Starting phenix.real_space_refine on Wed Mar 4 17:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.map" model { file = "/net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a2t_15106/03_2026/8a2t_15106.cif" } resolution = 2.24 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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 100 5.16 5 C 9145 2.51 5 N 2445 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15046 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 2870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2870 Classifications: {'peptide': 366} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "A" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "B" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Classifications: {'water': 113} Link IDs: {None: 112} Chain: "E" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 88 Classifications: {'water': 88} Link IDs: {None: 87} Restraints were copied for chains: A, B, D, E Time building chain proxies: 2.49, per 1000 atoms: 0.17 Number of scatterers: 15046 At special positions: 0 Unit cell: (96.605, 91.045, 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 100 16.00 P 10 15.00 Mg 5 11.99 O 3341 8.00 N 2445 7.00 C 9145 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 703.5 milliseconds 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3400 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 30 sheets defined 52.7% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 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 97 through 101 removed outlier: 3.631A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.008A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.797A 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 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 349 No H-bonds generated for 'chain 'C' and resid 348 through 349' Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.752A 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 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.629A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.009A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.796A 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 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 349 No H-bonds generated for 'chain 'A' and resid 348 through 349' Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.751A 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 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.631A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.008A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.797A 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 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 349 No H-bonds generated for 'chain 'B' and resid 348 through 349' Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.752A 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 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.630A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.009A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.550A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.797A 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 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 349 No H-bonds generated for 'chain 'D' and resid 348 through 349' Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.752A 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 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.630A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.010A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 removed outlier: 3.549A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 194 removed outlier: 3.797A 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 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 308 through 321 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 348 through 349 No H-bonds generated for 'chain 'E' and resid 348 through 349' Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.751A 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 Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.074A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 41 through 42 removed outlier: 4.074A pdb=" N GLN C 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.228A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.911A pdb=" N GLN E 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AA9, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'B' and resid 176 through 178 removed outlier: 6.228A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.180A pdb=" N GLN D 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.566A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.370A pdb=" N CYS 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: 6.228A pdb=" N ASN 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: 6.567A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N CYS 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: 6.228A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 238 through 241 743 hydrogen bonds defined for protein. 