Starting phenix.real_space_refine on Sat May 17 06:38:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oid_16889/05_2025/8oid_16889.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oid_16889/05_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_16889/05_2025/8oid_16889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oid_16889/05_2025/8oid_16889.map" model { file = "/net/cci-nas-00/data/ceres_data/8oid_16889/05_2025/8oid_16889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oid_16889/05_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-5687/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: 8.16, per 1000 atoms: 0.54 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: 3.65 Conformation dependent library (CDL) restraints added in 3.8 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: 2.06 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: 5.30 Time building geometry restraints manager: 4.20 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: 2.860 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.540 Find NCS groups from input model: 0.330 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:10.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.210 ------------------------------------------------------------------------------- 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 : 1.632 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: 1.5202 time to fit residues: 473.3423 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 : 1.609 ------------------------------------------------------------------------------- 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 = 0.092729 restraints weight = 18592.073| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.47 r_work: 0.2873 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 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 : 1.784 Fit side-chains REVERT: C 47 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5720 (tpt) REVERT: C 180 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8619 (tp) REVERT: A 180 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8649 (tt) REVERT: A 276 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8151 (mm-30) REVERT: B 47 MET cc_start: 0.4544 (mmt) cc_final: 0.4158 (tpt) REVERT: B 68 LYS cc_start: 0.9014 (mptt) cc_final: 0.8795 (mmtt) REVERT: B 153 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8710 (ttp) REVERT: D 47 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5147 (tpt) REVERT: D 121 GLN cc_start: 0.8438 (tt0) cc_final: 0.8208 (tm-30) REVERT: D 180 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8687 (tt) REVERT: D 326 LYS cc_start: 0.8395 (tptt) cc_final: 0.7921 (pttm) REVERT: D 351 THR cc_start: 0.9066 (m) cc_final: 0.8769 (m) REVERT: D 353 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8152 (mm-40) REVERT: E 47 MET cc_start: 0.5408 (OUTLIER) cc_final: 0.4612 (tpt) REVERT: E 132 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8126 (ttp) outliers start: 32 outliers final: 5 residues processed: 220 average time/residue: 1.4207 time to fit residues: 341.5069 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 : 1.880 ------------------------------------------------------------------------------- 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: 8.9990 chunk 9 optimal weight: 6.9990 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: 0.0040 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 overall best weight: 2.3398 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.120284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092593 restraints weight = 24717.877| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.71 r_work: 0.2841 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2693 r_free = 0.2693 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 = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 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 : 0.005 0.050 14920 Z= 0.214 Angle : 0.659 8.780 20250 Z= 0.322 Chirality : 0.048 0.186 2245 Planarity : 0.005 0.041 2585 Dihedral : 12.232 172.341 2098 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.92 % Allowed : 8.78 % Favored : 89.29 % 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: 1.38 (0.20), residues: 1830 helix: 0.61 (0.19), residues: 770 sheet: 0.80 (0.26), residues: 345 loop : 1.69 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.013 0.002 PHE D 262 TYR 0.013 0.001 TYR A 143 ARG 0.008 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.04645 ( 715) hydrogen bonds : angle 4.77539 ( 1885) covalent geometry : bond 0.00496 (14920) covalent geometry : angle 0.65938 (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 228 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.765 Fit side-chains REVERT: C 47 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5786 (tpt) REVERT: C 180 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8624 (tp) REVERT: A 64 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9103 (pp) REVERT: A 180 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8630 (tt) REVERT: A 205 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8381 (mt-10) REVERT: A 276 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: B 47 MET cc_start: 0.4592 (mmt) cc_final: 0.4197 (tpt) REVERT: B 64 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9077 (pp) REVERT: B 68 LYS cc_start: 0.9031 (mptt) cc_final: 0.8803 (mmtt) REVERT: B 72 GLU cc_start: 0.7972 (mp0) cc_final: 0.7727 (mp0) REVERT: B 153 