Starting phenix.real_space_refine on Tue Nov 18 15:17:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t24_10366/11_2025/6t24_10366.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 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 15 5.49 5 Mg 5 5.21 5 S 105 5.16 5 C 9425 2.51 5 N 2495 2.21 5 O 2865 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {' MG': 1, '9ZK': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D, E Time building chain proxies: 3.09, per 1000 atoms: 0.21 Number of scatterers: 14910 At special positions: 0 Unit cell: (96.32, 92.96, 192.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 105 16.00 P 15 15.00 Mg 5 11.99 O 2865 8.00 N 2495 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 674.1 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 30 sheets defined 53.6% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.214A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 181 through 193 Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.921A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 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 296 removed outlier: 4.421A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.605A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) 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 348 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 372 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.214A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 removed outlier: 3.921A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 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 296 removed outlier: 4.422A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.606A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) 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 348 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.214A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 193 Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.921A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 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 296 removed outlier: 4.422A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.605A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) 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 348 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 367 through 372 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.215A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 removed outlier: 3.921A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 237 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 296 removed outlier: 4.422A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.605A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) 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 348 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 78 through 92 Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.214A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 146 Processing helix chain 'E' and resid 172 through 175 Processing helix chain 'E' and resid 181 through 193 Processing helix chain 'E' and resid 194 through 197 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 removed outlier: 3.920A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 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 296 removed outlier: 4.421A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.605A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) 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 348 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 6.600A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.142A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.141A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.141A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.599A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.399A 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: 6.600A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.502A 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: 6.141A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.400A 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 241 765 hydrogen bonds defined for protein. 