Starting phenix.real_space_refine on Sat Sep 12 10:17:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.cif" model { file = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2026/6t20_10364.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 10 5.49 5 Mg 5 5.21 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14915 Number of models: 1 Model: "" Number of chains: 4 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: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.58, per 1000 atoms: 0.17 Number of scatterers: 14915 At special positions: 0 Unit cell: (98.56, 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 110 16.00 P 10 15.00 Mg 5 11.99 O 2870 8.00 N 2510 7.00 C 9410 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 Links applied TRANS " TRP F 1 " - " ALA F 7 " " DTH F 4 " - " ALA F 3 " " TRP G 1 " - " ALA G 7 " " DTH G 4 " - " ALA G 3 " " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 579.9 milliseconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH F 4 " pdb=" CB DTH G 4 " pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 3490 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 25 sheets defined 52.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 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: 4.082A 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 171 through 175 Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.557A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 231 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: 4.497A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP A 292 " --> pdb=" O ASP A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.644A 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 349 Processing helix chain 'A' and resid 350 through 356 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: 4.083A 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 171 through 175 Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.558A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 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: 4.496A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.644A 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 349 Processing helix chain 'B' and resid 350 through 356 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: 4.083A 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 171 through 175 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.558A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 231 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: 4.496A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.644A 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 349 Processing helix chain 'C' and resid 350 through 356 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: 4.082A 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 171 through 175 Processing helix chain 'D' and resid 181 through 197 removed outlier: 3.558A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 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: 4.497A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.644A 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 349 Processing helix chain 'D' and resid 350 through 356 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: 4.083A 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 171 through 175 Processing helix chain 'E' and resid 181 through 197 removed outlier: 3.557A pdb=" N GLU E 195 " --> pdb=" O LYS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 231 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: 4.496A pdb=" N LYS E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.643A 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 349 Processing helix chain 'E' and resid 350 through 356 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: 6.762A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.521A 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 176 through 178 removed outlier: 7.426A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 6.762A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 7.426A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.762A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 7.426A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.761A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 7.427A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 29 through 32 removed outlier: 6.762A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC5, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC6, first strand: chain 'E' and resid 176 through 178 removed outlier: 7.426A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 755 hydrogen bonds defined for protein. 