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8785 (ttp) REVERT: B 314 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8162 (tp40) REVERT: D 47 MET cc_start: 0.5705 (OUTLIER) cc_final: 0.5195 (tpt) REVERT: D 121 GLN cc_start: 0.8565 (tt0) cc_final: 0.8295 (tm-30) REVERT: D 292 ASP cc_start: 0.8762 (m-30) cc_final: 0.8537 (m-30) REVERT: D 326 LYS cc_start: 0.8460 (tptt) cc_final: 0.7978 (pttm) REVERT: D 351 THR cc_start: 0.9042 (m) cc_final: 0.8785 (m) REVERT: D 353 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8278 (mm110) REVERT: E 47 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4637 (tpt) REVERT: E 64 ILE cc_start: 0.9410 (OUTLIER) cc_final: 0.8890 (pp) REVERT: E 95 ARG cc_start: 0.7908 (mtt-85) cc_final: 0.7654 (mtt-85) outliers start: 30 outliers final: 6 residues processed: 217 average time/residue: 1.4600 time to fit residues: 345.4189 Evaluate side-chains 205 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 205 GLU 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 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 81 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 145 optimal weight: 0.1980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 E 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094716 restraints weight = 30873.514| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.94 r_work: 0.2868 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14920 Z= 0.119 Angle : 0.592 8.098 20250 Z= 0.281 Chirality : 0.044 0.183 2245 Planarity : 0.004 0.037 2585 Dihedral : 11.967 173.748 2098 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.35 % Allowed : 10.19 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.20), residues: 1830 helix: 0.88 (0.19), residues: 775 sheet: 0.90 (0.26), residues: 345 loop : 1.88 (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 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 0.03441 ( 715) hydrogen bonds : angle 4.49962 ( 1885) covalent geometry : bond 0.00264 (14920) covalent geometry : angle 0.59162 (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 222 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 2.025 Fit side-chains REVERT: C 47 MET cc_start: 0.6373 (OUTLIER) cc_final: 0.5896 (tpt) REVERT: C 180 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8436 (tp) REVERT: A 180 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 205 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: B 47 MET cc_start: 0.4664 (mmt) cc_final: 0.4263 (tpt) REVERT: B 64 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9000 (pp) REVERT: B 68 LYS cc_start: 0.9052 (mptt) cc_final: 0.8813 (mmtt) REVERT: B 72 GLU cc_start: 0.8012 (mp0) cc_final: 0.7791 (mp0) REVERT: B 314 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8163 (tp40) REVERT: D 47 MET cc_start: 0.5732 (OUTLIER) cc_final: 0.5207 (tpt) REVERT: D 64 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8739 (pp) REVERT: D 121 GLN cc_start: 0.8615 (tt0) cc_final: 0.8329 (tm-30) REVERT: D 292 ASP cc_start: 0.8778 (m-30) cc_final: 0.8568 (m-30) REVERT: D 326 LYS cc_start: 0.8477 (tptt) cc_final: 0.7915 (pttm) REVERT: D 351 THR cc_start: 0.9038 (m) cc_final: 0.8753 (m) REVERT: D 353 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8288 (mm-40) REVERT: E 47 MET cc_start: 0.5449 (OUTLIER) cc_final: 0.4693 (tpt) REVERT: E 95 ARG cc_start: 0.7937 (mtt-85) cc_final: 0.7703 (mtt-85) outliers start: 21 outliers final: 3 residues processed: 215 average time/residue: 1.5284 time to fit residues: 358.2060 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.653 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain B residue 64 ILE 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 E residue 47 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 154 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.094960 restraints weight = 22287.309| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.65 r_work: 0.2916 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2774 r_free = 0.2774 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 = 0.2774 r_free = 0.2774 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14920 Z= 0.117 Angle : 0.581 7.880 20250 Z= 0.274 Chirality : 0.044 0.177 2245 Planarity : 0.004 0.036 2585 Dihedral : 11.888 174.401 2098 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.67 % Allowed : 10.38 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 775 sheet: 0.96 (0.26), residues: 345 loop : 2.01 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS B 88 PHE 0.007 0.001 PHE D 262 TYR 0.013 0.001 TYR A 143 ARG 0.008 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 715) hydrogen bonds : angle 4.40025 ( 1885) covalent geometry : bond 0.00259 (14920) covalent geometry : angle 0.58085 (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 223 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.679 Fit side-chains REVERT: C 47 MET cc_start: 0.6311 (OUTLIER) cc_final: 0.5814 (tpt) REVERT: C 180 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 180 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8659 (tt) REVERT: B 47 MET cc_start: 0.4678 (mmt) cc_final: 0.4293 (tpt) REVERT: B 64 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 68 LYS cc_start: 0.9003 (mptt) cc_final: 0.8753 (mmtt) REVERT: B 72 GLU cc_start: 0.7901 (mp0) cc_final: 0.7633 (mp0) REVERT: B 314 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8092 (tp40) REVERT: D 47 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5206 (tpt) REVERT: D 64 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8709 (pp) REVERT: D 121 GLN cc_start: 0.8548 (tt0) cc_final: 0.8281 (tm-30) REVERT: D 222 ASP cc_start: 0.8536 (t70) cc_final: 0.8248 (t70) REVERT: D 292 ASP cc_start: 0.8697 (m-30) cc_final: 0.8464 (m-30) REVERT: D 314 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: D 326 LYS cc_start: 0.8414 (tptt) cc_final: 0.7917 (pttm) REVERT: D 351 THR cc_start: 0.9025 (m) cc_final: 0.8718 (m) REVERT: E 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8828 (pp) REVERT: E 95 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7677 (mtt-85) REVERT: E 326 LYS cc_start: 0.8218 (tptt) cc_final: 0.7877 (tttm) REVERT: E 351 THR cc_start: 0.9135 (p) cc_final: 0.8934 (t) outliers start: 26 outliers final: 6 residues processed: 217 average time/residue: 1.4281 time to fit residues: 338.2883 Evaluate side-chains 204 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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 A residue 171 LEU Chi-restraints excluded: chain A residue 180 LEU 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 D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 44 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.119471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.091483 restraints weight = 21754.976| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.57 r_work: 0.2841 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 14920 Z= 0.286 Angle : 0.713 9.060 20250 Z= 0.350 Chirality : 0.051 0.184 2245 Planarity : 0.005 0.048 2585 Dihedral : 12.363 169.607 2098 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.05 % Allowed : 10.38 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.20), residues: 1830 helix: 0.84 (0.19), residues: 770 sheet: 0.91 (0.27), residues: 345 loop : 1.92 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.014 0.002 PHE B 262 TYR 0.010 0.002 TYR D 143 ARG 0.008 0.001 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.05124 ( 715) hydrogen bonds : angle 4.78459 ( 1885) covalent geometry : bond 0.00670 (14920) covalent geometry : angle 0.71335 (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 221 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.744 Fit side-chains REVERT: C 47 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5862 (tpt) REVERT: C 51 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7825 (p0) REVERT: C 180 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8651 (tp) REVERT: A 64 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 180 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8682 (tt) REVERT: A 276 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8174 (mm-30) REVERT: B 47 MET cc_start: 0.4645 (mmt) cc_final: 0.4328 (tpt) REVERT: B 68 LYS cc_start: 0.9077 (mptt) cc_final: 0.8832 (mmtt) REVERT: B 153 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8758 (ttp) REVERT: B 286 ASP cc_start: 0.8120 (m-30) cc_final: 0.7738 (m-30) REVERT: B 314 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8071 (tp40) REVERT: D 47 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5317 (tpt) REVERT: D 64 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8769 (pp) REVERT: D 121 GLN cc_start: 0.8493 (tt0) cc_final: 0.8235 (tm-30) REVERT: D 292 ASP cc_start: 0.8761 (m-30) cc_final: 0.8536 (m-30) REVERT: D 314 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8371 (tt0) REVERT: D 326 LYS cc_start: 0.8456 (tptt) cc_final: 0.8008 (pttm) REVERT: E 326 LYS cc_start: 0.8201 (tptt) cc_final: 0.7869 (tttm) outliers start: 32 outliers final: 10 residues processed: 211 average time/residue: 1.4399 time to fit residues: 332.1035 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 : 1.767 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 57 GLU 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 153 MET Chi-restraints excluded: chain B residue 171 LEU 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 D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 97 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 150 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.123147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095484 restraints weight = 20953.819| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.55 r_work: 0.2918 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2772 r_free = 0.2772 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 = 0.2772 r_free = 0.2772 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14920 Z= 0.115 Angle : 0.590 8.075 20250 Z= 0.279 Chirality : 0.044 0.186 2245 Planarity : 0.003 0.037 2585 Dihedral : 11.960 173.364 2098 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.35 % Allowed : 11.09 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.20), residues: 1830 helix: 1.05 (0.19), residues: 775 sheet: 0.92 (0.27), residues: 345 loop : 2.07 (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 B 88 PHE 0.008 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.010 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 715) hydrogen bonds : angle 4.42486 ( 1885) covalent geometry : bond 0.00255 (14920) covalent geometry : angle 0.59038 (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 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 1.794 Fit side-chains REVERT: C 47 MET cc_start: 0.6274 (OUTLIER) cc_final: 0.5791 (tpt) REVERT: C 180 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 180 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8672 (tt) REVERT: B 47 MET cc_start: 0.4672 (mmt) cc_final: 0.4370 (tpt) REVERT: B 64 