1875 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2478 1.29 - 1.43: 3885 1.43 - 1.56: 8566 1.56 - 1.69: 126 1.69 - 1.83: 185 Bond restraints: 15240 Sorted by residual: bond pdb=" C22 9ZK E 379 " pdb=" N23 9ZK E 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 8.03e+01 bond pdb=" C22 9ZK D 379 " pdb=" N23 9ZK D 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 8.01e+01 bond pdb=" C22 9ZK C 379 " pdb=" N23 9ZK C 379 " ideal model delta sigma weight residual 1.350 1.529 -0.179 2.00e-02 2.50e+03 7.99e+01 bond pdb=" C22 9ZK B 379 " pdb=" N23 9ZK B 379 " ideal model delta sigma weight residual 1.350 1.528 -0.178 2.00e-02 2.50e+03 7.96e+01 bond pdb=" C22 9ZK A 379 " pdb=" N23 9ZK A 379 " ideal model delta sigma weight residual 1.350 1.528 -0.178 2.00e-02 2.50e+03 7.93e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 17762 2.43 - 4.85: 2469 4.85 - 7.28: 339 7.28 - 9.70: 115 9.70 - 12.13: 5 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C GLY A 366 " pdb=" N PRO A 367 " pdb=" CA PRO A 367 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.95e+01 angle pdb=" C GLY C 366 " pdb=" N PRO C 367 " pdb=" CA PRO C 367 " ideal model delta sigma weight residual 119.56 128.06 -8.50 1.02e+00 9.61e-01 6.95e+01 angle pdb=" C GLY E 366 " pdb=" N PRO E 367 " pdb=" CA PRO E 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.93e+01 angle pdb=" C GLY D 366 " pdb=" N PRO D 367 " pdb=" CA PRO D 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.92e+01 angle pdb=" C GLY B 366 " pdb=" N PRO B 367 " pdb=" CA PRO B 367 " ideal model delta sigma weight residual 119.56 128.05 -8.49 1.02e+00 9.61e-01 6.92e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 8970 35.87 - 71.74: 145 71.74 - 107.61: 40 107.61 - 143.48: 10 143.48 - 179.35: 75 Dihedral angle restraints: 9240 sinusoidal: 3880 harmonic: 5360 Sorted by residual: dihedral pdb=" O1B ADP A 376 " pdb=" O3A ADP A 376 " pdb=" PB ADP A 376 " pdb=" PA ADP A 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.82 -149.83 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP D 376 " pdb=" O3A ADP D 376 " pdb=" PB ADP D 376 " pdb=" PA ADP D 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.80 -149.81 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" O1B ADP C 376 " pdb=" O3A ADP C 376 " pdb=" PB ADP C 376 " pdb=" PA ADP C 376 " ideal model delta sinusoidal sigma weight residual -60.00 89.80 -149.80 1 2.00e+01 2.50e-03 4.47e+01 ... (remaining 9237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1353 0.074 - 0.148: 697 0.148 - 0.222: 188 0.222 - 0.296: 32 0.296 - 0.370: 10 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C25 9ZK A 379 " pdb=" C26 9ZK A 379 " pdb=" C36 9ZK A 379 " pdb=" N23 9ZK A 379 " both_signs ideal model delta sigma weight residual False 2.15 2.52 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C25 9ZK C 379 " pdb=" C26 9ZK C 379 " pdb=" C36 9ZK C 379 " pdb=" N23 9ZK C 379 " both_signs ideal model delta sigma weight residual False 2.15 2.51 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" C25 9ZK B 379 " pdb=" C26 9ZK B 379 " pdb=" C36 9ZK B 379 " pdb=" N23 9ZK B 379 " both_signs ideal model delta sigma weight residual False 2.15 2.51 -0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 2277 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 375 " -0.031 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" C PHE A 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE A 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE A 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE E 375 " -0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE E 375 " 0.110 2.00e-02 2.50e+03 pdb=" O PHE E 375 " -0.039 2.00e-02 2.50e+03 pdb=" OXT PHE E 375 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 375 " 0.031 2.00e-02 2.50e+03 6.34e-02 4.02e+01 pdb=" C PHE B 375 " -0.110 2.00e-02 2.50e+03 pdb=" O PHE B 375 " 0.039 2.00e-02 2.50e+03 pdb=" OXT PHE B 375 " 0.039 2.00e-02 2.50e+03 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 490 2.66 - 3.22: 14670 3.22 - 3.78: 23581 3.78 - 4.34: 33890 4.34 - 4.90: 53672 Nonbonded interactions: 126303 Sorted by model distance: nonbonded pdb=" N SER B 14 " pdb=" O1 PO4 B 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER E 14 " pdb=" O1 PO4 E 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER C 14 " pdb=" O1 PO4 C 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER A 14 " pdb=" O1 PO4 A 377 " model vdw 2.104 3.120 nonbonded pdb=" N SER D 14 " pdb=" O1 PO4 D 377 " model vdw 2.105 3.120 ... (remaining 126298 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 375) selection = (chain 'B' and resid 5 through 375) selection = (chain 'C' and resid 5 through 375) selection = (chain 'D' and resid 5 through 375) selection = (chain 'E' and resid 5 through 375) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.600 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.021 0.179 15240 Z= 1.128 Angle : 1.811 12.126 20690 Z= 1.165 Chirality : 0.091 0.370 2280 Planarity : 0.009 0.063 2630 Dihedral : 23.396 179.349 5810 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.74 (0.20), residues: 1830 helix: -0.66 (0.16), residues: 760 sheet: 0.72 (0.31), residues: 270 loop : 2.00 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 183 TYR 0.045 0.008 TYR B 188 PHE 0.030 0.005 PHE A 200 TRP 0.075 0.013 TRP A 340 HIS 0.004 0.001 HIS B 161 Details of bonding type rmsd covalent geometry : bond 0.02087 (15240) covalent geometry : angle 1.81075 (20690) hydrogen bonds : bond 0.17414 ( 755) hydrogen bonds : angle 7.63737 ( 1875) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.8886 (mt) cc_final: 0.8577 (mp) REVERT: A 226 GLU cc_start: 0.8228 (tp30) cc_final: 0.7823 (mm-30) REVERT: A 259 GLU cc_start: 0.8580 (tp30) cc_final: 0.7698 (tp30) REVERT: A 283 MET cc_start: 0.7975 (mmm) cc_final: 0.7616 (mmm) REVERT: A 290 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7837 (mtm180) REVERT: B 25 ASP cc_start: 0.7361 (p0) cc_final: 0.7070 (t0) REVERT: B 118 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7848 (mmtt) REVERT: B 157 ASP cc_start: 0.6615 (t70) cc_final: 0.5982 (t0) REVERT: B 269 MET cc_start: 0.7406 (mtt) cc_final: 0.7160 (mtp) REVERT: B 283 MET cc_start: 0.8554 (mmm) cc_final: 0.8336 (mmt) REVERT: B 284 LYS cc_start: 0.8204 (mttm) cc_final: 0.7868 (tptp) REVERT: B 309 ILE cc_start: 0.8527 (tp) cc_final: 0.8259 (tt) REVERT: B 316 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8174 (mm-30) REVERT: C 39 ARG cc_start: 0.6726 (ttp-170) cc_final: 0.6134 (ttp80) REVERT: C 123 MET cc_start: 0.8212 (mmt) cc_final: 0.7938 (mmm) REVERT: C 152 VAL cc_start: 0.9026 (t) cc_final: 0.8775 (p) REVERT: C 187 ASP cc_start: 0.8049 (t70) cc_final: 0.7842 (m-30) REVERT: C 190 MET cc_start: 0.8412 (mtp) cc_final: 0.8198 (mtp) REVERT: D 64 ILE cc_start: 0.8925 (tt) cc_final: 0.8691 (mt) REVERT: D 81 ASP cc_start: 0.7872 (m-30) cc_final: 0.7637 (m-30) REVERT: D 116 ARG cc_start: 0.7697 (mtp85) cc_final: 0.7428 (mtm-85) REVERT: D 152 VAL cc_start: 0.9503 (t) cc_final: 0.9291 (p) REVERT: D 180 LEU cc_start: 0.8111 (tp) cc_final: 0.7799 (pp) REVERT: D 283 MET cc_start: 0.7688 (mmm) cc_final: 0.7236 (ttp) REVERT: D 346 LEU cc_start: 0.8679 (tp) cc_final: 0.8292 (tp) REVERT: E 104 LEU cc_start: 0.8917 (tp) cc_final: 0.8679 (tt) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.1354 time to fit residues: 120.4597 Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 HIS ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 GLN D 225 ASN D 371 HIS E 12 ASN E 111 ASN ** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.127088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.110940 restraints weight = 22035.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.114506 restraints weight = 12241.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116870 restraints weight = 7801.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.118523 restraints weight = 5493.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.119588 restraints weight = 4154.991| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15240 Z= 0.143 Angle : 0.675 7.110 20690 Z= 0.330 Chirality : 0.047 0.218 2280 Planarity : 0.005 0.042 2630 Dihedral : 31.942 179.902 2330 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 2.62 % Allowed : 12.27 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.20), residues: 1830 helix: 0.79 (0.18), residues: 730 sheet: 1.06 (0.29), residues: 315 loop : 2.16 (0.24), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 147 TYR 0.021 0.002 TYR E 294 PHE 0.013 0.001 PHE C 255 TRP 0.025 0.002 TRP A 340 HIS 0.006 0.002 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00320 (15240) covalent geometry : angle 0.67511 (20690) hydrogen bonds : bond 0.03776 ( 755) hydrogen bonds : angle 5.13531 ( 1875) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 344 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 154 ASP cc_start: 0.8652 (t0) cc_final: 0.8127 (t70) REVERT: A 227 MET cc_start: 0.8371 (tpt) cc_final: 0.7737 (tpp) REVERT: A 259 GLU cc_start: 0.8323 (tp30) cc_final: 0.7605 (tp30) REVERT: A 283 MET cc_start: 0.7916 (mmm) cc_final: 0.7436 (mmm) REVERT: A 290 ARG cc_start: 0.7523 (mtt180) cc_final: 0.7079 (mtm180) REVERT: B 118 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7771 (mmtt) REVERT: B 244 ASP cc_start: 0.8163 (p0) cc_final: 0.7328 (t0) REVERT: B 259 GLU cc_start: 0.8101 (tp30) cc_final: 0.7651 (tp30) REVERT: B 269 MET cc_start: 0.7197 (mtt) cc_final: 0.6967 (mtp) REVERT: B 283 MET cc_start: 0.8415 (mmm) cc_final: 0.7789 (mpp) REVERT: B 284 LYS cc_start: 0.8110 (mttm) cc_final: 0.7877 (tptp) REVERT: B 299 MET cc_start: 0.7833 (mmm) cc_final: 0.7552 (mtp) REVERT: C 244 ASP cc_start: 0.8689 (p0) cc_final: 0.7558 (t0) REVERT: C 267 ILE cc_start: 0.8180 (pt) cc_final: 0.7436 (tp) REVERT: C 288 ASP cc_start: 0.7254 (m-30) cc_final: 0.6945 (m-30) REVERT: D 115 ASN cc_start: 0.8431 (t0) cc_final: 0.8222 (t0) REVERT: D 162 ASN cc_start: 0.8027 (m110) cc_final: 0.7803 (m110) REVERT: D 167 GLU cc_start: 0.7281 (mm-30) cc_final: 0.7062 (mp0) REVERT: D 246 GLN cc_start: 0.8319 (mt0) cc_final: 0.8105 (mt0) REVERT: D 283 MET cc_start: 0.7500 (mmm) cc_final: 0.7242 (ttp) REVERT: D 346 LEU cc_start: 0.8728 (tp) cc_final: 0.8337 (tp) REVERT: E 14 SER cc_start: 0.7576 (m) cc_final: 0.7030 (p) REVERT: E 226 GLU cc_start: 0.7733 (tp30) cc_final: 0.7394 (tp30) REVERT: E 346 LEU cc_start: 0.8915 (tp) cc_final: 0.8578 (tp) REVERT: E 360 GLN cc_start: 0.8002 (pp30) cc_final: 0.7571 (pp30) outliers start: 41 outliers final: 27 residues processed: 370 average time/residue: 0.1024 time to fit residues: 59.6539 Evaluate side-chains 293 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 130 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 178 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN C 115 ASN D 246 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.102534 restraints weight = 23023.