1890 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: 2.66 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3450 1.32 - 1.44: 3694 1.44 - 1.56: 7901 1.56 - 1.68: 5 1.68 - 1.80: 190 Bond restraints: 15240 Sorted by residual: bond pdb=" CA EEP F 2 " pdb=" C EEP F 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" CA EEP G 2 " pdb=" C EEP G 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 15235 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18380 2.41 - 4.82: 1928 4.82 - 7.23: 242 7.23 - 9.64: 105 9.64 - 12.06: 35 Bond angle restraints: 20690 Sorted by residual: angle pdb=" C HIS E 101 " pdb=" N PRO E 102 " pdb=" CA PRO E 102 " ideal model delta sigma weight residual 119.78 129.31 -9.53 1.03e+00 9.43e-01 8.56e+01 angle pdb=" C HIS A 101 " pdb=" N PRO A 102 " pdb=" CA PRO A 102 " ideal model delta sigma weight residual 119.78 129.31 -9.53 1.03e+00 9.43e-01 8.56e+01 angle pdb=" C HIS C 101 " pdb=" N PRO C 102 " pdb=" CA PRO C 102 " ideal model delta sigma weight residual 119.78 129.29 -9.51 1.03e+00 9.43e-01 8.52e+01 angle pdb=" C HIS B 101 " pdb=" N PRO B 102 " pdb=" CA PRO B 102 " ideal model delta sigma weight residual 119.78 129.27 -9.49 1.03e+00 9.43e-01 8.50e+01 angle pdb=" C HIS D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta sigma weight residual 119.78 129.27 -9.49 1.03e+00 9.43e-01 8.49e+01 ... (remaining 20685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.06: 8940 27.06 - 54.12: 130 54.12 - 81.19: 50 81.19 - 108.25: 5 108.25 - 135.31: 10 Dihedral angle restraints: 9135 sinusoidal: 3680 harmonic: 5455 Sorted by residual: dihedral pdb=" CA HYP H 6 " pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta harmonic sigma weight residual 180.00 147.87 32.13 0 5.00e+00 4.00e-02 4.13e+01 dihedral pdb=" CA HYP G 6 " pdb=" C HYP G 6 " pdb=" N ALA G 7 " pdb=" CA ALA G 7 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA HYP J 6 " pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta harmonic sigma weight residual 180.00 147.91 32.09 0 5.00e+00 4.00e-02 4.12e+01 ... (remaining 9132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.032: 2295 1.032 - 2.063: 0 2.063 - 3.095: 0 3.095 - 4.126: 0 4.126 - 5.158: 10 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CB DTH G 4 " pdb=" CA DTH G 4 " pdb=" OG1 DTH G 4 " pdb=" CG2 DTH G 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.61 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CB DTH I 4 " pdb=" CA DTH I 4 " pdb=" OG1 DTH I 4 " pdb=" CG2 DTH I 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.61 5.16 2.00e-01 2.50e+01 6.65e+02 chirality pdb=" CB DTH J 4 " pdb=" CA DTH J 4 " pdb=" OG1 DTH J 4 " pdb=" CG2 DTH J 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.61 5.16 2.00e-01 2.50e+01 6.65e+02 ... (remaining 2302 not shown) Planarity restraints: 2635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 306 " -0.089 2.00e-02 2.50e+03 5.24e-02 5.50e+01 pdb=" CG TYR A 306 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 306 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 306 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 306 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 306 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 306 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 306 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 306 " -0.089 2.00e-02 2.50e+03 5.24e-02 5.48e+01 pdb=" CG TYR C 306 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 306 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 306 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR C 306 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR C 306 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR C 306 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR C 306 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 306 " 0.089 2.00e-02 2.50e+03 5.23e-02 5.48e+01 pdb=" CG TYR D 306 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR D 306 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR D 306 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR D 306 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TYR D 306 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR D 306 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 306 " 0.090 2.00e-02 2.50e+03 ... (remaining 2632 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 45 2.37 - 3.00: 10037 3.00 - 3.63: 21828 3.63 - 4.27: 36360 4.27 - 4.90: 57245 Nonbonded