Starting phenix.real_space_refine on Mon Nov 18 03:47:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_16889.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_16889.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_16889.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_16889.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oid_16889/11_2024/8oid_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15206 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 370, 2883 Classifications: {'peptide': 370} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2937 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 159 Classifications: {'water': 159} Link IDs: {None: 158} Chain: "A" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "B" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "E" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 77 Classifications: {'water': 77} Link IDs: {None: 76} Restraints were copied for chains: C, B, E, D Time building chain proxies: 9.93, per 1000 atoms: 0.65 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: 4.25 Conformation dependent library (CDL) restraints added in 3.7 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: 2.02 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: 8.23 Time building geometry restraints manager: 4.78 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'B' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'C' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'D' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) selection = (chain 'E' and (resid 6 through 160 or resid 162 through 375 or resid 401 throug \ h 402)) } 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: 11.010 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: 0.000 Extract box with map and model: 1.400 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 42.810 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:12.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.600 ------------------------------------------------------------------------------- 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= 0.273 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 *********************** 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 : 1.793 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: 1.6276 time to fit residues: 505.8791 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 : 1.811 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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= 0.336 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 *********************** 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 : 1.928 Fit side-chains REVERT: C 47 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5934 (tpt) REVERT: C 51 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7158 (p0) REVERT: C 180 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8642 (tp) REVERT: A 180 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8708 (tt) REVERT: A 276 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: B 47 MET cc_start: 0.4349 (mmt) cc_final: 0.4049 (tpt) REVERT: B 153 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: D 47 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5169 (tpt) REVERT: D 180 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8683 (tt) REVERT: D 351 THR cc_start: 0.8955 (m) cc_final: 0.8665 (m) REVERT: D 353 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8214 (mm-40) REVERT: E 47 MET cc_start: 0.5320 (OUTLIER) cc_final: 0.4696 (tpt) REVERT: E 72 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6708 (mt-10) outliers start: 32 outliers final: 5 residues processed: 220 average time/residue: 1.5718 time to fit residues: 376.7239 Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 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 72 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14920 Z= 0.157 Angle : 0.574 7.957 20250 Z= 0.272 Chirality : 0.044 0.177 2245 Planarity : 0.004 0.036 2585 Dihedral : 11.881 173.885 2098 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.73 % Allowed : 9.17 % Favored : 89.10 % 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: 1.51 (0.20), residues: 1830 helix: 0.73 (0.19), residues: 775 sheet: 0.77 (0.26), residues: 345 loop : 1.79 (0.24), residues: 710 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 0.007 0.001 PHE D 262 TYR 0.012 0.001 TYR A 143 ARG 0.007 0.000 ARG E 28 *********************** 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 222 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.817 Fit side-chains REVERT: C 47 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5904 (tpt) REVERT: C 180 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8441 (tp) REVERT: A 180 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8690 (tt) REVERT: B 47 MET cc_start: 0.4340 (mmt) cc_final: 0.4037 (tpt) REVERT: B 64 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8932 (pp) REVERT: B 314 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7783 (tp40) REVERT: D 47 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.5119 (tpt) REVERT: D 351 THR cc_start: 0.8943 (m) cc_final: 0.8648 (m) REVERT: E 47 MET cc_start: 0.5343 (OUTLIER) cc_final: 0.4711 (tpt) outliers start: 27 outliers final: 4 residues processed: 211 average time/residue: 1.5923 time to fit residues: 365.6112 Evaluate side-chains 194 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 183 time to evaluate : 1.814 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 225 GLN A 128 ASN A 246 GLN B 12 ASN B 128 ASN B 225 GLN E 12 ASN E 78 ASN E 246 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 14920 Z= 0.504 Angle : 0.751 9.184 20250 Z= 0.372 Chirality : 0.053 0.182 2245 Planarity : 0.006 0.055 2585 Dihedral : 12.455 168.731 2098 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 9.62 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1830 helix: 0.56 (0.18), residues: 785 sheet: 0.83 (0.27), residues: 345 loop : 1.65 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 340 HIS 0.005 0.002 HIS B 88 PHE 0.016 0.002 PHE B 262 TYR 0.011 0.002 TYR D 143 ARG 0.009 0.001 ARG E 28 *********************** 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 217 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 2.192 Fit side-chains REVERT: C 47 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.6054 (tpt) REVERT: C 51 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7240 (p0) REVERT: C 180 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8734 (tp) REVERT: A 180 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8725 (tt) REVERT: A 276 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7410 (mm-30) REVERT: B 47 MET cc_start: 0.4417 (mmt) cc_final: 0.4128 (tpt) REVERT: B 153 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7906 (ttp) REVERT: B 286 ASP cc_start: 0.7440 (m-30) cc_final: 