Starting phenix.real_space_refine on Fri Jun 13 20:04:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.map" model { file = "/net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oid_16889/06_2025/8oid_16889.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9210 2.51 5 N 2460 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15206 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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 bond proxies already assigned to first conformer: 2937 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Classifications: {'water': 159} Link IDs: {None: 158} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Restraints were copied for chains: C, B, E, D Time building chain proxies: 9.15, per 1000 atoms: 0.60 Number of scatterers: 15206 At special positions: 0 Unit cell: (93.13, 92.435, 193.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 10 15.00 Mg 5 11.99 O 3416 8.00 N 2460 7.00 C 9210 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: 3.98 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 100 helices and 30 sheets defined 48.6% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS C 371 " --> pdb=" O SER C 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 367 through 371' Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 260 Proline residue: A 258 - end of helix Processing helix chain 'A' and resid 261 through 262 No H-bonds generated for 'chain 'A' and resid 261 through 262' Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS A 371 " --> pdb=" O SER A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 260 Proline residue: B 258 - end of helix Processing helix chain 'B' and resid 261 through 262 No H-bonds generated for 'chain 'B' and resid 261 through 262' Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.104A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N HIS B 371 " --> pdb=" O SER B 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 367 through 371' Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.735A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 260 Proline residue: D 258 - end of helix Processing helix chain 'D' and resid 261 through 262 No H-bonds generated for 'chain 'D' and resid 261 through 262' Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.105A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 371 removed outlier: 3.614A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS D 371 " --> pdb=" O SER D 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 367 through 371' Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.966A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.734A pdb=" N THR E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 197 No H-bonds generated for 'chain 'E' and resid 195 through 197' Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 260 Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 261 through 262 No H-bonds generated for 'chain 'E' and resid 261 through 262' Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 351 through 355 removed outlier: 4.106A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.613A pdb=" N VAL E 370 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N HIS E 371 " --> pdb=" O SER E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.562A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.356A pdb=" N THR B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.354A pdb=" N THR D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.563A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC9, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'E' and resid 169 through 170 removed outlier: 6.355A pdb=" N THR E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 725 hydrogen bonds defined for protein. 1885 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: 5.70 Time building geometry restraints manager: 4.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4716 1.34 - 1.46: 2340 1.46 - 1.57: 7664 1.57 - 1.69: 15 1.69 - 1.81: 185 Bond restraints: 14920 Sorted by residual: bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.87e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.81e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.76e+00 ... (remaining 14915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 19729 1.50 - 3.00: 358 3.00 - 4.50: 113 4.50 - 6.00: 41 6.00 - 7.49: 9 Bond angle restraints: 20250 Sorted by residual: angle pdb=" N HIC B 73 " pdb=" CA HIC B 73 " pdb=" CB HIC B 73 " ideal model delta sigma weight residual 110.50 115.96 -5.46 1.70e+00 3.46e-01 1.03e+01 angle pdb=" N HIC E 73 " pdb=" CA HIC E 73 " pdb=" CB HIC E 73 " ideal model delta sigma weight residual 110.50 115.94 -5.44 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC A 73 " pdb=" CA HIC A 73 " pdb=" CB HIC A 73 " ideal model delta sigma weight residual 110.50 115.93 -5.43 1.70e+00 3.46e-01 1.02e+01 angle pdb=" N HIC D 73 " pdb=" CA HIC D 73 " pdb=" CB HIC D 