interactions: 125515 Sorted by model distance: nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.734 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.734 3.620 nonbonded pdb=" CD1 TRP F 1 " pdb=" SG CYS F 5 " model vdw 1.734 3.620 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.735 3.620 nonbonded pdb=" CD1 TRP G 1 " pdb=" SG CYS G 5 " model vdw 1.735 3.620 ... (remaining 125510 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.670 Find NCS groups from input model: 0.270 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.019 0.119 15250 Z= 1.191 Angle : 1.689 12.055 20720 Z= 1.117 Chirality : 0.350 5.158 2305 Planarity : 0.006 0.052 2625 Dihedral : 12.066 135.311 5615 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.10 (0.18), residues: 1830 helix: -0.92 (0.15), residues: 750 sheet: -0.26 (0.29), residues: 290 loop : -0.50 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 177 TYR 0.090 0.009 TYR A 306 PHE 0.013 0.004 PHE E 31 TRP 0.031 0.006 TRP A 340 HIS 0.007 0.003 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01855 / 1.19 (15240) covalent geometry : angle 1.68438 / 1.11 (20690) hydrogen bonds : bond 0.18648 / 12.37 ( 755) hydrogen bonds : angle 7.44332 / 5.36 ( 1890) link_TRANS : bond 0.01225 / 0.80 ( 10) link_TRANS : angle 3.68248 / 2.32 ( 30) *********************** 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 580 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7544 (p0) cc_final: 0.7267 (p0) REVERT: A 56 ASP cc_start: 0.7114 (m-30) cc_final: 0.6816 (t0) REVERT: A 246 GLN cc_start: 0.8159 (mt0) cc_final: 0.7954 (mt0) REVERT: A 258 PRO cc_start: 0.8477 (Cg_exo) cc_final: 0.8027 (Cg_endo) REVERT: A 283 MET cc_start: 0.8871 (mmp) cc_final: 0.8643 (mmp) REVERT: A 329 ILE cc_start: 0.8686 (mm) cc_final: 0.8067 (tt) REVERT: A 361 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7572 (mt-10) REVERT: B 41 GLN cc_start: 0.7597 (tp40) cc_final: 0.7334 (tt0) REVERT: B 195 GLU cc_start: 0.8327 (tt0) cc_final: 0.8111 (tt0) REVERT: B 201 VAL cc_start: 0.9004 (m) cc_final: 0.8709 (t) REVERT: B 246 GLN cc_start: 0.7925 (mt0) cc_final: 0.7540 (tt0) REVERT: B 325 MET cc_start: 0.6907 (mmm) cc_final: 0.6436 (mmt) REVERT: B 355 MET cc_start: 0.8223 (mmm) cc_final: 0.7945 (mmt) REVERT: C 201 VAL cc_start: 0.9157 (m) cc_final: 0.8738 (p) REVERT: C 211 ASP cc_start: 0.7538 (t70) cc_final: 0.7290 (m-30) REVERT: C 311 ASP cc_start: 0.7320 (m-30) cc_final: 0.7096 (t0) REVERT: D 149 THR cc_start: 0.8139 (m) cc_final: 0.7922 (t) REVERT: D 287 ILE cc_start: 0.8354 (tt) cc_final: 0.8013 (tt) REVERT: D 349 LEU cc_start: 0.7174 (tp) cc_final: 0.6896 (mt) REVERT: E 56 ASP cc_start: 0.7163 (m-30) cc_final: 0.6787 (t0) REVERT: E 59 GLN cc_start: 0.7852 (mm-40) cc_final: 0.6922 (tp40) REVERT: E 115 ASN cc_start: 0.8438 (t0) cc_final: 0.8181 (t0) REVERT: E 173 HIS cc_start: 0.8406 (p-80) cc_final: 0.8116 (p90) REVERT: E 244 ASP cc_start: 0.7812 (p0) cc_final: 0.7059 (p0) REVERT: E 299 MET cc_start: 0.8328 (mmp) cc_final: 0.8109 (mmt) REVERT: E 371 HIS cc_start: 0.8258 (m-70) cc_final: 0.8039 (m-70) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.1317 time to fit residues: 110.3941 Evaluate side-chains 280 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 HIS C 41 GLN D 162 ASN D 296 ASN D 360 GLN E 40 HIS E 59 GLN E 297 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.124478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109569 restraints weight = 22153.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113047 restraints weight = 12495.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115438 restraints weight = 7918.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117071 restraints weight = 5473.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118184 restraints weight = 4037.922| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15250 Z= 0.154 Angle : 0.691 8.059 20720 Z= 0.347 Chirality : 0.048 0.243 2305 Planarity : 0.005 0.031 2625 Dihedral : 11.381 147.708 2120 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.73 % Allowed : 9.90 % Favored : 87.37 % Cbeta Deviations : 0.29 % 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: 0.44 (0.20), residues: 1830 helix: 0.66 (0.18), residues: 800 sheet: 0.28 (0.29), residues: 305 loop : 0.07 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 256 TYR 0.019 0.002 TYR D 294 PHE 0.039 0.002 PHE D 352 TRP 0.014 0.002 TRP A 340 HIS 0.004 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (15240) covalent geometry : angle 0.69104 / 0.35 (20690) hydrogen bonds : bond 0.04431 / 