1878 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: 3.03 Time building geometry restraints manager: 1.54 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: 4701 1.34 - 1.46: 2868 1.46 - 1.57: 7046 1.57 - 1.69: 15 1.69 - 1.81: 175 Bond restraints: 14805 Sorted by residual: 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 7.79e+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 7.79e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.67e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.53e+00 ... (remaining 14800 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 19642 1.46 - 2.91: 312 2.91 - 4.37: 98 4.37 - 5.83: 28 5.83 - 7.28: 10 Bond angle restraints: 20090 Sorted by residual: angle pdb=" N VAL B 43 " pdb=" CA VAL B 43 " pdb=" C VAL B 43 " ideal model delta sigma weight residual 113.71 110.30 3.41 9.50e-01 1.11e+00 1.29e+01 angle pdb=" N VAL D 43 " pdb=" CA VAL D 43 " pdb=" C VAL D 43 " ideal model delta sigma weight residual 113.71 110.31 3.40 9.50e-01 1.11e+00 1.28e+01 angle pdb=" N VAL A 43 " pdb=" CA VAL A 43 " pdb=" C VAL A 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 113.71 110.36 3.35 9.50e-01 1.11e+00 1.24e+01 angle pdb=" N VAL C 43 " pdb=" CA VAL C 43 " pdb=" C VAL C 43 " ideal model delta sigma weight residual 113.71 110.37 3.34 9.50e-01 1.11e+00 1.24e+01 ... (remaining 20085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.63: 8790 33.63 - 67.27: 80 67.27 - 100.90: 30 100.90 - 134.54: 5 134.54 - 168.17: 5 Dihedral angle restraints: 8910 sinusoidal: 3610 harmonic: 5300 Sorted by residual: 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 -60.00 108.18 -168.17 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 108.16 -168.16 1 2.00e+01 2.50e-03 4.75e+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 -60.00 108.14 -168.14 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 8907 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1239 0.031 - 0.062: 696 0.062 - 0.094: 176 0.094 - 0.125: 113 0.125 - 0.156: 6 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C3' ADP B 401 " pdb=" C2' ADP B 401 " pdb=" C4' ADP B 401 " pdb=" O3' ADP B 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" C3' ADP E 401 " pdb=" C2' ADP E 401 " pdb=" C4' ADP E 401 " pdb=" O3' ADP E 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.79e-01 chirality pdb=" C3' ADP A 401 " pdb=" C2' ADP A 401 " pdb=" C4' ADP A 401 " pdb=" O3' ADP A 401 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.77e-01 ... (remaining 2227 not shown) Planarity restraints: 2565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 163 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO C 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO E 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO E 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO E 164 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 163 " -0.017 5.00e-02 4.00e+02 2.59e-02 1.08e+00 pdb=" N PRO A 164 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.014 5.00e-02 4.00e+02 ... (remaining 2562 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 133 2.48 - 3.09: 10361 3.09 - 3.69: 24256 3.69 - 4.30: 39521 4.30 - 4.90: 61090 Nonbonded interactions: 135361 Sorted by model distance: nonbonded pdb="MG MG E 402 " pdb=" O HOH E 522 " model vdw 1.880 2.170 nonbonded pdb="MG MG B 402 " pdb=" O HOH B 528 " model vdw 1.891 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 544 " model vdw 1.892 2.170 nonbonded pdb="MG MG D 402 " pdb=" O HOH D 536 " model vdw 1.925 2.170 nonbonded pdb="MG MG C 402 " pdb=" O HOH C 545 " model vdw 1.928 2.170 ... (remaining 135356 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.680 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.056 14805 Z= 0.174 Angle : 0.564 7.282 20090 Z= 0.286 Chirality : 0.044 0.156 2230 Planarity : 0.004 0.026 2565 Dihedral : 13.196 168.175 5510 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.19), residues: 1795 helix: -2.37 (0.14), residues: 785 sheet: -1.01 (0.25), residues: 305 loop : 0.95 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 177 TYR 0.009 0.001 TYR E 143 PHE 0.007 0.001 PHE E 262 TRP 0.013 0.002 TRP C 340 HIS 0.003 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.00387 (14805) covalent geometry : angle 0.56422 (20090) hydrogen bonds : bond 0.22866 ( 728) hydrogen bonds : angle 8.01184 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 246 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7078 (mp10) cc_final: 0.6659 (mp10) REVERT: B 41 GLN cc_start: 0.6963 (mp10) cc_final: 0.6663 (mp10) REVERT: B 72 GLU cc_start: 0.7419 (tp30) cc_final: 0.7020 (tp30) REVERT: B 121 GLN cc_start: 0.8126 (tt0) cc_final: 0.7901 (tt0) REVERT: B 123 MET cc_start: 0.8970 (mmt) cc_final: 0.8715 (mmp) REVERT: D 25 ASP cc_start: 0.7743 (p0) cc_final: 0.7349 (m-30) REVERT: D 41 GLN cc_start: 0.6559 (mp10) cc_final: 0.6338 (mp10) REVERT: E 41 GLN cc_start: 0.6894 (mp10) cc_final: 0.6554 (mp10) outliers start: 5 outliers final: 1 residues processed: 250 average time/residue: 0.7497 time to fit residues: 202.4488 Evaluate side-chains 188 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 178 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN A 225 ASN A 246 GLN A 354 GLN B 354 GLN D 40 HIS D 246 GLN D 353 GLN E 40 HIS E 88 HIS E 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.112074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092994 restraints weight = 15626.477| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.22 r_work: 0.2940 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14805 Z= 0.216 Angle : 0.655 9.302 20090 Z= 0.327 Chirality : 0.048 0.211 2230 Planarity : 0.004 0.039 2565 Dihedral : 12.203 167.397 2057 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.61 % Allowed : 6.97 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.19), residues: 1795 helix: -0.34 (0.17), residues: 775 sheet: -0.53 (0.26), residues: 315 loop : 1.73 (0.25), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.016 0.001 TYR E 143 PHE 0.017 0.002 PHE D 262 TRP 0.019 0.003 TRP C 340 HIS 0.004 0.001 HIS B 173 Details of bonding type rmsd covalent geometry : bond 0.00498 (14805) covalent geometry : angle 0.65525 (20090) hydrogen bonds : bond 0.05039 ( 728) hydrogen bonds : angle 5.29413 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 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: 25 poor density : 190 time to evaluate : 0.585 Fit side-chains REVERT: C 41 GLN cc_start: 0.7321 (mp10) cc_final: 0.7009 (mp10) REVERT: C 211 ASP cc_start: 0.8570 (t70) cc_final: 0.8316 (t70) REVERT: C 328 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8581 (tttt) REVERT: A 57 GLU cc_start: 0.8283 (tt0) cc_final: 0.7838 (pt0) REVERT: A 64 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.8608 (pp) REVERT: A 326 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8383 (mmtt) REVERT: B 41 GLN cc_start: 0.7348 (mp10) cc_final: 0.7012 (mp10) REVERT: B 57 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: B 72 GLU cc_start: 0.8070 (tp30) cc_final: 0.7724 (tp30) REVERT: B 354 GLN cc_start: 0.8365 (pt0) cc_final: 0.8052 (pm20) REVERT: D 25 ASP cc_start: 0.8346 (p0) cc_final: 0.7744 (m-30) REVERT: D 95 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7921 (mtp180) REVERT: E 41 GLN cc_start: 0.7354 (mp10) cc_final: 0.7015 (mp10) REVERT: E 50 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7584 (mtpt) REVERT: E 121 GLN cc_start: 0.8346 (tt0) cc_final: 0.8142 (tm-30) outliers start: 25 outliers final: 7 residues processed: 203 average time/residue: 0.7554 time to fit residues: 165.4547 Evaluate side-chains 186 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 160 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS A 225 ASN A 353 GLN A 354 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.114955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.096274 restraints weight = 15734.048| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.21 r_work: 0.3004 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14805 Z= 0.149 Angle : 0.593 8.329 20090 Z= 0.289 Chirality : 0.045 0.203 2230 Planarity : 0.004 0.039 2565 Dihedral : 12.003 171.032 2055 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.81 % Allowed : 7.55 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.20), residues: 1795 helix: 0.47 (0.18), residues: 775 sheet: -0.20 (0.25), residues: 345 loop : 2.03 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.011 0.001 TYR E 143 PHE 0.013 0.001 PHE D 262 TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00336 (14805) covalent geometry : angle 0.59296 (20090) hydrogen bonds : bond 0.03982 ( 728) hydrogen bonds : angle 4.89279 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 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: 28 poor density : 184 time to evaluate : 0.581 Fit side-chains REVERT: C 