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8986 (pp) REVERT: B 68 LYS cc_start: 0.8999 (mptt) cc_final: 0.8758 (mmtt) REVERT: B 314 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8099 (tp40) REVERT: D 47 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.5308 (tpt) REVERT: D 64 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8733 (pp) REVERT: D 121 GLN cc_start: 0.8519 (tt0) cc_final: 0.8259 (tm-30) REVERT: D 222 ASP cc_start: 0.8516 (t70) cc_final: 0.8242 (t70) REVERT: D 292 ASP cc_start: 0.8681 (m-30) cc_final: 0.8479 (m-30) REVERT: D 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8385 (tt0) REVERT: D 326 LYS cc_start: 0.8399 (tptt) cc_final: 0.7937 (pttm) REVERT: E 47 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.4611 (tpt) REVERT: E 95 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7635 (mtt-85) REVERT: E 326 LYS cc_start: 0.8216 (tptt) cc_final: 0.7851 (tttm) outliers start: 21 outliers final: 7 residues processed: 209 average time/residue: 1.4835 time to fit residues: 337.7390 Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.681 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 9.9990 chunk 167 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 32 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.123850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.096862 restraints weight = 23730.949| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.60 r_work: 0.2926 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 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 = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14920 Z= 0.125 Angle : 0.593 8.028 20250 Z= 0.281 Chirality : 0.044 0.179 2245 Planarity : 0.004 0.038 2585 Dihedral : 11.943 173.392 2098 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.47 % Allowed : 11.03 % 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: 1.99 (0.20), residues: 1830 helix: 1.12 (0.19), residues: 775 sheet: 0.94 (0.27), residues: 345 loop : 2.12 (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 D 275 PHE 0.008 0.001 PHE B 262 TYR 0.011 0.001 TYR B 143 ARG 0.010 0.000 ARG E 28 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 715) hydrogen bonds : angle 4.40331 ( 1885) covalent geometry : bond 0.00278 (14920) covalent geometry : angle 0.59297 (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 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 1.830 Fit side-chains REVERT: C 47 MET cc_start: 0.6301 (OUTLIER) cc_final: 0.5842 (tpt) REVERT: C 180 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 180 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8658 (tt) REVERT: B 47 MET cc_start: 0.4681 (mmt) cc_final: 0.4384 (tpt) REVERT: B 64 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8946 (pp) REVERT: B 68 LYS cc_start: 0.9015 (mptt) cc_final: 0.8756 (mmtt) REVERT: B 314 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8076 (tp40) REVERT: D 47 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5314 (tpt) REVERT: D 64 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8705 (pp) REVERT: D 121 GLN cc_start: 0.8526 (tt0) cc_final: 0.8258 (tm-30) REVERT: D 222 ASP cc_start: 0.8508 (t70) cc_final: 0.8231 (t70) REVERT: D 292 ASP cc_start: 0.8697 (m-30) cc_final: 0.8462 (m-30) REVERT: D 314 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8357 (tt0) REVERT: D 326 LYS cc_start: 0.8405 (tptt) cc_final: 0.7928 (pttm) REVERT: E 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8867 (pp) REVERT: E 95 ARG cc_start: 0.7859 (mtt-85) cc_final: 0.7639 (mtt-85) REVERT: E 326 LYS cc_start: 0.8245 (tptt) cc_final: 0.7942 (tttm) outliers start: 23 outliers final: 8 residues processed: 203 average time/residue: 1.4480 time to fit residues: 321.2155 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 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 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 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: 0.7980 chunk 158 optimal weight: 0.0770 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 D 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096647 restraints weight = 24694.777| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.61 r_work: 0.2923 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 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 = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.1766 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= 0.133 Angle : 0.598 8.090 20250 Z= 0.284 Chirality : 0.045 0.180 2245 Planarity : 0.004 0.038 2585 Dihedral : 11.965 173.480 2098 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 2.00 (0.20), residues: 1830 helix: 1.12 (0.19), residues: 775 sheet: 0.93 (0.27), residues: 345 loop : 2.14 (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 0.011 0.001 TYR C 143 ARG 0.009 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 715) hydrogen bonds : angle 4.41394 ( 1885) covalent geometry : bond 0.00299 (14920) covalent geometry : angle 0.59798 (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 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 1.838 Fit side-chains REVERT: C 47 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5871 (tpt) REVERT: C 51 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7766 (p0) REVERT: C 64 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8618 (pp) REVERT: C 180 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8435 (tp) REVERT: A 180 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8666 (tt) REVERT: B 47 MET cc_start: 0.4706 (mmt) cc_final: 