2.94 ( 755) hydrogen bonds : angle 5.14551 / 3.71 ( 1890) link_TRANS : bond 0.00310 / 0.22 ( 10) link_TRANS : angle 0.55372 / 0.32 ( 30) *********************** 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 428 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8288 (mm) cc_final: 0.7900 (pt) REVERT: A 78 ASN cc_start: 0.6367 (t0) cc_final: 0.6140 (t0) REVERT: A 166 TYR cc_start: 0.8564 (t80) cc_final: 0.8259 (t80) REVERT: A 250 ILE cc_start: 0.7469 (mm) cc_final: 0.7180 (mm) REVERT: A 258 PRO cc_start: 0.8571 (Cg_exo) cc_final: 0.8298 (Cg_endo) REVERT: A 315 LYS cc_start: 0.8098 (tttt) cc_final: 0.7765 (ttmm) REVERT: A 329 ILE cc_start: 0.8618 (mm) cc_final: 0.8403 (mm) REVERT: B 176 MET cc_start: 0.7767 (mmt) cc_final: 0.6959 (mmm) REVERT: B 201 VAL cc_start: 0.8909 (m) cc_final: 0.8601 (t) REVERT: B 221 LEU cc_start: 0.7998 (mm) cc_final: 0.7776 (pt) REVERT: B 226 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 246 GLN cc_start: 0.7841 (mt0) cc_final: 0.7445 (tt0) REVERT: B 349 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6609 (tt) REVERT: B 364 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7741 (tm-30) REVERT: C 75 ILE cc_start: 0.8675 (mt) cc_final: 0.8285 (tt) REVERT: C 201 VAL cc_start: 0.8827 (m) cc_final: 0.8446 (p) REVERT: C 211 ASP cc_start: 0.7566 (t70) cc_final: 0.7268 (m-30) REVERT: C 259 GLU cc_start: 0.7532 (tp30) cc_final: 0.7290 (tp30) REVERT: D 78 ASN cc_start: 0.7856 (t0) cc_final: 0.7298 (m-40) REVERT: D 152 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (m) REVERT: D 211 ASP cc_start: 0.7891 (t70) cc_final: 0.7682 (t0) REVERT: D 292 ASP cc_start: 0.7275 (t0) cc_final: 0.6926 (t0) REVERT: D 364 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7916 (mt-10) REVERT: E 50 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7582 (mtmt) REVERT: E 78 ASN cc_start: 0.8269 (t0) cc_final: 0.7863 (t0) REVERT: E 87 HIS cc_start: 0.8021 (t70) cc_final: 0.7778 (t-90) REVERT: E 169 TYR cc_start: 0.8255 (m-80) cc_final: 0.7852 (m-80) outliers start: 43 outliers final: 22 residues processed: 413 average time/residue: 0.1059 time to fit residues: 68.7114 Evaluate side-chains 306 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 281 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain E residue 50 LYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 163 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 92 ASN A 162 ASN B 111 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN D 101 HIS D 111 ASN D 162 ASN D 360 GLN E 40 HIS E 296 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094959 restraints weight = 23664.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098117 restraints weight = 13676.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100321 restraints weight = 8916.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.101832 restraints weight = 6333.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102967 restraints weight = 4836.619| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15250 Z= 0.245 Angle : 0.759 8.968 20720 Z= 0.378 Chirality : 0.050 0.267 2305 Planarity : 0.005 0.041 2625 Dihedral : 11.269 147.943 2120 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.94 % Allowed : 12.13 % Favored : 83.94 % Cbeta Deviations : 0.29 % 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: 0.67 (0.19), residues: 1830 helix: 1.00 (0.18), residues: 740 sheet: 0.20 (0.29), residues: 315 loop : 0.17 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 372 TYR 0.027 0.002 TYR D 294 PHE 0.019 0.002 PHE D 262 TRP 0.017 0.003 TRP A 79 HIS 0.007 0.001 HIS D 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (15240) covalent geometry : angle 0.75909 / 0.38 (20690) hydrogen bonds : bond 0.05101 / 3.35 ( 755) hydrogen bonds : angle 5.04831 / 3.62 ( 1890) link_TRANS : bond 0.00180 / 0.12 ( 10) link_TRANS : angle 0.52055 / 0.29 ( 30) *********************** 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 363 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8481 (mm) cc_final: 0.8266 (pt) REVERT: A 166 TYR cc_start: 0.8518 (t80) cc_final: 0.8174 (t80) REVERT: A 217 CYS cc_start: 0.9113 (m) cc_final: 0.8863 (m) REVERT: A 246 GLN cc_start: 0.7848 (mt0) cc_final: 0.7586 (mt0) REVERT: A 258 PRO cc_start: 0.8890 (Cg_exo) cc_final: 0.8586 (Cg_endo) REVERT: A 329 ILE cc_start: 0.8832 (mm) cc_final: 0.8507 (tt) REVERT: B 14 SER cc_start: 0.7634 (t) cc_final: 0.7331 (p) REVERT: B 201 VAL cc_start: 0.8879 (m) cc_final: 0.8558 (t) REVERT: B 227 MET cc_start: 0.8595 (mmm) cc_final: 0.8346 (mmm) REVERT: B 311 ASP cc_start: 