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 angle pdb=" N HIC C 73 " pdb=" CA HIC C 73 " pdb=" CB HIC C 73 " ideal model delta sigma weight residual 110.50 115.91 -5.41 1.70e+00 3.46e-01 1.01e+01 ... (remaining 20245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.43: 8805 32.43 - 64.86: 140 64.86 - 97.28: 20 97.28 - 129.71: 5 129.71 - 162.14: 5 Dihedral angle restraints: 8975 sinusoidal: 3615 harmonic: 5360 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.14 -162.14 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PA ADP D 401 " pdb=" PB ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.10 -162.10 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 102.08 -162.07 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1189 0.029 - 0.058: 693 0.058 - 0.087: 177 0.087 - 0.115: 159 0.115 - 0.144: 27 Chirality restraints: 2245 Sorted by residual: chirality pdb=" C3' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C4' ADP C 401 " pdb=" O3' ADP C 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 2242 not shown) Planarity restraints: 2585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.025 5.00e-02 4.00e+02 3.85e-02 2.38e+00 pdb=" N PRO C 164 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 163 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO D 164 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 164 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 164 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO E 164 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.021 5.00e-02 4.00e+02 ... (remaining 2582 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 138 2.45 - 3.06: 10189 3.06 - 3.68: 24368 3.68 - 4.29: 40105 4.29 - 4.90: 62710 Nonbonded interactions: 137510 Sorted by model distance: nonbonded pdb="MG MG C 402 " pdb=" O HOH C 557 " model vdw 1.840 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 548 " model vdw 1.857 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 514 " model vdw 1.873 2.170 nonbonded pdb="MG MG A 402 " pdb=" O HOH A 526 " model vdw 1.877 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 532 " model vdw 1.880 2.170 ... (remaining 137505 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 39.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14920 Z= 0.185 Angle : 0.608 7.494 20250 Z= 0.303 Chirality : 0.044 0.144 2245 Planarity : 0.004 0.039 2585 Dihedral : 13.008 162.140 5545 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.96 % Allowed : 4.17 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.19), residues: 1830 helix: -1.33 (0.16), residues: 790 sheet: 0.07 (0.26), residues: 335 loop : 0.83 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.002 0.001 HIS E 173 PHE 0.006 0.001 PHE B 262 TYR 0.012 0.001 TYR C 143 ARG 0.003 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.13645 ( 715) hydrogen bonds : angle 6.23939 ( 1885) covalent geometry : bond 0.00413 (14920) covalent geometry : angle 0.60841 (20250) *********************** 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 295 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 280 time to evaluate : 1.797 Fit side-chains REVERT: C 47 MET cc_start: 0.6146 (OUTLIER) cc_final: 0.5836 (tpt) REVERT: C 180 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8581 (tp) REVERT: C 269 MET cc_start: 0.8436 (mtp) cc_final: 0.8207 (mtt) REVERT: A 180 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8753 (tp) REVERT: D 47 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.5143 (tpt) REVERT: D 121 GLN cc_start: 0.7959 (tt0) cc_final: 0.7674 (tm130) REVERT: D 325 MET cc_start: 0.8917 (mmp) cc_final: 0.8625 (mmp) REVERT: D 351 THR cc_start: 0.8906 (m) cc_final: 0.8674 (m) REVERT: E 47 MET cc_start: 0.5398 (OUTLIER) cc_final: 0.4766 (tpt) outliers start: 15 outliers final: 0 residues processed: 287 average time/residue: 1.5231 time to fit residues: 474.4032 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 0.0270 chunk 107 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN C 128 ASN C 225 GLN C 246 GLN A 128 ASN A 353 GLN B 12 ASN B 41 GLN B 128 ASN B 225 GLN B 353 GLN E 78 ASN E 121 GLN E 353 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.092730 restraints weight = 18592.067| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.47 r_work: 0.2872 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14920 Z= 0.222 Angle : 0.679 8.834 20250 Z= 0.333 Chirality : 0.048 0.190 2245 Planarity : 0.005 0.042 2585 Dihedral : 12.223 170.303 2098 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.05 % Allowed : 8.08 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1830 helix: 0.19 (0.19), residues: 770 sheet: 0.55 (0.26), residues: 345 loop : 1.45 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.012 0.002 PHE D 262 TYR 0.014 0.001 TYR A 143 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 715) hydrogen bonds : angle 4.93337 ( 1885) covalent geometry : bond 0.00513 (14920) covalent geometry : angle 0.67868 (20250) *********************** 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 233 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.783 Fit side-chains REVERT: C 47 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5738 (tpt) REVERT: C 180 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 180 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8651 (tt) REVERT: A 276 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8130 (mm-30) REVERT: B 47 MET cc_start: 0.4562 (mmt) cc_final: 0.4178 (tpt) REVERT: B 68 LYS cc_start: 0.9015 (mptt) cc_final: 0.8795 (mmtt) REVERT: B 153 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8714 (ttp) REVERT: D 47 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5158 (tpt) REVERT: D 121 GLN cc_start: 0.8466 (tt0) cc_final: 0.8239 (tm-30) REVERT: D 180 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8687 (tt) REVERT: D 326 LYS cc_start: 0.8392 (tptt) cc_final: 0.7925 (pttm) REVERT: D 351 THR cc_start: 0.9069 (m) cc_final: 0.8772 (m) REVERT: D 353 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8159 (mm-40) REVERT: E 47 MET cc_start: 0.5419 (OUTLIER) cc_final: 0.4629 (tpt) REVERT: E 132 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8131 (ttp) outliers start: 32 outliers final: 5 residues processed: 220 average time/residue: 1.6689 time to fit residues: 400.9204 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 132 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 40 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 179 optimal weight: 8.9990 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN A 354 GLN B 12 ASN B 128 ASN B 225 GLN E 12 ASN E 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.091984 restraints weight = 24458.338| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.69 r_work: 0.2834 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14920 Z= 0.251 Angle : 0.688 8.961 20250 Z= 0.338 Chirality : 0.049 0.187 2245 Planarity : 0.005 0.044 2585 Dihedral : 12.311 170.944 2098 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.18 % Allowed : 8.46 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.20), residues: 1830 helix: 0.54 (0.19), residues: 770 sheet: 0.77 (0.26), residues: 345 loop : 1.65 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.014 0.002 PHE D 262 TYR 0.013 0.001 TYR A 143 ARG 0.007 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.04985 ( 715) hydrogen bonds : angle 4.86074 ( 1885) covalent geometry : bond 0.00586 (14920) covalent geometry : angle 0.68791 (20250) *********************** 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 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 1.708 Fit side-chains REVERT: C 47 MET cc_start: 0.6293 (OUTLIER) cc_final: 0.5838 (tpt) REVERT: C 180 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8665 (tp) REVERT: A 64 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9103 (pp) REVERT: A 180 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 276 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8215 (mm-30) REVERT: B 47 MET cc_start: 0.4597 (mmt) cc_final: 0.4202 (tpt) REVERT: B 64 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9077 (pp) REVERT: B 68 LYS cc_start: 0.9070 (mptt) cc_final: 0.8837 (mmtt) REVERT: B 72 GLU cc_start: 0.7975 (mp0) cc_final: 0.7716 (mp0) REVERT: B 153 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8773 (ttp) REVERT: B 314 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8157 (tp40) REVERT: D 47 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5217 (tpt) REVERT: D 121 GLN cc_start: 0.8563 (tt0) cc_final: 0.8306 (tm-30) REVERT: D 292 ASP cc_start: 0.8781 (m-30) cc_final: 0.8553 (m-30) REVERT: D 326 LYS cc_start: 0.8461 (tptt) cc_final: 0.7990 (pttm) REVERT: D 351 THR cc_start: 0.9051 (m) cc_final: 0.8787 (m) REVERT: E 47 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.4654 (tpt) REVERT: E 132 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8127 (ttp) outliers start: 34 outliers final: 8 residues processed: 217 average time/residue: 1.4339 time to fit residues: 340.2205 Evaluate side-chains 208 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 132 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN E 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092909 restraints weight = 29303.540| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.89 r_work: 0.2843 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14920 Z= 0.175 Angle : 0.636 8.626 20250 Z= 0.308 Chirality : 0.046 0.186 2245 Planarity : 0.004 0.040 2585 Dihedral : 12.168 172.454 2098 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.99 % Allowed : 9.42 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.20), residues: 1830 helix: 0.79 (0.19), residues: 770 sheet: 0.88 (0.27), residues: 345 loop : 1.79 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.011 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 715) hydrogen bonds : angle 4.66939 ( 1885) covalent geometry : bond 0.00403 (14920) covalent geometry : angle 0.63645 (20250) *********************** 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 230 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 2.162 Fit side-chains REVERT: C 47 MET cc_start: 0.6334 (OUTLIER) cc_final: 0.5811 (tpt) REVERT: C 51 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7873 (p0) REVERT: C 180 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8555 (tp) REVERT: A 64 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9123 (pp) REVERT: A 180 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8661 (tt) REVERT: A 276 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: B 47 MET cc_start: 0.4665 (mmt) cc_final: 0.4261 (tpt) REVERT: B 64 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9051 (pp) REVERT: B 68 LYS cc_start: 0.9075 (mptt) cc_final: 0.8826 (mmtt) REVERT: B 72 GLU cc_start: 0.8030 (mp0) cc_final: 0.7773 (mp0) REVERT: B 153 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8836 (ttp) REVERT: B 314 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8160 (tp40) REVERT: D 47 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5235 (tpt) REVERT: D 64 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8736 (pp) REVERT: D 121 GLN cc_start: 0.8596 (tt0) cc_final: 0.8327 (tm-30) REVERT: D 292 ASP cc_start: 0.8787 (m-30) cc_final: 0.8573 (m-30) REVERT: D 326 LYS cc_start: 0.8493 (tptt) cc_final: 0.7972 (pttm) REVERT: E 47 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4697 (tpt) REVERT: E 64 ILE cc_start: 0.9400 (OUTLIER) cc_final: 0.8866 (pp) REVERT: E 95 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7662 (mtt-85) outliers start: 31 outliers final: 9 residues processed: 218 average time/residue: 1.6111 time to fit residues: 383.4144 Evaluate side-chains 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 139 optimal weight: 0.6980 chunk 179 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.092555 restraints weight = 19229.337| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.52 r_work: 0.2880 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14920 Z= 0.223 Angle : 0.670 8.869 20250 Z= 0.327 Chirality : 0.048 0.186 2245 Planarity : 0.005 0.041 2585 Dihedral : 12.275 171.624 2098 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.31 % Allowed : 9.29 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.20), residues: 1830 helix: 0.81 (0.19), residues: 770 sheet: 0.89 (0.27), residues: 345 loop : 1.80 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.012 0.002 PHE B 262 TYR 0.012 0.001 TYR C 143 ARG 0.008 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 715) hydrogen bonds : angle 4.73675 ( 1885) covalent geometry : bond 0.00520 (14920) covalent geometry : angle 0.66951 (20250) *********************** 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 225 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.795 Fit side-chains REVERT: C 47 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.5830 (tpt) REVERT: C 51 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7833 (p0) REVERT: C 180 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (tp) REVERT: A 180 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8657 (tt) REVERT: A 276 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8154 (mm-30) REVERT: B 47 MET cc_start: 0.4669 (mmt) cc_final: 0.4284 (tpt) REVERT: B 64 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9049 (pp) REVERT: B 68 LYS cc_start: 0.9050 (mptt) cc_final: 0.8804 (mmtt) REVERT: B 72 GLU cc_start: 0.7906 (mp0) cc_final: 0.7669 (mp0) REVERT: B 153 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8753 (ttp) REVERT: B 314 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8095 (tp40) REVERT: D 47 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.5284 (tpt) REVERT: D 64 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8722 (pp) REVERT: D 121 GLN cc_start: 0.8508 (tt0) cc_final: 0.8229 (tm-30) REVERT: D 132 MET cc_start: 0.8402 (ttp) cc_final: 0.8192 (ppp) REVERT: D 292 ASP cc_start: 0.8691 (m-30) cc_final: 0.8463 (m-30) REVERT: D 314 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8346 (tt0) REVERT: D 326 LYS cc_start: 0.8459 (tptt) cc_final: 0.7984 (pttm) outliers start: 36 outliers final: 10 residues processed: 213 average time/residue: 1.4139 time to fit residues: 329.1806 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 44 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 111 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.095016 restraints weight = 22405.201| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.65 r_work: 0.2899 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14920 Z= 0.123 Angle : 0.594 8.224 20250 Z= 0.283 Chirality : 0.044 0.181 2245 Planarity : 0.004 0.038 2585 Dihedral : 11.998 173.702 2098 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.35 % Allowed : 10.51 