0.4430 (tpt) REVERT: B 64 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.8952 (pp) REVERT: B 68 LYS cc_start: 0.9015 (mptt) cc_final: 0.8758 (mmtt) REVERT: B 314 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8069 (tp40) REVERT: D 47 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5331 (tpt) REVERT: D 64 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8732 (pp) REVERT: D 121 GLN cc_start: 0.8511 (tt0) cc_final: 0.8258 (tm-30) REVERT: D 222 ASP cc_start: 0.8517 (t70) cc_final: 0.8233 (t70) REVERT: D 292 ASP cc_start: 0.8709 (m-30) cc_final: 0.8476 (m-30) REVERT: D 314 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: D 326 LYS cc_start: 0.8412 (tptt) cc_final: 0.7957 (pttm) REVERT: E 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8876 (pp) REVERT: E 95 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7629 (mtt-85) REVERT: E 326 LYS cc_start: 0.8240 (tptt) cc_final: 0.7875 (tttm) outliers start: 25 outliers final: 9 residues processed: 205 average time/residue: 1.4183 time to fit residues: 317.4359 Evaluate side-chains 206 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 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 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE 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: 0.2980 chunk 89 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 170 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 179 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.125985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098035 restraints weight = 20760.440| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.57 r_work: 0.2969 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2825 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2825 r_free = 0.2825 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 = 0.2825 r_free = 0.2825 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2825 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14920 Z= 0.094 Angle : 0.563 7.445 20250 Z= 0.263 Chirality : 0.043 0.174 2245 Planarity : 0.003 0.038 2585 Dihedral : 11.674 174.514 2098 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.41 % Allowed : 11.15 % Favored : 87.44 % 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: 2.14 (0.20), residues: 1830 helix: 1.24 (0.20), residues: 775 sheet: 1.00 (0.27), residues: 335 loop : 2.19 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 PHE 0.006 0.001 PHE D 31 TYR 0.011 0.001 TYR B 143 ARG 0.010 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.02814 ( 715) hydrogen bonds : angle 4.24001 ( 1885) covalent geometry : bond 0.00202 (14920) covalent geometry : angle 0.56269 (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 215 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 1.885 Fit side-chains REVERT: C 47 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5872 (tpt) REVERT: C 51 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7742 (p0) REVERT: C 180 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8357 (tp) REVERT: B 47 MET cc_start: 0.4606 (mmt) cc_final: 0.4352 (tpt) REVERT: B 64 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 68 LYS cc_start: 0.8992 (mptt) cc_final: 0.8746 (mmtt) REVERT: B 314 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8056 (tp40) REVERT: D 47 MET cc_start: 0.5674 (OUTLIER) cc_final: 0.5328 (tpt) REVERT: D 64 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8685 (pp) REVERT: D 121 GLN cc_start: 0.8536 (tt0) cc_final: 0.8283 (tm-30) REVERT: D 222 ASP cc_start: 0.8485 (t70) cc_final: 0.8177 (t70) REVERT: D 292 ASP cc_start: 0.8681 (m-30) cc_final: 0.8468 (m-30) REVERT: D 314 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: D 326 LYS cc_start: 0.8405 (tptt) cc_final: 0.7952 (pttm) REVERT: E 95 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7619 (mtt-85) REVERT: E 326 LYS cc_start: 0.8250 (tptt) cc_final: 0.7943 (tttm) outliers start: 22 outliers final: 8 residues processed: 207 average time/residue: 1.4852 time to fit residues: 334.9877 Evaluate side-chains 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 B residue 64 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 276 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 152 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 123 optimal weight: 0.8980 chunk 178 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.094679 restraints weight = 16648.073| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.40 r_work: 0.2916 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- 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 = 0.36 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: 0.8767 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14920 Z= 0.201 Angle : 0.660 8.527 20250 Z= 0.318 Chirality : 0.047 0.187 2245 Planarity : 0.004 0.038 2585 Dihedral : 12.143 171.861 2096 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.22 % Allowed : 11.54 % 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: 1.94 (0.20), residues: 1830 helix: 1.10 (0.19), residues: 770 sheet: 0.86 (0.27), residues: 345 loop : 2.08 (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 0.012 0.001 PHE D 262 TYR 0.011 0.001 TYR C 143 ARG 0.010 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 715) hydrogen bonds : angle 4.55979 ( 1885) covalent geometry : bond 0.00463 (14920) covalent geometry : angle 0.65971 (20250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14763.49 seconds wall clock time: 254 minutes 19.99 seconds (15259.99 seconds total)