0.7970 (m-30) cc_final: 0.7588 (m-30) REVERT: B 354 GLN cc_start: 0.8129 (mm110) cc_final: 0.7798 (mm-40) REVERT: C 153 LEU cc_start: 0.8889 (tp) cc_final: 0.8495 (tp) REVERT: C 157 ASP cc_start: 0.8301 (t70) cc_final: 0.8022 (t0) REVERT: C 201 VAL cc_start: 0.8759 (m) cc_final: 0.8409 (p) REVERT: C 259 GLU cc_start: 0.7774 (tp30) cc_final: 0.7337 (tp30) REVERT: C 329 ILE cc_start: 0.9058 (mm) cc_final: 0.8811 (mm) REVERT: D 311 ASP cc_start: 0.8250 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: E 100 GLU cc_start: 0.6937 (tm-30) cc_final: 0.6529 (tm-30) REVERT: E 271 SER cc_start: 0.8827 (t) cc_final: 0.8493 (m) REVERT: E 298 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8914 (p) outliers start: 62 outliers final: 45 residues processed: 337 average time/residue: 0.1031 time to fit residues: 55.2967 Evaluate side-chains 291 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 173 HIS B 12 ASN B 59 GLN B 296 ASN C 41 GLN D 49 GLN D 296 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101701 restraints weight = 22944.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.105085 restraints weight = 12802.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.107429 restraints weight = 8129.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108938 restraints weight = 5644.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110156 restraints weight = 4260.131| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15250 Z= 0.125 Angle : 0.620 8.059 20720 Z= 0.298 Chirality : 0.045 0.220 2305 Planarity : 0.004 0.035 2625 Dihedral : 10.937 158.903 2120 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.86 % Allowed : 15.24 % Favored : 81.90 % Cbeta Deviations : 0.29 % 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: 1.04 (0.19), residues: 1830 helix: 1.38 (0.19), residues: 740 sheet: 0.24 (0.29), residues: 315 loop : 0.36 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 206 TYR 0.013 0.001 TYR D 294 PHE 0.011 0.001 PHE A 352 TRP 0.014 0.002 TRP A 340 HIS 0.004 0.001 HIS E 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (15240) covalent geometry : angle 0.62014 / 0.30 (20690) hydrogen bonds : bond 0.03516 / 2.31 ( 755) hydrogen bonds : angle 4.71488 / 3.42 ( 1890) link_TRANS : bond 0.00069 / 0.05 ( 10) link_TRANS : angle 0.34663 / 0.19 ( 30) *********************** 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 334 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8414 (mm) cc_final: 0.8207 (pt) REVERT: A 166 TYR cc_start: 0.8532 (t80) cc_final: 0.8136 (t80) REVERT: A 195 GLU cc_start: 0.8375 (tt0) cc_final: 0.8063 (tt0) REVERT: A 246 GLN cc_start: 0.7850 (mt0) cc_final: 0.7564 (mt0) REVERT: A 258 PRO cc_start: 0.8902 (Cg_exo) cc_final: 0.8591 (Cg_endo) REVERT: A 283 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8281 (mmm) REVERT: B 14 SER cc_start: 0.7677 (t) cc_final: 0.7448 (p) REVERT: B 176 MET cc_start: 0.7778 (mmt) cc_final: 0.6975 (mmm) REVERT: B 201 VAL cc_start: 0.8712 (m) cc_final: 0.8377 (t) REVERT: B 364 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7799 (tm-30) REVERT: B 372 ARG cc_start: 0.6988 (mtt90) cc_final: 0.6506 (mtp180) REVERT: C 157 ASP cc_start: 0.8227 (t70) cc_final: 0.7816 (t0) REVERT: C 217 CYS cc_start: 0.8932 (m) cc_final: 0.7895 (m) REVERT: C 259 GLU cc_start: 0.7767 (tp30) cc_final: 0.7257 (tp30) REVERT: C 355 MET cc_start: 0.7660 (mmm) cc_final: 0.7320 (mmt) REVERT: D 152 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.9025 (m) REVERT: D 190 MET cc_start: 0.7447 (mtm) cc_final: 0.7145 (mtm) REVERT: D 329 ILE cc_start: 0.8555 (mm) cc_final: 0.8340 (mm) REVERT: E 145 SER cc_start: 0.8638 (m) cc_final: 0.8381 (t) REVERT: E 271 SER cc_start: 0.8850 (t) cc_final: 0.8476 (m) REVERT: E 283 MET cc_start: 0.7640 (mmp) cc_final: 0.7229 (mmp) outliers start: 45 outliers final: 30 residues processed: 315 average time/residue: 0.0969 time to fit residues: 48.9305 Evaluate side-chains 291 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 259 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS B 59 GLN B 296 ASN C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.107046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.091882 restraints weight = 24000.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094895 restraints weight = 13825.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.097039 restraints weight = 9046.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098557 restraints weight = 6439.