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.034 0.001 TYR A 166 PHE 0.020 0.001 PHE A 223 TRP 0.020 0.002 TRP A 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00374 (15220) covalent geometry : angle 0.67922 (20660) hydrogen bonds : bond 0.03549 ( 765) hydrogen bonds : angle 4.41799 ( 1920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 223 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8908 (mt) cc_final: 0.8662 (mt) REVERT: A 103 THR cc_start: 0.8814 (m) cc_final: 0.8475 (p) REVERT: A 223 PHE cc_start: 0.6741 (p90) cc_final: 0.6496 (p90) REVERT: A 283 MET cc_start: 0.8431 (mmt) cc_final: 0.8125 (mmt) REVERT: A 305 MET cc_start: 0.8924 (mtm) cc_final: 0.8696 (mtp) REVERT: B 136 ILE cc_start: 0.8912 (mp) cc_final: 0.8684 (mt) REVERT: B 269 MET cc_start: 0.7210 (mtt) cc_final: 0.6967 (mtt) REVERT: C 40 HIS cc_start: 0.8313 (OUTLIER) cc_final: 0.8006 (m-70) REVERT: C 47 MET cc_start: 0.7838 (tpp) cc_final: 0.6557 (ttt) REVERT: C 78 ASN cc_start: 0.8293 (t0) cc_final: 0.7312 (t0) REVERT: C 81 ASP cc_start: 0.8613 (m-30) cc_final: 0.8251 (m-30) REVERT: C 132 MET cc_start: 0.8188 (ppp) cc_final: 0.7815 (ptt) REVERT: C 269 MET cc_start: 0.7315 (tpt) cc_final: 0.6982 (tpt) REVERT: C 313 MET cc_start: 0.8258 (tpp) cc_final: 0.7764 (ttp) REVERT: C 336 LYS cc_start: 0.8271 (mttt) cc_final: 0.7701 (ttpt) REVERT: C 337 TYR cc_start: 0.8641 (m-80) cc_final: 0.8044 (m-80) REVERT: D 72 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7313 (pt0) REVERT: D 149 THR cc_start: 0.8771 (m) cc_final: 0.8328 (t) REVERT: D 353 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: E 82 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8748 (tpt) REVERT: E 162 ASN cc_start: 0.8299 (m110) cc_final: 0.7971 (m-40) REVERT: E 246 GLN cc_start: 0.8770 (mt0) cc_final: 0.8467 (mt0) REVERT: E 353 GLN cc_start: 0.7684 (mp-120) cc_final: 0.7135 (mp10) outliers start: 46 outliers final: 37 residues processed: 253 average time/residue: 0.1010 time to fit residues: 41.2563 Evaluate side-chains 259 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 165 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.116698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101221 restraints weight = 23470.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.104277 restraints weight = 12104.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.106326 restraints weight = 7604.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107659 restraints weight = 5455.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108599 restraints weight = 4312.943| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15220 Z= 0.115 Angle : 0.650 8.941 20660 Z= 0.314 Chirality : 0.044 0.180 2280 Planarity : 0.005 0.047 2630 Dihedral : 26.708 179.741 2330 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.87 % Allowed : 3.17 % Favored : 95.96 % Rotamer: Outliers : 2.43 % Allowed : 18.34 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1830 helix: 1.37 (0.20), residues: 735 sheet: -0.51 (0.30), residues: 305 loop : 0.28 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.033 0.001 TYR A 166 PHE 0.019 0.001 PHE A 223 TRP 0.023 0.001 TRP A 86 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00256 (15220) covalent geometry : angle 0.64962 (20660) hydrogen bonds : bond 0.02965 ( 765) hydrogen bonds : angle 4.32212 ( 1920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 65 LEU cc_start: 0.8802 (mt) cc_final: 0.8588 (mt) REVERT: A 103 THR cc_start: 0.8770 (m) cc_final: 0.8429 (p) REVERT: A 223 PHE cc_start: 0.6713 (p90) cc_final: 0.6475 (p90) REVERT: A 283 MET cc_start: 0.8455 (mmt) cc_final: 0.8173 (mmt) REVERT: A 285 CYS cc_start: 0.8379 (m) cc_final: 0.8119 (m) REVERT: A 305 MET cc_start: 0.8799 (mtm) cc_final: 0.8542 (mtp) REVERT: B 136 ILE cc_start: 0.8926 (mp) cc_final: 0.8694 (mt) REVERT: B 269 MET cc_start: 0.7139 (mtt) cc_final: 0.6913 (mtt) REVERT: C 40 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7816 (m-70) REVERT: C 47 MET cc_start: 0.7873 (tpp) cc_final: 0.6503 (ttt) REVERT: C 78 ASN cc_start: 0.8263 (t0) cc_final: 0.7292 (t0) REVERT: C 81 ASP cc_start: 0.8602 (m-30) cc_final: 0.8260 (m-30) REVERT: C 132 MET cc_start: 0.8116 (ppp) cc_final: 0.7761 (ptt) REVERT: C 217 CYS cc_start: 0.8604 (m) cc_final: 0.7825 (m) REVERT: C 269 MET cc_start: 0.7187 (tpt) cc_final: 0.6868 (tpt) REVERT: C 283 MET cc_start: 0.7808 (mmp) cc_final: 0.7436 (mmt) REVERT: C 336 LYS cc_start: 0.8254 (mttt) cc_final: 0.7654 (ttpt) REVERT: C 337 TYR cc_start: 0.8596 (m-80) cc_final: 0.7937 (m-80) REVERT: D 72 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7422 (pt0) REVERT: D 149 THR cc_start: 0.8779 (m) cc_final: 0.8522 (t) REVERT: D 353 GLN cc_start: 0.7484 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: E 246 GLN cc_start: 0.8691 (mt0) cc_final: 0.8167 (mt0) REVERT: E 325 MET cc_start: 0.7949 (mmp) cc_final: 0.7265 (mmm) REVERT: E 353 GLN cc_start: 0.7534 (mp-120) cc_final: 0.6997 (mp10) outliers start: 38 outliers final: 29 residues processed: 267 average time/residue: 0.1076 time to fit residues: 45.2654 Evaluate side-chains 255 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 238 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain C residue 40 HIS Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 289 ILE Chi-restraints excluded: chain E residue 334 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 177 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.116201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.100825 restraints weight = 23552.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103858 restraints weight = 12174.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105926 restraints weight = 7641.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.107309 restraints weight = 5478.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108246 restraints weight = 4298.665| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15220 Z= 0.124 Angle : 0.658 9.578 20660 Z= 0.317 Chirality : 0.044 0.163 2280 Planarity : 0.005 0.045 2630 Dihedral : 26.590 179.901 2330 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.82 % Allowed : 3.50 % Favored : 95.68 % Rotamer: Outliers : 2.30 % Allowed : 18.59 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.20), residues: 1830 helix: 1.35 (0.20), residues: 735 sheet: -0.44 (0.30), residues: 305 loop : 0.27 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 206 TYR 0.032 0.001 TYR A 166 PHE 0.020 0.001 PHE A 223 TRP 0.022 0.002 TRP A 86 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd covalent geometry : bond 0.00284 (15220) covalent geometry : angle 0.65780 (20660) hydrogen bonds : bond 0.03113 ( 765) hydrogen bonds : angle 4.31777 ( 1920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2304.56 seconds wall clock time: 40 minutes 50.00 seconds (2450.00 seconds total)