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105948 restraints weight = 12852.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108278 restraints weight = 8213.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.109862 restraints weight = 5827.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.110952 restraints weight = 4464.046| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15240 Z= 0.122 Angle : 0.615 8.019 20690 Z= 0.294 Chirality : 0.044 0.164 2280 Planarity : 0.004 0.031 2630 Dihedral : 30.385 178.819 2330 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.94 % Allowed : 14.82 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.18 (0.20), residues: 1830 helix: 1.19 (0.19), residues: 730 sheet: 1.21 (0.27), residues: 345 loop : 2.17 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 372 TYR 0.014 0.001 TYR A 294 PHE 0.025 0.001 PHE E 352 TRP 0.015 0.002 TRP A 79 HIS 0.005 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00278 (15240) covalent geometry : angle 0.61540 (20690) hydrogen bonds : bond 0.03300 ( 755) hydrogen bonds : angle 4.77753 ( 1875) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 294 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 154 ASP cc_start: 0.8641 (t0) cc_final: 0.8217 (t70) REVERT: A 227 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7674 (tpp) REVERT: A 283 MET cc_start: 0.7833 (mmm) cc_final: 0.7567 (mmm) REVERT: B 47 MET cc_start: 0.3325 (ptp) cc_final: 0.1377 (tpp) REVERT: B 118 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7636 (mmtp) REVERT: B 176 MET cc_start: 0.7581 (mmm) cc_final: 0.7152 (mpp) REVERT: B 244 ASP cc_start: 0.8383 (p0) cc_final: 0.7404 (t0) REVERT: B 283 MET cc_start: 0.8388 (mmm) cc_final: 0.8128 (mmt) REVERT: C 225 ASN cc_start: 0.7699 (m-40) cc_final: 0.7491 (t0) REVERT: C 244 ASP cc_start: 0.8819 (p0) cc_final: 0.7599 (t0) REVERT: C 338 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8429 (p) REVERT: D 81 ASP cc_start: 0.7565 (m-30) cc_final: 0.7210 (m-30) REVERT: D 115 ASN cc_start: 0.8318 (t0) cc_final: 0.7855 (t0) REVERT: D 162 ASN cc_start: 0.8096 (m110) cc_final: 0.7871 (m110) REVERT: D 167 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7012 (mp0) REVERT: D 283 MET cc_start: 0.7638 (mmm) cc_final: 0.7295 (ttp) REVERT: D 346 LEU cc_start: 0.8744 (tp) cc_final: 0.8351 (tp) REVERT: E 14 SER cc_start: 0.7690 (m) cc_final: 0.7147 (p) REVERT: E 226 GLU cc_start: 0.7716 (tp30) cc_final: 0.7402 (tp30) REVERT: E 346 LEU cc_start: 0.8994 (tp) cc_final: 0.8620 (tp) REVERT: E 354 GLN cc_start: 0.7410 (mt0) cc_final: 0.7069 (pm20) outliers start: 46 outliers final: 27 residues processed: 322 average time/residue: 0.1068 time to fit residues: 54.0903 Evaluate side-chains 270 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 14 SER Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 120 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 92 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 97 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 115 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 ASN A 353 GLN B 137 GLN B 162 ASN C 101 HIS ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN E 360 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.120714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104642 restraints weight = 22685.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.108029 restraints weight = 12729.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110310 restraints weight = 8163.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111899 restraints weight = 5797.