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099619 restraints weight = 4903.817| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 15250 Z= 0.321 Angle : 0.803 9.459 20720 Z= 0.397 Chirality : 0.053 0.296 2305 Planarity : 0.006 0.047 2625 Dihedral : 11.274 154.081 2120 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.57 % Allowed : 15.37 % Favored : 80.06 % Cbeta Deviations : 0.29 % 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: 0.42 (0.19), residues: 1830 helix: 0.85 (0.19), residues: 745 sheet: -0.01 (0.29), residues: 315 loop : 0.01 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 196 TYR 0.021 0.002 TYR D 294 PHE 0.024 0.002 PHE D 262 TRP 0.018 0.003 TRP H 1 HIS 0.008 0.002 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00765 / 0.32 (15240) covalent geometry : angle 0.80298 / 0.40 (20690) hydrogen bonds : bond 0.05297 / 3.47 ( 755) hydrogen bonds : angle 5.06022 / 3.63 ( 1890) link_TRANS : bond 0.00306 / 0.21 ( 10) link_TRANS : angle 0.88077 / 0.47 ( 30) *********************** 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 339 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 267 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.7260 (t0) cc_final: 0.6999 (t0) REVERT: A 166 TYR cc_start: 0.8640 (t80) cc_final: 0.8178 (t80) REVERT: A 246 GLN cc_start: 0.8002 (mt0) cc_final: 0.7667 (mt0) REVERT: B 14 SER cc_start: 0.7646 (OUTLIER) cc_final: 0.7428 (p) REVERT: B 176 MET cc_start: 0.7775 (mmt) cc_final: 0.7442 (mmt) REVERT: B 201 VAL cc_start: 0.8811 (m) cc_final: 0.8407 (t) REVERT: C 157 ASP cc_start: 0.8320 (t70) cc_final: 0.8007 (t70) REVERT: C 259 GLU cc_start: 0.7758 (tp30) cc_final: 0.7223 (tp30) REVERT: C 292 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7242 (t0) REVERT: D 107 GLU cc_start: 0.7830 (pt0) cc_final: 0.7199 (pt0) REVERT: D 184 ASP cc_start: 0.7946 (t0) cc_final: 0.7721 (t0) REVERT: E 143 TYR cc_start: 0.7818 (m-80) cc_final: 0.7428 (m-80) REVERT: E 222 ASP cc_start: 0.7872 (t0) cc_final: 0.7641 (t0) REVERT: E 271 SER cc_start: 0.9013 (t) cc_final: 0.8633 (m) REVERT: E 283 MET cc_start: 0.7829 (mmp) cc_final: 0.7429 (mmp) outliers start: 72 outliers final: 51 residues processed: 310 average time/residue: 0.0987 time to fit residues: 48.9463 Evaluate side-chains 297 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 244 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN C 41 GLN E 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.098291 restraints weight = 23197.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101432 restraints weight = 13197.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103655 restraints weight = 8503.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105169 restraints weight = 5962.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106259 restraints weight = 4466.654| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15250 Z= 0.127 Angle : 0.634 8.766 20720 Z= 0.304 Chirality : 0.046 0.231 2305 Planarity : 0.004 0.035 2625 Dihedral : 11.051 172.755 2120 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.24 % Allowed : 17.02 % Favored : 79.75 % Cbeta Deviations : 0.29 % 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: 0.78 (0.20), residues: 1830 helix: 1.11 (0.19), residues: 770 sheet: 0.08 (0.28), residues: 315 loop : 0.26 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 116 TYR 0.018 0.001 TYR D 166 PHE 0.008 0.001 PHE D 255 TRP 0.015 0.002 TRP D 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (15240) covalent geometry : angle 0.63382 / 0.30 (20690) hydrogen bonds : bond 0.03544 / 2.33 ( 755) hydrogen bonds : angle 4.72141 / 3.43 ( 1890) link_TRANS : bond 0.00084 / 0.06 ( 10) link_TRANS : angle 0.40422 / 0.22 ( 30) *********************** 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 341 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8631 (t80) cc_final: 0.8229 (t80) REVERT: A 246 GLN cc_start: 0.7952 (mt0) cc_final: 0.7637 (mt0) REVERT: A 283 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8176 (mmm) REVERT: B 14 SER cc_start: 0.7976 (t) cc_final: 0.7699 (p) REVERT: B 176 MET cc_start: 0.7740 (mmt) cc_final: 0.7027 (mmm) REVERT: B 215 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8356 (mttm) REVERT: C 157 ASP cc_start: 0.8264 (t70) cc_final: 0.7861 (t0) REVERT: C 211 ASP cc_start: 0.7678 (t0) cc_final: 0.6885 (m-30) REVERT: C 217 CYS cc_start: 0.8767 (m) cc_final: 0.7903 (m) REVERT: C 259 GLU cc_start: 0.7814 (tp30) cc_final: 0.7215 (tp30) REVERT: C 355 MET cc_start: 0.7595 (mmm) cc_final: 0.7250 (mmt) REVERT: D 152 VAL cc_start: 0.9104 (m) cc_final: 0.8770 (p) REVERT: D 190 MET cc_start: 0.7512 (mtm) cc_final: 0.7228 (mtm) REVERT: D 329 ILE cc_start: 0.8710 (mm) cc_final: 0.8461 (mm) REVERT: E 222 ASP cc_start: 0.7637 (t0) cc_final: 0.7430 (t0) REVERT: E 271 SER cc_start: 0.9027 (t) cc_final: 0.8653 (m) REVERT: E 283 MET cc_start: 0.7810 (mmp) cc_final: 0.7190 (mmp) outliers start: 51 outliers final: 34 residues processed: 316 average time/residue: 0.0977 time to fit residues: 49.1010 Evaluate side-chains 300 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 0.0030 chunk 46 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 162 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN E 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094853 restraints weight = 23434.