41 GLN cc_start: 0.7375 (mp10) cc_final: 0.7106 (mp10) REVERT: C 211 ASP cc_start: 0.8628 (t70) cc_final: 0.8346 (t70) REVERT: C 328 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8578 (tttt) REVERT: A 57 GLU cc_start: 0.8327 (tt0) cc_final: 0.7947 (pt0) REVERT: B 41 GLN cc_start: 0.7341 (mp10) cc_final: 0.7102 (mp10) REVERT: B 57 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: B 72 GLU cc_start: 0.8068 (tp30) cc_final: 0.7666 (tp30) REVERT: B 299 MET cc_start: 0.8775 (mtt) cc_final: 0.8552 (mtp) REVERT: B 354 GLN cc_start: 0.8386 (pt0) cc_final: 0.8086 (pm20) REVERT: D 25 ASP cc_start: 0.8300 (p0) cc_final: 0.7785 (m-30) REVERT: D 95 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7953 (mtp180) REVERT: D 351 THR cc_start: 0.8791 (m) cc_final: 0.8545 (m) REVERT: E 41 GLN cc_start: 0.7368 (mp10) cc_final: 0.7022 (mp10) REVERT: E 50 LYS cc_start: 0.7802 (mtmm) cc_final: 0.7597 (mtpt) REVERT: E 314 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8161 (tt0) outliers start: 28 outliers final: 6 residues processed: 201 average time/residue: 0.7269 time to fit residues: 157.8411 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 54 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.111762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092861 restraints weight = 15740.704| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.21 r_work: 0.2946 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14805 Z= 0.287 Angle : 0.698 9.716 20090 Z= 0.350 Chirality : 0.052 0.215 2230 Planarity : 0.005 0.044 2565 Dihedral : 12.380 165.090 2055 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.68 % Allowed : 8.26 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.20), residues: 1795 helix: 0.49 (0.18), residues: 790 sheet: -0.29 (0.27), residues: 315 loop : 1.71 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 210 TYR 0.013 0.002 TYR E 143 PHE 0.021 0.002 PHE D 262 TRP 0.023 0.004 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00668 (14805) covalent geometry : angle 0.69817 (20090) hydrogen bonds : bond 0.05128 ( 728) hydrogen bonds : angle 5.06023 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7380 (mp10) cc_final: 0.7144 (mp10) REVERT: C 64 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.8951 (pp) REVERT: C 121 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8144 (tt0) REVERT: C 328 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8570 (tttt) REVERT: A 57 GLU cc_start: 0.8396 (tt0) cc_final: 0.7860 (pt0) REVERT: A 64 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.8686 (pp) REVERT: B 41 GLN cc_start: 0.7267 (mp10) cc_final: 0.7010 (mp10) REVERT: B 72 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7706 (tp30) REVERT: B 299 MET cc_start: 0.8799 (mtt) cc_final: 0.8574 (mtp) REVERT: B 354 GLN cc_start: 0.8413 (pt0) cc_final: 0.8105 (pm20) REVERT: D 25 ASP cc_start: 0.8408 (p0) cc_final: 0.7848 (m-30) REVERT: D 64 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8844 (pp) REVERT: D 95 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7954 (mtp180) REVERT: E 41 GLN cc_start: 0.7346 (mp10) cc_final: 0.6946 (mp10) REVERT: E 314 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8140 (tt0) outliers start: 26 outliers final: 10 residues processed: 189 average time/residue: 0.7561 time to fit residues: 154.5797 Evaluate side-chains 191 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN A 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.093454 restraints weight = 15686.360| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.21 r_work: 0.2956 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14805 Z= 0.237 Angle : 0.661 9.304 20090 Z= 0.329 Chirality : 0.049 0.210 2230 Planarity : 0.004 0.044 2565 Dihedral : 12.292 166.146 2055 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.74 % Allowed : 8.65 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 1795 helix: 0.62 (0.19), residues: 790 sheet: -0.29 (0.27), residues: 315 loop : 1.75 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 177 TYR 0.012 0.001 TYR D 188 PHE 0.018 0.002 PHE D 262 TRP 0.021 0.003 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00550 (14805) covalent geometry : angle 0.66149 (20090) hydrogen bonds : bond 0.04697 ( 728) hydrogen bonds : angle 4.94676 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7381 (mp10) cc_final: 0.7161 (mp10) REVERT: C 64 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8949 (pp) REVERT: C 121 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: C 328 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8562 (tttt) REVERT: A 57 GLU cc_start: 0.8406 (tt0) cc_final: 0.7888 (pt0) REVERT: A 64 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.8702 (pp) REVERT: B 72 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7694 (tp30) REVERT: B 299 MET cc_start: 0.8791 (mtt) cc_final: 0.8582 (mtp) REVERT: B 354 GLN cc_start: 0.8382 (pt0) cc_final: 0.8098 (pm20) REVERT: D 25 ASP cc_start: 0.8368 (p0) cc_final: 0.7816 (m-30) REVERT: D 64 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8797 (pp) REVERT: D 95 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7973 (mtp180) REVERT: E 41 GLN cc_start: 0.7330 (mp10) cc_final: 0.6914 (mp10) REVERT: E 314 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8147 (tt0) outliers start: 27 outliers final: 10 residues processed: 188 average time/residue: 0.7389 time to fit residues: 150.3063 Evaluate side-chains 184 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 110 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.114176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.095601 restraints weight = 15631.982| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.20 r_work: 0.2992 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14805 Z= 0.140 Angle : 0.588 8.241 20090 Z= 0.286 Chirality : 0.045 0.201 2230 Planarity : 0.004 0.041 2565 Dihedral : 12.013 170.603 2055 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.23 % Allowed : 9.55 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.20), residues: 1795 helix: 0.95 (0.19), residues: 775 sheet: -0.10 (0.25), residues: 345 loop : 2.16 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.010 0.001 TYR B 143 PHE 0.011 0.001 PHE D 262 TRP 0.018 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00314 (14805) covalent geometry : angle 0.58819 (20090) hydrogen bonds : bond 0.03694 ( 728) hydrogen bonds : angle 4.69937 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.599 Fit side-chains REVERT: C 41 GLN cc_start: 0.7380 (mp10) cc_final: 0.7147 (mp10) REVERT: C 64 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8900 (pp) REVERT: C 121 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: C 211 ASP cc_start: 0.8631 (t70) cc_final: 0.8314 (t70) REVERT: C 328 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8578 (tttt) REVERT: A 41 GLN cc_start: 0.7636 (mm-40) cc_final: 0.7274 (mp10) REVERT: A 57 GLU cc_start: 0.8353 (tt0) cc_final: 0.7912 (pt0) REVERT: A 64 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.8698 (pp) REVERT: A 326 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (mmtt) REVERT: B 57 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7565 (pt0) REVERT: B 72 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: B 354 GLN cc_start: 0.8355 (pt0) cc_final: 0.8074 (pm20) REVERT: D 25 ASP cc_start: 0.8329 (p0) cc_final: 0.7817 (m-30) REVERT: D 95 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7996 (mtp180) REVERT: E 41 GLN cc_start: 0.7348 (mp10) cc_final: 0.6942 (mp10) REVERT: E 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8142 (tt0) outliers start: 19 outliers final: 8 residues processed: 191 average time/residue: 0.7534 time to fit residues: 155.8098 Evaluate side-chains 189 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 169 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.096427 restraints weight = 15539.375| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.20 r_work: 0.3005 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14805 Z= 0.123 Angle : 0.572 7.770 20090 Z= 0.275 Chirality : 0.044 0.199 2230 Planarity : 0.003 0.040 2565 Dihedral : 11.845 175.341 2055 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.55 % Allowed : 9.55 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1795 helix: 1.08 (0.19), residues: 775 sheet: -0.06 (0.26), residues: 345 loop : 2.25 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 28 TYR 0.009 0.001 TYR B 143 PHE 0.010 0.001 PHE D 262 TRP 0.016 0.002 TRP C 340 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00271 (14805) covalent geometry : angle 0.57187 (20090) hydrogen bonds : bond 0.03440 ( 728) hydrogen bonds : angle 4.58852 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.631 Fit side-chains REVERT: C 41 GLN cc_start: 0.7396 (mp10) cc_final: 0.7165 (mp10) REVERT: C 64 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8895 (pp) REVERT: C 121 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: C 211 ASP cc_start: 0.8618 (t70) cc_final: 0.8309 (t70) REVERT: C 328 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8593 (tttt) REVERT: A 41 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7302 (mp10) REVERT: A 57 GLU cc_start: 0.8318 (tt0) cc_final: 0.7917 (pt0) REVERT: A 64 ILE cc_start: 0.9369 