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.20), residues: 1830 helix: 1.00 (0.19), residues: 775 sheet: 0.96 (0.27), residues: 345 loop : 1.98 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS B 88 PHE 0.008 0.001 PHE B 262 TYR 0.012 0.001 TYR A 143 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 715) hydrogen bonds : angle 4.47537 ( 1885) covalent geometry : bond 0.00276 (14920) covalent geometry : angle 0.59363 (20250) *********************** 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 218 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 1.621 Fit side-chains REVERT: C 47 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5816 (tpt) REVERT: C 180 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8373 (tp) REVERT: A 180 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 205 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8270 (mt-10) REVERT: B 47 MET cc_start: 0.4690 (mmt) cc_final: 0.4315 (tpt) REVERT: B 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8960 (pp) REVERT: B 68 LYS cc_start: 0.9017 (mptt) cc_final: 0.8767 (mmtt) REVERT: B 72 GLU cc_start: 0.7875 (mp0) cc_final: 0.7673 (mp0) REVERT: B 286 ASP cc_start: 0.8009 (m-30) cc_final: 0.7637 (m-30) REVERT: B 314 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8123 (tp40) REVERT: D 47 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.5343 (tpt) REVERT: D 64 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8730 (pp) REVERT: D 121 GLN cc_start: 0.8543 (tt0) cc_final: 0.8293 (tm-30) REVERT: D 222 ASP cc_start: 0.8527 (t70) cc_final: 0.8196 (t70) REVERT: D 292 ASP cc_start: 0.8701 (m-30) cc_final: 0.8467 (m-30) REVERT: D 314 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8389 (tt0) REVERT: D 326 LYS cc_start: 0.8421 (tptt) cc_final: 0.7930 (pttm) REVERT: E 47 MET cc_start: 0.5358 (OUTLIER) cc_final: 0.4676 (tpt) REVERT: E 95 ARG cc_start: 0.7877 (mtt-85) cc_final: 0.7648 (mtt-85) REVERT: E 326 LYS cc_start: 0.8210 (tptt) cc_final: 0.7874 (tttm) REVERT: E 351 THR cc_start: 0.9142 (p) cc_final: 0.8936 (t) outliers start: 21 outliers final: 6 residues processed: 211 average time/residue: 1.4307 time to fit residues: 329.8463 Evaluate side-chains 207 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 114 optimal weight: 9.9990 chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 150 optimal weight: 5.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.095303 restraints weight = 19561.422| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.55 r_work: 0.2919 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14920 Z= 0.155 Angle : 0.615 8.382 20250 Z= 0.295 Chirality : 0.046 0.182 2245 Planarity : 0.004 0.038 2585 Dihedral : 12.067 173.097 2098 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.54 % Allowed : 10.71 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.20), residues: 1830 helix: 1.04 (0.19), residues: 770 sheet: 0.98 (0.27), residues: 345 loop : 1.99 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.009 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 715) hydrogen bonds : angle 4.51090 ( 1885) covalent geometry : bond 0.00353 (14920) covalent geometry : angle 0.61515 (20250) *********************** 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 219 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.772 Fit side-chains REVERT: C 47 MET cc_start: 0.6294 (OUTLIER) cc_final: 0.5820 (tpt) REVERT: C 51 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7765 (p0) REVERT: C 132 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8231 (tmt) REVERT: C 180 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8451 (tp) REVERT: A 180 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8626 (tt) REVERT: A 205 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: A 276 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: B 47 MET cc_start: 0.4681 (mmt) cc_final: 0.4364 (tpt) REVERT: B 64 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.8964 (pp) REVERT: B 68 LYS cc_start: 0.9013 (mptt) cc_final: 0.8746 (mmtt) REVERT: B 72 GLU cc_start: 0.7882 (mp0) cc_final: 0.7656 (mp0) REVERT: B 286 ASP cc_start: 0.7978 (m-30) cc_final: 0.7606 (m-30) REVERT: B 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8081 (tp40) REVERT: D 47 MET cc_start: 0.5741 (OUTLIER) cc_final: 0.5326 (tpt) REVERT: D 64 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8725 (pp) REVERT: D 121 GLN cc_start: 0.8509 (tt0) cc_final: 0.8237 (tm-30) REVERT: D 222 ASP cc_start: 0.8494 (t70) cc_final: 0.8159 (t70) REVERT: D 292 ASP cc_start: 0.8684 (m-30) cc_final: 0.8450 (m-30) REVERT: D 314 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8331 (tt0) REVERT: D 326 LYS cc_start: 0.8391 (tptt) cc_final: 0.7925 (pttm) REVERT: E 95 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7622 (mtt-85) REVERT: E 326 LYS cc_start: 0.8203 (tptt) cc_final: 0.7871 (tttm) REVERT: E 351 THR cc_start: 0.9155 (p) cc_final: 0.8948 (t) outliers start: 24 outliers final: 