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.097939 restraints weight = 13366.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100090 restraints weight = 8629.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101590 restraints weight = 6065.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102665 restraints weight = 4573.529| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15250 Z= 0.171 Angle : 0.673 9.218 20720 Z= 0.323 Chirality : 0.047 0.253 2305 Planarity : 0.004 0.039 2625 Dihedral : 10.889 177.556 2120 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.49 % Allowed : 18.22 % Favored : 78.29 % Cbeta Deviations : 0.29 % 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: 0.80 (0.20), residues: 1830 helix: 1.18 (0.19), residues: 745 sheet: 0.10 (0.29), residues: 315 loop : 0.23 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 116 TYR 0.013 0.001 TYR A 362 PHE 0.010 0.001 PHE D 262 TRP 0.015 0.002 TRP A 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15240) covalent geometry : angle 0.67311 / 0.32 (20690) hydrogen bonds : bond 0.03946 / 2.58 ( 755) hydrogen bonds : angle 4.71804 / 3.42 ( 1890) link_TRANS : bond 0.00122 / 0.08 ( 10) link_TRANS : angle 0.49980 / 0.28 ( 30) *********************** 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 327 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8634 (t80) cc_final: 0.8215 (t80) REVERT: A 246 GLN cc_start: 0.8008 (mt0) cc_final: 0.7673 (mt0) REVERT: A 270 GLU cc_start: 0.5528 (mm-30) cc_final: 0.5156 (mm-30) REVERT: A 279 TYR cc_start: 0.8252 (t80) cc_final: 0.8052 (t80) REVERT: A 283 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8168 (mmm) REVERT: B 14 SER cc_start: 0.7992 (t) cc_final: 0.7752 (p) REVERT: B 116 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7670 (mtp85) REVERT: B 176 MET cc_start: 0.7721 (mmt) cc_final: 0.7030 (mmm) REVERT: B 215 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (mttm) REVERT: C 157 ASP cc_start: 0.8256 (t70) cc_final: 0.7823 (t0) REVERT: C 217 CYS cc_start: 0.8880 (m) cc_final: 0.8232 (m) REVERT: C 286 ASP cc_start: 0.5869 (OUTLIER) cc_final: 0.5452 (m-30) REVERT: C 292 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7150 (t0) REVERT: E 222 ASP cc_start: 0.7795 (t0) cc_final: 0.7536 (t0) REVERT: E 283 MET cc_start: 0.7845 (mmp) cc_final: 0.7489 (mmp) outliers start: 55 outliers final: 42 residues processed: 306 average time/residue: 0.0972 time to fit residues: 47.6096 Evaluate side-chains 300 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 101 HIS Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 131 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 139 optimal weight: 0.0870 chunk 130 optimal weight: 0.0980 chunk 127 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN B 49 GLN C 41 GLN C 173 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.099049 restraints weight = 23329.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102241 restraints weight = 13199.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104451 restraints weight = 8444.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105987 restraints weight = 5886.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107079 restraints weight = 4387.921| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15250 Z= 0.121 Angle : 0.638 9.579 20720 Z= 0.303 Chirality : 0.045 0.225 2305 Planarity : 0.004 0.036 2625 Dihedral : 9.856 164.240 2120 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.11 % Allowed : 19.24 % Favored : 77.65 % Cbeta Deviations : 0.29 % 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: 0.91 (0.20), residues: 1830 helix: 1.22 (0.19), residues: 770 sheet: 0.19 (0.29), residues: 315 loop : 0.30 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.013 0.001 TYR D 306 PHE 0.009 0.001 PHE B 124 TRP 0.014 0.002 TRP D 340 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (15240) covalent