0.7178 (m-30) REVERT: B 314 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7763 (tp40) REVERT: D 47 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.5262 (tpt) REVERT: D 241 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: D 314 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8097 (tt0) outliers start: 31 outliers final: 8 residues processed: 204 average time/residue: 1.5866 time to fit residues: 353.9015 Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.851 ------------------------------------------------------------------------------- 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 C residue 351 THR Chi-restraints excluded: chain A residue 57 GLU 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 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 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 324 THR 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 148 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 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 E 12 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1681 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= 0.173 Angle : 0.592 8.176 20250 Z= 0.282 Chirality : 0.044 0.186 2245 Planarity : 0.004 0.037 2585 Dihedral : 12.001 173.628 2098 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.35 % Allowed : 10.45 % Favored : 88.21 % 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: 1.77 (0.20), residues: 1830 helix: 0.94 (0.19), residues: 775 sheet: 0.93 (0.27), residues: 345 loop : 1.92 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS B 88 PHE 0.008 0.001 PHE B 262 TYR 0.012 0.001 TYR A 143 ARG 0.009 0.000 ARG B 95 *********************** 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 212 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.793 Fit side-chains REVERT: C 47 MET cc_start: 0.6391 (OUTLIER) cc_final: 0.5952 (tpt) REVERT: C 51 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.7224 (p0) REVERT: C 64 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8525 (pp) REVERT: C 180 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 180 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8684 (tt) REVERT: A 276 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7390 (mm-30) REVERT: B 47 MET cc_start: 0.4430 (mmt) cc_final: 0.4149 (tpt) REVERT: B 64 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8943 (pp) REVERT: B 314 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7746 (tp40) REVERT: D 47 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.5223 (tpt) REVERT: E 47 MET cc_start: 0.5253 (OUTLIER) cc_final: 0.4722 (tpt) outliers start: 21 outliers final: 6 residues processed: 206 average time/residue: 1.4953 time to fit residues: 337.0015 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 : 1.869 ------------------------------------------------------------------------------- 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 C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 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 E residue 47 MET Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 E 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1682 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= 0.354 Angle : 0.677 8.820 20250 Z= 0.330 Chirality : 0.049 0.185 2245 Planarity : 0.005 0.041 2585 Dihedral : 12.253 171.368 2098 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.79 % Allowed : 10.83 % 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: 1.74 (0.20), residues: 1830 helix: 0.90 (0.19), residues: 770 sheet: 0.93 (0.27), residues: 345 loop : 1.91 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP C 340 HIS 0.005 0.001 HIS B 88 PHE 0.012 0.002 PHE B 262 TYR 0.011 0.001 TYR C 143 ARG 0.008 0.001 ARG E 28 *********************** 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 213 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.886 Fit side-chains REVERT: C 47 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5987 (tpt) REVERT: C 51 ASP cc_start: 0.7532 (OUTLIER) cc_final: 0.7267 (p0) REVERT: C 64 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8598 (pp) REVERT: C 180 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 180 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 276 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: B 47 MET cc_start: 0.4428 (mmt) cc_final: 0.4226 (tpt) REVERT: B 286 ASP cc_start: 0.7395 (m-30) cc_final: 0.7142 (m-30) REVERT: B 314 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: D 47 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5344 (tpt) REVERT: D 64 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8641 (pp) REVERT: D 241 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: E 64 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.8785 (pp) outliers start: 28 outliers final: 10 residues processed: 204 average time/residue: 1.5466 time to fit residues: 344.4844 Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 241 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 E 12 ASN E 78 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14920 Z= 0.252 Angle : 0.630 8.564 20250 Z= 0.303 Chirality : 0.046 0.185 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.142 172.859 2098 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.73 % Allowed : 11.15 % Favored : 87.12 % 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: 1.83 (0.20), residues: 1830 helix: 0.99 (0.19), residues: 770 sheet: 0.96 (0.27), residues: 345 loop : 1.95 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.010 0.001 PHE B 262 TYR 0.011 0.001 TYR A 143 ARG 0.009 0.001 ARG B 95 *********************** 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 213 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 1.723 Fit side-chains REVERT: C 47 MET cc_start: 0.6376 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: C 51 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7256 (p0) REVERT: C 64 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8568 (pp) REVERT: C 180 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8513 (tp) REVERT: A 180 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8700 (tt) REVERT: A 276 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7393 (mm-30) REVERT: B 47 MET cc_start: 0.4440 (mmt) cc_final: 0.4239 (tpt) REVERT: B 314 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7756 (tp40) REVERT: D 47 MET cc_start: 0.5630 (OUTLIER) cc_final: 0.5342 (tpt) REVERT: D 314 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8112 (tt0) REVERT: E 64 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8773 (pp) outliers start: 27 outliers final: 9 residues processed: 203 average time/residue: 1.5435 time to fit residues: 342.2865 Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 2.102 ------------------------------------------------------------------------------- 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 