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 326 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8417 (mmtt) REVERT: B 57 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: B 72 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7658 (tp30) REVERT: B 354 GLN cc_start: 0.8346 (pt0) cc_final: 0.8078 (pm20) REVERT: D 25 ASP cc_start: 0.8272 (p0) cc_final: 0.7744 (m-30) REVERT: D 64 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8894 (pp) REVERT: D 95 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7977 (mtp180) REVERT: E 41 GLN cc_start: 0.7382 (mp10) cc_final: 0.7008 (mp10) REVERT: E 314 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8175 (tt0) outliers start: 24 outliers final: 8 residues processed: 192 average time/residue: 0.7060 time to fit residues: 147.0655 Evaluate side-chains 192 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 174 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 164 optimal weight: 0.1980 chunk 139 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.114407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095713 restraints weight = 15706.851| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.21 r_work: 0.2994 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14805 Z= 0.140 Angle : 0.588 7.978 20090 Z= 0.285 Chirality : 0.045 0.200 2230 Planarity : 0.003 0.039 2565 Dihedral : 11.884 176.151 2055 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.48 % Allowed : 9.87 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.20), residues: 1795 helix: 1.07 (0.19), residues: 775 sheet: -0.04 (0.26), residues: 345 loop : 2.26 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 28 TYR 0.012 0.001 TYR B 143 PHE 0.011 0.001 PHE D 262 TRP 0.016 0.002 TRP C 340 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00315 (14805) covalent geometry : angle 0.58832 (20090) hydrogen bonds : bond 0.03661 ( 728) hydrogen bonds : angle 4.63528 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7407 (mp10) cc_final: 0.7173 (mp10) REVERT: C 64 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8894 (pp) REVERT: C 121 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: C 328 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8594 (tttt) REVERT: A 41 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7291 (mp10) REVERT: A 57 GLU cc_start: 0.8333 (tt0) cc_final: 0.7925 (pt0) REVERT: A 64 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.8672 (pp) REVERT: B 57 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: B 72 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: B 354 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: D 25 ASP cc_start: 0.8308 (p0) cc_final: 0.7793 (m-30) REVERT: D 64 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8842 (pp) REVERT: D 95 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7999 (mtp180) REVERT: E 41 GLN cc_start: 0.7401 (mp10) cc_final: 0.7021 (mp10) REVERT: E 314 GLN cc_start: 0.8916 (OUTLIER) cc_final: 0.8195 (tt0) outliers start: 23 outliers final: 10 residues processed: 191 average time/residue: 0.7232 time to fit residues: 149.6056 Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 121 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.093903 restraints weight = 15624.230| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.21 r_work: 0.2962 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14805 Z= 0.219 Angle : 0.650 8.726 20090 Z= 0.322 Chirality : 0.048 0.211 2230 Planarity : 0.004 0.039 2565 Dihedral : 12.219 170.875 2055 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.42 % Allowed : 10.06 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.20), residues: 1795 helix: 0.83 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 315 loop : 1.90 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 28 TYR 0.011 0.001 TYR D 188 PHE 0.017 0.002 PHE D 262 TRP 0.019 0.003 TRP C 340 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00507 (14805) covalent geometry : angle 0.64952 (20090) hydrogen bonds : bond 0.04474 ( 728) hydrogen bonds : angle 4.84074 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7363 (mp10) cc_final: 0.7128 (mp10) REVERT: C 64 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8936 (pp) REVERT: C 121 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: C 328 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8558 (tttt) REVERT: A 41 GLN cc_start: 0.7621 (mm-40) cc_final: 0.7268 (mp10) REVERT: A 57 GLU cc_start: 0.8379 (tt0) cc_final: 0.7897 (pt0) REVERT: A 64 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 72 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7666 (tp30) REVERT: B 354 