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.112948 restraints weight = 4430.249| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15240 Z= 0.110 Angle : 0.593 6.784 20690 Z= 0.279 Chirality : 0.044 0.208 2280 Planarity : 0.004 0.036 2630 Dihedral : 29.195 179.735 2330 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.62 % Allowed : 15.21 % Favored : 82.17 % 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: 2.28 (0.20), residues: 1830 helix: 1.36 (0.20), residues: 730 sheet: 1.15 (0.28), residues: 345 loop : 2.17 (0.25), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.010 0.001 TYR E 169 PHE 0.026 0.001 PHE E 352 TRP 0.016 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00248 (15240) covalent geometry : angle 0.59348 (20690) hydrogen bonds : bond 0.02983 ( 755) hydrogen bonds : angle 4.62537 ( 1875) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 261 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 227 MET cc_start: 0.8409 (tpt) cc_final: 0.7823 (tpp) REVERT: A 270 GLU cc_start: 0.7273 (tt0) cc_final: 0.7058 (mp0) REVERT: B 118 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7573 (mmtp) REVERT: B 244 ASP cc_start: 0.8304 (p0) cc_final: 0.7572 (t0) REVERT: B 283 MET cc_start: 0.8314 (mmm) cc_final: 0.8034 (mmt) REVERT: C 225 ASN cc_start: 0.7614 (m-40) cc_final: 0.7394 (t0) REVERT: C 244 ASP cc_start: 0.8805 (p0) cc_final: 0.7770 (t0) REVERT: C 279 TYR cc_start: 0.8142 (t80) cc_final: 0.7880 (t80) REVERT: C 338 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8454 (p) REVERT: D 81 ASP cc_start: 0.7575 (m-30) cc_final: 0.7284 (m-30) REVERT: D 115 ASN cc_start: 0.8341 (t0) cc_final: 0.7927 (t0) REVERT: D 167 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6967 (mp0) REVERT: D 269 MET cc_start: 0.8093 (mtp) cc_final: 0.7753 (ttm) REVERT: D 283 MET cc_start: 0.7539 (mmm) cc_final: 0.7213 (ttp) REVERT: D 292 ASP cc_start: 0.7860 (m-30) cc_final: 0.7624 (m-30) REVERT: D 346 LEU cc_start: 0.8779 (tp) cc_final: 0.8441 (tp) REVERT: E 14 SER cc_start: 0.7882 (m) cc_final: 0.7400 (p) REVERT: E 132 MET cc_start: 0.6855 (ptm) cc_final: 0.6653 (ttt) REVERT: E 203 THR cc_start: 0.7535 (m) cc_final: 0.5751 (t) REVERT: E 223 PHE cc_start: 0.8611 (t80) cc_final: 0.8107 (t80) REVERT: E 226 GLU cc_start: 0.7668 (tp30) cc_final: 0.7443 (tp30) REVERT: E 271 SER cc_start: 0.8565 (m) cc_final: 0.8056 (p) REVERT: E 346 LEU cc_start: 0.8967 (tp) cc_final: 0.8640 (tp) outliers start: 41 outliers final: 24 residues processed: 289 average time/residue: 0.0981 time to fit residues: 45.3672 Evaluate side-chains 264 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 24 ASP Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 339 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 147 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 180 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.119073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102580 restraints weight = 22791.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.106020 restraints weight = 12499.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.108371 restraints weight = 7941.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.109993 restraints weight = 5606.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.111107 restraints weight = 4268.960| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15240 Z= 0.137 Angle : 0.617 8.887 20690 Z= 0.288 Chirality : 0.045 0.190 2280 Planarity : 0.004 0.036 2630 Dihedral : 28.303 179.945 2330 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.81 % Allowed : 16.29 % Favored : 80.89 % 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: 2.10 (0.20), residues: 1830 helix: 1.32 (0.20), residues: 730 sheet: 1.03 (0.27), residues: 345 loop : 1.96 (0.24), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 147 TYR 0.010 0.001 TYR A 294 PHE 0.018 0.001 PHE E 352 TRP 0.017 0.002 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00320 (15240) covalent geometry : angle 0.61696 (20690) hydrogen bonds : bond 0.03219 ( 755) hydrogen bonds : angle 4.62379 ( 1875) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7822 (ttp) REVERT: A 328 LYS cc_start: 0.8471 (tttp) cc_final: 0.8244 (tttm) REVERT: A 352 PHE cc_start: 0.8517 (t80) cc_final: 0.8281 (t80) REVERT: B 103 THR cc_start: 0.8616 (m) cc_final: 0.8178 (t) REVERT: B 118 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7686 (mmtp) REVERT: B 244 ASP cc_start: 0.8315 (p0) cc_final: 0.7789 (t0) REVERT: C 244 ASP cc_start: 0.8825 (p0) cc_final: 0.7876 (t0) REVERT: C 338 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8531 (p) REVERT: D 81 ASP cc_start: 0.7486 (m-30) cc_final: 0.7072 (m-30) REVERT: D 283 MET cc_start: 0.7624 (mmm) cc_final: 0.7323 (ttp) REVERT: D 346 LEU cc_start: 0.8912 (tp) cc_final: 0.8513 (tp) REVERT: D 348 SER cc_start: 0.8043 (m) cc_final: 0.7784 (t) REVERT: E 14 SER cc_start: 0.8086 (m) cc_final: 0.7500 (p) REVERT: E 78 ASN cc_start: 0.8343 (t0) cc_final: 0.7740 (t0) REVERT: E 203 THR cc_start: 0.7616 (m) cc_final: 0.5943 (t) REVERT: E 346 LEU cc_start: 0.9020 (tp) cc_final: 0.8650 (tp) outliers start: 44 outliers final: 33 residues processed: 287 average time/residue: 0.1024 time to fit residues: 46.8116 Evaluate side-chains 259 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 224 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 338 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 339 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 150 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 115 optimal weight: 0.0000 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN C 128 ASN D 59 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.089843 restraints weight = 23723.