11 residues processed: 209 average time/residue: 1.6372 time to fit residues: 375.2318 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 175 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.093114 restraints weight = 23350.754| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.71 r_work: 0.2876 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14920 Z= 0.198 Angle : 0.649 8.668 20250 Z= 0.315 Chirality : 0.047 0.186 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.203 172.346 2098 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.86 % Allowed : 10.64 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.20), residues: 1830 helix: 0.98 (0.19), residues: 770 sheet: 0.93 (0.27), residues: 345 loop : 1.99 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.011 0.001 PHE B 262 TYR 0.011 0.001 TYR C 143 ARG 0.009 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04354 ( 715) hydrogen bonds : angle 4.61800 ( 1885) covalent geometry : bond 0.00458 (14920) covalent geometry : angle 0.64944 (20250) *********************** 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 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.602 Fit side-chains REVERT: C 47 MET cc_start: 0.6321 (OUTLIER) cc_final: 0.5858 (tpt) REVERT: C 51 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7823 (p0) REVERT: C 132 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8277 (tmt) REVERT: C 180 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8531 (tp) REVERT: A 180 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8641 (tt) REVERT: A 205 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8360 (mt-10) REVERT: A 276 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8166 (mm-30) REVERT: B 47 MET cc_start: 0.4679 (mmt) cc_final: 0.4361 (tpt) REVERT: B 68 LYS cc_start: 0.9056 (mptt) cc_final: 0.8804 (mmtt) REVERT: B 72 GLU cc_start: 0.7936 (mp0) cc_final: 0.7679 (mp0) REVERT: B 286 ASP cc_start: 0.8072 (m-30) cc_final: 0.7709 (m-30) REVERT: B 314 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: D 47 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5450 (tpt) REVERT: D 64 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8747 (pp) REVERT: D 121 GLN cc_start: 0.8554 (tt0) cc_final: 0.8291 (tm-30) REVERT: D 292 ASP cc_start: 0.8762 (m-30) cc_final: 0.8541 (m-30) REVERT: D 314 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8372 (tt0) REVERT: D 326 LYS cc_start: 0.8438 (tptt) cc_final: 0.7968 (pttm) REVERT: E 64 ILE cc_start: 0.9397 (OUTLIER) cc_final: 0.8892 (pp) REVERT: E 95 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7628 (mtt-85) REVERT: E 326 LYS cc_start: 0.8226 (tptt) cc_final: 0.7893 (tttm) REVERT: E 351 THR cc_start: 0.9157 (p) cc_final: 0.8951 (t) outliers start: 29 outliers final: 12 residues processed: 210 average time/residue: 1.5461 time to fit residues: 354.9276 Evaluate side-chains 210 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 chunk 158 optimal weight: 0.0870 chunk 168 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095071 restraints weight = 24182.682| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.63 r_work: 0.2896 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14920 Z= 0.164 Angle : 0.625 8.547 20250 Z= 0.301 Chirality : 0.046 0.185 2245 Planarity : 0.004 0.038 2585 Dihedral : 12.132 172.544 2098 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.86 % Allowed : 10.90 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1830 helix: 1.04 (0.19), residues: 770 sheet: 0.93 (0.27), residues: 345 loop : 2.01 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.010 0.001 PHE B 262 TYR 0.011 0.001 TYR A 143 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 715) hydrogen bonds : angle 4.54209 ( 1885) covalent geometry : bond 0.00377 (14920) covalent geometry : angle 0.62454 (20250) *********************** 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 220 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 1.734 Fit side-chains REVERT: C 47 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5871 (tpt) REVERT: C 64 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.8610 (pp) REVERT: C 132 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8267 (tmt) REVERT: C 180 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8463 (tp) REVERT: A 180 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8648 (tt) REVERT: A 205 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8303 (mt-10) REVERT: A 276 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8147 (mm-30) REVERT: B 47 MET cc_start: 0.4694 (mmt) cc_final: 0.4382 (tpt) REVERT: B 64 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8978 (pp) REVERT: B 68 LYS cc_start: 0.9042 (mptt) cc_final: 0.8790 (mmtt) REVERT: B 72 GLU cc_start: 0.7916 (mp0) cc_final: 0.7662 (mp0) REVERT: B 153 MET cc_start: 0.9061 (OUTLIER) cc_final: 0.8773 (ttp) REVERT: B 314 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8113 (tp40) REVERT: D 47 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5469 (tpt) REVERT: D 64 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8744 (pp) REVERT: D 121 GLN cc_start: 0.8550 (tt0) cc_final: 0.8289 (tm-30) REVERT: D 292 ASP cc_start: 0.8737 (m-30) cc_final: 0.8501 (m-30) REVERT: D 314 GLN cc_start: 0.8981 (OUTLIER) cc_final: 0.8366 (tt0) REVERT: D 326 LYS cc_start: 0.8413 (tptt) cc_final: 0.7955 (pttm) REVERT: E 64 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.8884 (pp) REVERT: E 95 ARG cc_start: 0.7846 (mtt-85) cc_final: 0.7618 (mtt-85) REVERT: E 326 LYS cc_start: 0.8224 (tptt) cc_final: 0.7856 (tttm) outliers start: 29 outliers final: 11 residues processed: 208 average time/residue: 1.4855 time to fit residues: 338.0677 Evaluate side-chains 211 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 179 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN E 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.124701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097617 restraints weight = 19822.524| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 1.50 r_work: 0.2958 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14920 Z= 0.105 Angle : 0.575 7.834 20250 Z= 0.271 Chirality : 0.044 0.178 2245 Planarity : 0.003 0.037 2585 Dihedral : 11.874 173.122 2098 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.60 % Allowed : 11.03 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.20), residues: 1830 helix: 1.15 (0.19), residues: 775 sheet: 0.95 (0.27), residues: 345 loop : 2.13 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 PHE 0.006 0.001 PHE B 262 TYR 0.013 0.001 TYR A 143 ARG 0.010 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 715) hydrogen bonds : angle 4.34020 ( 1885) covalent geometry : bond 0.00230 (14920) covalent geometry : angle 0.57498 (20250) ********************** 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 229 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.601 Fit side-chains REVERT: C 47 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5849 (tpt) REVERT: C 51 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7747 (p0) REVERT: C 64 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 132 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8244 (tmt) REVERT: C 180 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8403 (tp) REVERT: A 180 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8673 (tt) REVERT: A 205 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8070 (mt-10) REVERT: B 47 MET cc_start: 0.4700 (mmt) cc_final: 0.4401 (tpt) REVERT: B 64 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 68 LYS cc_start: 0.9001 (mptt) cc_final: 0.8746 (mmtt) REVERT: B 72 GLU cc_start: 0.7851 (mp0) cc_final: 0.7628 (mp0) REVERT: B 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: D 47 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5416 (tpt) REVERT: D 64 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8702 (pp) REVERT: D 121 GLN cc_start: 0.8508 (tt0) cc_final: 0.8241 (tm-30) REVERT: D 222 ASP cc_start: 0.8487 (t70) cc_final: 0.8183 (t70) REVERT: D 292 ASP cc_start: 0.8667 (m-30) cc_final: 0.8449 (m-30) REVERT: D 314 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: D 326 LYS cc_start: 0.8389 (tptt) cc_final: 0.7926 (pttm) REVERT: E 47 MET cc_start: 0.5254 (OUTLIER) cc_final: 0.4549 (tpt) REVERT: E 64 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.8841 (pp) REVERT: E 95 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7618 (mtt-85) REVERT: E 326 LYS cc_start: 0.8241 (tptt) cc_final: 0.7945 (tttm) outliers start: 25 outliers final: 9 residues processed: 219 average time/residue: 1.4934 time to fit residues: 356.3545 Evaluate side-chains 216 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 152 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 178 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 ASN C 128 ASN C 225 GLN B 12 ASN B 128 ASN B 225 GLN B 246 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.095297 restraints weight = 17647.713| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.45 r_work: 0.2926 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14920 Z= 0.159 Angle : 0.618 8.343 20250 Z= 0.296 Chirality : 0.046 0.184 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.050 172.645 2098 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.92 % Allowed : 11.03 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1830 helix: 1.13 (0.19), residues: 770 sheet: 0.92 (0.27), residues: 345 loop : 2.09 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.010 0.001 PHE D 262 TYR 0.011 0.001 TYR A 143 ARG 0.010 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 715) hydrogen bonds : angle 4.46893 ( 1885) covalent geometry : bond 0.00362 (14920) covalent geometry : angle 0.61835 (20250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15582.09 seconds wall clock time: 269 minutes 6.33 seconds (16146.33 seconds total)