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: D 25 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: D 64 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8867 (pp) REVERT: D 95 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7989 (mtp180) REVERT: E 41 GLN cc_start: 0.7413 (mp10) cc_final: 0.7011 (mp10) REVERT: E 57 GLU cc_start: 0.8161 (pt0) cc_final: 0.7931 (pt0) REVERT: E 314 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8135 (tt0) outliers start: 22 outliers final: 11 residues processed: 188 average time/residue: 0.7379 time to fit residues: 150.5552 Evaluate side-chains 195 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 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 225 ASN A 225 ASN D 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096093 restraints weight = 15733.721| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.23 r_work: 0.2996 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14805 Z= 0.112 Angle : 0.566 7.645 20090 Z= 0.272 Chirality : 0.044 0.193 2230 Planarity : 0.003 0.039 2565 Dihedral : 11.791 175.589 2055 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.23 % Allowed : 10.13 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.20), residues: 1795 helix: 1.15 (0.19), residues: 775 sheet: -0.03 (0.26), residues: 345 loop : 2.28 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 28 TYR 0.014 0.001 TYR B 143 PHE 0.009 0.001 PHE E 31 TRP 0.016 0.002 TRP B 79 HIS 0.003 0.001 HIS E 87 Details of bonding type rmsd covalent geometry : bond 0.00246 (14805) covalent geometry : angle 0.56640 (20090) hydrogen bonds : bond 0.03253 ( 728) hydrogen bonds : angle 4.53964 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3590 Ramachandran restraints generated. 1795 Oldfield, 0 Emsley, 1795 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: C 41 GLN cc_start: 0.7386 (mp10) cc_final: 0.7136 (mp10) REVERT: C 64 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8857 (pp) REVERT: C 121 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: C 328 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8603 (tttt) REVERT: A 41 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7253 (mp10) REVERT: A 44 MET cc_start: 0.8191 (mtp) cc_final: 0.7986 (mtt) REVERT: A 57 GLU cc_start: 0.8306 (tt0) cc_final: 0.7895 (pt0) REVERT: A 64 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8650 (pp) REVERT: A 326 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8402 (mmtt) REVERT: B 57 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7464 (pt0) REVERT: B 72 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7639 (tp30) REVERT: B 354 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: D 25 ASP cc_start: 0.8301 (p0) cc_final: 0.7779 (m-30) REVERT: D 64 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8847 (pp) REVERT: D 72 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: D 95 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8061 (mtp180) REVERT: E 41 GLN cc_start: 0.7414 (mp10) cc_final: 0.7008 (mp10) REVERT: E 314 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8212 (tt0) outliers start: 19 outliers final: 7 residues processed: 190 average time/residue: 0.7289 time to fit residues: 150.1476 Evaluate side-chains 193 residues out of total 1550 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 88 HIS Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain C residue 328 LYS Chi-restraints excluded: chain C residue 374 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 88 HIS Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 72 GLU Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN D 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.092233 restraints weight = 15670.021| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.23 r_work: 0.2932 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14805 Z= 0.272 Angle : 0.692 9.110 20090 Z= 0.345 Chirality : 0.051 0.214 2230 Planarity : 0.004 0.040 2565 Dihedral : 12.351 169.127 2055 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.48 % Allowed : 10.13 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.20), residues: 1795 helix: 0.78 (0.19), residues: 790 sheet: -0.22 (0.27), residues: 315 loop : 1.89 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 28 TYR 0.013 0.002 TYR D 188 PHE 0.019 0.002 PHE D 262 TRP 0.022 0.003 TRP C 340 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00635 (14805) covalent geometry : angle 0.69161 (20090) hydrogen bonds : bond 0.04888 ( 728) hydrogen bonds : angle 4.91743 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6042.36 seconds wall clock time: 103 minutes 33.82 seconds (6213.82 seconds total)