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.093025 restraints weight = 13405.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.095283 restraints weight = 8746.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096806 restraints weight = 6287.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.097934 restraints weight = 4884.755| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15240 Z= 0.239 Angle : 0.704 8.742 20690 Z= 0.336 Chirality : 0.048 0.201 2280 Planarity : 0.005 0.044 2630 Dihedral : 28.176 179.490 2330 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.71 % Allowed : 16.23 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.20), residues: 1830 helix: 1.16 (0.20), residues: 700 sheet: 0.24 (0.28), residues: 305 loop : 1.55 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 254 TYR 0.014 0.002 TYR A 294 PHE 0.027 0.002 PHE E 352 TRP 0.020 0.002 TRP A 79 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00568 (15240) covalent geometry : angle 0.70393 (20690) hydrogen bonds : bond 0.04251 ( 755) hydrogen bonds : angle 4.99810 ( 1875) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 241 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: A 283 MET cc_start: 0.8174 (mmp) cc_final: 0.7866 (mmp) REVERT: B 64 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8518 (tp) REVERT: B 103 THR cc_start: 0.8795 (m) cc_final: 0.8460 (t) REVERT: B 118 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7916 (mttm) REVERT: C 346 LEU cc_start: 0.9131 (tp) cc_final: 0.8900 (tt) REVERT: D 81 ASP cc_start: 0.7520 (m-30) cc_final: 0.7142 (m-30) REVERT: D 283 MET cc_start: 0.7479 (mmm) cc_final: 0.7272 (ttp) REVERT: D 346 LEU cc_start: 0.9021 (tp) cc_final: 0.8560 (tp) REVERT: E 14 SER cc_start: 0.7906 (m) cc_final: 0.7399 (p) REVERT: E 78 ASN cc_start: 0.8473 (t0) cc_final: 0.8065 (t0) REVERT: E 107 GLU cc_start: 0.7445 (tt0) cc_final: 0.7034 (tt0) REVERT: E 123 MET cc_start: 0.7689 (tpp) cc_final: 0.7096 (mtm) REVERT: E 187 ASP cc_start: 0.7604 (m-30) cc_final: 0.7301 (m-30) REVERT: E 346 LEU cc_start: 0.9186 (tp) cc_final: 0.8919 (tp) REVERT: E 360 GLN cc_start: 0.7586 (pp30) cc_final: 0.7277 (pp30) outliers start: 58 outliers final: 40 residues processed: 286 average time/residue: 0.1013 time to fit residues: 46.5066 Evaluate side-chains 263 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 50 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 65 optimal weight: 0.0970 chunk 123 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS ** E 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100397 restraints weight = 22682.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103626 restraints weight = 12787.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.105849 restraints weight = 8256.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.107363 restraints weight = 5884.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.108461 restraints weight = 4529.476| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15240 Z= 0.102 Angle : 0.603 8.989 20690 Z= 0.280 Chirality : 0.044 0.157 2280 Planarity : 0.004 0.052 2630 Dihedral : 27.497 179.413 2330 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.04 % Allowed : 18.02 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.20), residues: 1830 helix: 1.55 (0.20), residues: 700 sheet: 0.51 (0.27), residues: 335 loop : 1.78 (0.24), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.011 0.001 TYR B 166 PHE 0.034 0.001 PHE E 352 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00231 (15240) covalent geometry : angle 0.60345 (20690) hydrogen bonds : bond 0.02785 ( 755) hydrogen bonds : angle 4.61685 ( 1875) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 283 MET cc_start: 0.8077 (mmp) cc_final: 0.7862 (mmp) REVERT: B 103 THR cc_start: 0.8642 (m) cc_final: 0.8278 (t) REVERT: B 118 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7853 (mttm) REVERT: B 244 ASP cc_start: 0.8197 (p0) cc_final: 0.7968 (t0) REVERT: D 81 ASP cc_start: 0.7461 (m-30) cc_final: 0.7112 (m-30) REVERT: D 283 MET cc_start: 0.7313 (mmm) cc_final: 0.6927 (ttp) REVERT: D 346 LEU cc_start: 0.8985 (tp) cc_final: 0.8723 (tp) REVERT: D 355 MET cc_start: 0.8305 (mmp) cc_final: 0.7940 (mmt) REVERT: E 14 SER cc_start: 0.7958 (m) cc_final: 0.7326 (p) REVERT: E 44 MET cc_start: -0.0920 (tpp) cc_final: -0.2408 (ptm) REVERT: E 78 ASN cc_start: 0.8481 (t0) cc_final: 0.7575 (t0) REVERT: E 81 ASP cc_start: 0.7742 (m-30) cc_final: 0.6552 (m-30) REVERT: E 123 MET cc_start: 0.7670 (tpp) cc_final: 0.7137 (mtm) REVERT: E 179 ASP cc_start: 0.7937 (t0) cc_final: 0.7643 (t0) REVERT: E 187 ASP cc_start: 0.7594 (m-30) cc_final: 0.7321 (m-30) REVERT: E 346 LEU cc_start: 0.9015 (tp) cc_final: 0.8680 (tp) REVERT: E 360 GLN cc_start: 0.7464 (pp30) cc_final: 0.7085 (pp30) outliers start: 32 outliers final: 20 residues processed: 267 average time/residue: 0.1002 time to fit residues: 42.7292 Evaluate side-chains 238 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 218 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 169 optimal weight: 5.9990 chunk 162 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.110956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.095319 restraints weight = 23166.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.098397 restraints weight = 13110.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.100542 restraints weight = 8520.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.101998 restraints weight = 6121.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.103044 restraints weight = 4744.362| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15240 Z= 0.234 Angle : 0.694 7.549 20690 Z= 0.331 Chirality : 0.048 0.166 2280 Planarity : 0.005 0.057 2630 Dihedral : 27.537 179.481 2330 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.94 % Allowed : 17.89 % Favored : 79.17 % 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: 1.47 (0.20), residues: 1830 helix: 1.24 (0.20), residues: 700 sheet: -0.03 (0.28), residues: 305 loop : 1.42 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 95 TYR 0.012 0.001 TYR A 306 PHE 0.034 0.002 PHE E 352 TRP 0.017 0.002 TRP A 79 HIS 0.005 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00557 (15240) covalent geometry : angle 0.69422 (20690) hydrogen bonds : bond 0.04009 ( 755) hydrogen bonds : angle 4.89896 ( 1875) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 64 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8522 (tp) REVERT: B 103 THR cc_start: 0.8705 (m) cc_final: 0.8393 (t) REVERT: B 118 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7926 (mttm) REVERT: D 81 ASP cc_start: 0.7420 (m-30) cc_final: 0.7085 (m-30) REVERT: D 283 MET cc_start: 0.7447 (mmm) cc_final: 0.7220 (ttp) REVERT: D 346 LEU cc_start: 0.9030 (tp) cc_final: 0.8705 (tp) REVERT: E 14 SER cc_start: 0.8002 (m) cc_final: 0.7566 (p) REVERT: E 78 ASN cc_start: 0.8535 (t0) cc_final: 0.8078 (m-40) REVERT: E 107 GLU cc_start: 0.7430 (tt0) cc_final: 0.7076 (tt0) REVERT: E 346 LEU cc_start: 0.9150 (tp) cc_final: 0.8787 (tp) REVERT: E 360 GLN cc_start: 0.7495 (pp30) cc_final: 0.7051 (pp30) outliers start: 46 outliers final: 37 residues processed: 254 average time/residue: 0.0986 time to fit residues: 40.2746 Evaluate side-chains 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 109 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.099478 restraints weight = 22840.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.102605 restraints weight = 12821.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.104786 restraints weight = 8292.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.106283 restraints weight = 5924.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107368 restraints weight = 4566.175| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.6175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15240 Z= 0.154 Angle : 0.644 10.433 20690 Z= 0.302 Chirality : 0.045 0.156 2280 Planarity : 0.004 0.049 2630 Dihedral : 27.335 179.397 2330 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.75 % Allowed : 18.85 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.59 (0.20), residues: 1830 helix: 1.42 (0.20), residues: 690 sheet: 0.18 (0.27), residues: 335 loop : 1.39 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.010 0.001 TYR A 306 PHE 0.040 0.002 PHE E 352 TRP 0.013 0.002 TRP A 79 HIS 0.008 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00366 (15240) covalent geometry : angle 0.64402 (20690) hydrogen bonds : bond 0.03297 ( 755) hydrogen bonds : angle 4.74644 ( 1875) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.9009 (m-10) cc_final: 0.8771 (m-80) REVERT: B 64 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8500 (tp) REVERT: B 103 THR cc_start: 0.8638 (m) cc_final: 0.8335 (t) REVERT: B 118 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7904 (mttm) REVERT: B 244 ASP cc_start: 0.8200 (p0) cc_final: 0.7451 (t0) REVERT: D 81 ASP cc_start: 0.7390 (m-30) cc_final: 0.7036 (m-30) REVERT: D 283 MET cc_start: 0.7395 (mmm) cc_final: 0.7169 (ttp) REVERT: D 346 LEU cc_start: 0.9037 (tp) cc_final: 0.8732 (tp) REVERT: E 14 SER cc_start: 0.8055 (m) cc_final: 0.7667 (p) REVERT: E 346 LEU cc_start: 0.9123 (tp) cc_final: 0.8823 (tp) REVERT: E 360 GLN cc_start: 0.7452 (pp30) cc_final: 0.7086 (pp30) outliers start: 43 outliers final: 34 residues processed: 255 average time/residue: 0.1070 time to fit residues: 43.7832 Evaluate side-chains 254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 122 ILE Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 173 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 350 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 2 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 53 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.115976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100026 restraints weight = 23063.