C residue 351 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain E residue 47 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.0980 chunk 121 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14920 Z= 0.137 Angle : 0.569 7.628 20250 Z= 0.266 Chirality : 0.043 0.176 2245 Planarity : 0.003 0.039 2585 Dihedral : 11.780 174.506 2098 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.22 % Allowed : 11.35 % 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: 2.11 (0.20), residues: 1830 helix: 1.17 (0.19), residues: 775 sheet: 1.12 (0.27), residues: 335 loop : 2.14 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.003 0.001 HIS D 275 PHE 0.006 0.001 PHE C 31 TYR 0.013 0.001 TYR A 143 ARG 0.010 0.000 ARG B 95 *********************** 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 219 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 1.777 Fit side-chains REVERT: C 47 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5949 (tpt) REVERT: C 64 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8520 (pp) REVERT: C 180 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8447 (tp) REVERT: B 47 MET cc_start: 0.4465 (mmt) cc_final: 0.4260 (tpt) REVERT: B 64 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.8863 (pp) REVERT: B 314 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.7729 (tp40) REVERT: D 47 MET cc_start: 0.5619 (OUTLIER) cc_final: 0.5321 (tpt) REVERT: D 64 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8599 (pp) REVERT: D 314 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: E 47 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4593 (tpt) outliers start: 19 outliers final: 3 residues processed: 214 average time/residue: 1.5430 time to fit residues: 360.3675 Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 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 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 E residue 47 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 0.0770 overall best weight: 1.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 128 ASN C 225 GLN A 128 ASN B 12 ASN B 128 ASN B 225 GLN D 12 ASN E 12 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14920 Z= 0.287 Angle : 0.643 8.530 20250 Z= 0.309 Chirality : 0.047 0.183 2245 Planarity : 0.004 0.039 2585 Dihedral : 12.089 172.429 2096 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.41 % Allowed : 11.54 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.20), residues: 1830 helix: 1.11 (0.19), residues: 770 sheet: 0.96 (0.27), residues: 345 loop : 2.09 (0.25), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 340 HIS 0.004 0.001 HIS B 88 PHE 0.011 0.001 PHE D 262 TYR 0.011 0.001 TYR C 143 ARG 0.009 0.001 ARG B 95 *********************** 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 209 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.815 Fit side-chains REVERT: C 47 MET cc_start: 0.6396 (OUTLIER) cc_final: 0.6007 (tpt) REVERT: C 64 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8602 (pp) REVERT: C 180 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8489 (tp) REVERT: B 47 MET cc_start: 0.4480 (mmt) cc_final: 0.4263 (tpt) REVERT: B 314 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7700 (tp40) REVERT: D 47 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5431 (tpt) REVERT: D 64 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8647 (pp) REVERT: D 241 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7697 (tt0) REVERT: D 314 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8108 (tt0) outliers start: 22 outliers final: 9 residues processed: 202 average time/residue: 1.6403 time to fit residues: 364.5124 Evaluate side-chains 201 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 241 GLU 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 175 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 83 optimal weight: 0.0050 chunk 122 optimal weight: 3.9990 chunk 184 optimal weight: 20.0000 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9396 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1811 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= 0.178 Angle : 0.593 8.082 20250 Z= 0.280 Chirality : 0.044 0.178 2245 Planarity : 0.004 0.037 2585 Dihedral : 11.920 173.037 2096 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.09 % Allowed : 12.05 % Favored : 86.86 % 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: 2.04 (0.20), residues: 1830 helix: 1.15 (0.19), residues: 775 sheet: 0.95 (0.27), residues: 345 loop : 2.17 (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 0.012 0.001 TYR A 143 ARG 0.010 0.000 ARG B 95 ********************** 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 202 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 1.777 Fit side-chains REVERT: C 47 MET cc_start: 0.6351 (OUTLIER) cc_final: 0.5967 (tpt) REVERT: C 64 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8563 (pp) REVERT: C 180 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8459 (tp) REVERT: B 314 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7723 (tp40) REVERT: D 47 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5406 (tpt) REVERT: D 64 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8643 (pp) REVERT: D 241 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: D 314 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.8126 (tt0) outliers start: 17 outliers final: 6 residues processed: 196 average time/residue: 1.5259 time to fit residues: 326.3919 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain A residue 57 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 171 LEU Chi-restraints excluded: chain D residue 241 GLU Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 323 SER 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 156 optimal weight: 0.2980 chunk 44 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.0030 chunk 61 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 = 0.3480 r_free = 0.3480 target = 0.124655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.096776 restraints weight = 19432.537| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.53 r_work: 0.2949 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.1857 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= 0.164 Angle : 0.583 7.801 20250 Z= 0.274 Chirality : 0.044 0.176 2245 Planarity : 0.003 0.038 2585 Dihedral : 11.810 173.826 2096 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.22 % Allowed : 11.86 % Favored : 86.92 % 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: 2.11 (0.20), residues: 1830 helix: 1.22 (0.19), residues: 775 sheet: 0.94 (0.27), residues: 345 loop : 2.21 (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 0.007 0.001 PHE B 262 TYR 0.012 0.001 TYR A 143 ARG 0.010 0.000 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.57 seconds wall clock time: 119 minutes 9.30 seconds (7149.30 seconds total)