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.103316 restraints weight = 12647.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105577 restraints weight = 8029.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.107124 restraints weight = 5651.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108210 restraints weight = 4315.188| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.6280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15240 Z= 0.111 Angle : 0.617 10.076 20690 Z= 0.288 Chirality : 0.044 0.137 2280 Planarity : 0.004 0.044 2630 Dihedral : 26.962 178.860 2330 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.30 % Allowed : 19.94 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1830 helix: 1.62 (0.20), residues: 690 sheet: 0.24 (0.27), residues: 335 loop : 1.46 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 95 TYR 0.008 0.001 TYR E 306 PHE 0.040 0.001 PHE E 352 TRP 0.012 0.001 TRP A 79 HIS 0.017 0.001 HIS E 173 Details of bonding type rmsd covalent geometry : bond 0.00257 (15240) covalent geometry : angle 0.61695 (20690) hydrogen bonds : bond 0.02878 ( 755) hydrogen bonds : angle 4.59589 ( 1875) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8928 (m-10) cc_final: 0.8718 (m-80) REVERT: B 64 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8522 (tp) REVERT: B 103 THR cc_start: 0.8647 (m) cc_final: 0.8402 (t) REVERT: B 118 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7812 (mttm) REVERT: B 244 ASP cc_start: 0.8293 (p0) cc_final: 0.7372 (t0) REVERT: D 81 ASP cc_start: 0.7533 (m-30) cc_final: 0.7210 (m-30) REVERT: D 283 MET cc_start: 0.7334 (mmm) cc_final: 0.7026 (ttp) REVERT: D 346 LEU cc_start: 0.8995 (tp) cc_final: 0.8707 (tp) REVERT: E 14 SER cc_start: 0.8167 (m) cc_final: 0.7451 (p) REVERT: E 44 MET cc_start: -0.1070 (tpp) cc_final: -0.2430 (ptm) REVERT: E 100 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7129 (tp30) REVERT: E 346 LEU cc_start: 0.9065 (tp) cc_final: 0.8821 (tp) REVERT: E 355 MET cc_start: 0.6658 (mmt) cc_final: 0.6370 (mmm) REVERT: E 360 GLN cc_start: 0.7527 (pp30) cc_final: 0.7123 (pp30) outliers start: 36 outliers final: 29 residues processed: 257 average time/residue: 0.1037 time to fit residues: 42.6517 Evaluate side-chains 252 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 222 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LEU Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 143 TYR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 12 ASN Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 88 HIS Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 338 SER Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 152 VAL Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain E residue 298 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 76 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 143 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.099090 restraints weight = 22950.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102358 restraints weight = 12650.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.104622 restraints weight = 8063.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.106173 restraints weight = 5697.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.107238 restraints weight = 4359.252| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15240 Z= 0.142 Angle : 0.632 9.617 20690 Z= 0.297 Chirality : 0.045 0.142 2280 Planarity : 0.004 0.044 2630 Dihedral : 26.838 179.716 2330 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.62 % Allowed : 19.74 % Favored : 77.64 % 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: 1.73 (0.20), residues: 1830 helix: 1.60 (0.20), residues: 690 sheet: 0.22 (0.27), residues: 335 loop : 1.42 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 95 TYR 0.009 0.001 TYR A 306 PHE 0.039 0.001 PHE E 352 TRP 0.014 0.002 TRP A 79 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00335 (15240) covalent geometry : angle 0.63194 (20690) hydrogen bonds : bond 0.03179 ( 755) hydrogen bonds : angle 4.61112 ( 1875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2285.70 seconds wall clock time: 40 minutes 29.68 seconds (2429.68 seconds total)