geometry : angle 0.63850 / 0.30 (20690) hydrogen bonds : bond 0.03312 / 2.19 ( 755) hydrogen bonds : angle 4.59049 / 3.34 ( 1890) link_TRANS : bond 0.00085 / 0.06 ( 10) link_TRANS : angle 0.39933 / 0.23 ( 30) *********************** 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 328 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.8454 (mtp) cc_final: 0.8245 (ttm) REVERT: A 166 TYR cc_start: 0.8594 (t80) cc_final: 0.8220 (t80) REVERT: A 227 MET cc_start: 0.8088 (mmm) cc_final: 0.7632 (mtp) REVERT: A 246 GLN cc_start: 0.7985 (mt0) cc_final: 0.7633 (mt0) REVERT: A 283 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: B 176 MET cc_start: 0.7753 (mmt) cc_final: 0.7022 (mmm) REVERT: B 215 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: C 217 CYS cc_start: 0.8731 (m) cc_final: 0.7841 (m) REVERT: C 286 ASP cc_start: 0.5772 (OUTLIER) cc_final: 0.5470 (m-30) REVERT: C 292 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7107 (t0) REVERT: C 355 MET cc_start: 0.7538 (mmm) cc_final: 0.7224 (mmt) REVERT: D 190 MET cc_start: 0.7547 (mtm) cc_final: 0.7255 (mtm) REVERT: D 313 MET cc_start: 0.8088 (ttm) cc_final: 0.7725 (ttm) REVERT: E 222 ASP cc_start: 0.7732 (t0) cc_final: 0.7526 (t0) REVERT: E 283 MET cc_start: 0.7854 (mmp) cc_final: 0.7304 (mmp) REVERT: E 340 TRP cc_start: 0.8930 (t60) cc_final: 0.8422 (t60) outliers start: 49 outliers final: 35 residues processed: 308 average time/residue: 0.0987 time to fit residues: 48.6027 Evaluate side-chains 299 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN A 41 GLN C 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.098005 restraints weight = 23507.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.101167 restraints weight = 13326.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.103330 restraints weight = 8551.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.104887 restraints weight = 5989.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.105967 restraints weight = 4471.539| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15250 Z= 0.130 Angle : 0.651 10.666 20720 Z= 0.310 Chirality : 0.046 0.237 2305 Planarity : 0.004 0.037 2625 Dihedral : 9.581 175.128 2120 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.86 % Allowed : 19.75 % Favored : 77.40 % Cbeta Deviations : 0.29 % 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: 1.03 (0.20), residues: 1830 helix: 1.42 (0.19), residues: 740 sheet: 0.22 (0.30), residues: 315 loop : 0.31 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.014 0.001 TYR A 362 PHE 0.009 0.001 PHE A 31 TRP 0.016 0.002 TRP E 86 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (15240) covalent geometry : angle 0.65123 / 0.31 (20690) hydrogen bonds : bond 0.03416 / 2.25 ( 755) hydrogen bonds : angle 4.58631 / 3.33 ( 1890) link_TRANS : bond 0.00079 / 0.05 ( 10) link_TRANS : angle 0.42541 / 0.25 ( 30) *********************** 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 318 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 273 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8550 (t80) cc_final: 0.8233 (t80) REVERT: A 227 MET cc_start: 0.8109 (mmm) cc_final: 0.7654 (mtp) REVERT: A 246 GLN cc_start: 0.7966 (mt0) cc_final: 0.7550 (mt0) REVERT: A 283 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8183 (mmm) REVERT: B 47 MET cc_start: 0.7238 (mmm) cc_final: 0.6564 (mmm) REVERT: B 176 MET cc_start: 0.7707 (mmt) cc_final: 0.6997 (mmm) REVERT: B 215 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8560 (mttm) REVERT: B 313 MET cc_start: 0.8305 (tpp) cc_final: 0.8046 (ttm) REVERT: C 217 CYS cc_start: 0.8751 (m) cc_final: 0.7798 (m) REVERT: C 286 ASP cc_start: 0.5687 (OUTLIER) cc_final: 0.5420 (m-30) REVERT: C 292 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7183 (t0) REVERT: D 121 GLN cc_start: 0.7930 (tt0) cc_final: 0.7351 (tp-100) REVERT: D 190 MET cc_start: 0.7558 (mtm) cc_final: 0.7278 (mtm) REVERT: D 313 MET cc_start: 0.8143 (ttm) cc_final: 0.7888 (ttm) REVERT: E 176 MET cc_start: 0.8113 (mmt) cc_final: 0.7840 (mmm) REVERT: E 222 ASP cc_start: 0.7781 (t0) cc_final: 0.7492 (t0) REVERT: E 283 MET cc_start: 0.7889 (mmp) cc_final: 0.7329 (mmp) REVERT: E 294 TYR cc_start: 0.8008 (m-10) cc_final: 0.7610 (m-10) REVERT: E 340 TRP cc_start: 0.8954 (t60) cc_final: 0.8457 (t60) outliers start: 45 outliers final: 37 residues processed: 294 average time/residue: 0.0961 time to fit residues: 45.5415 Evaluate side-chains 307 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 83 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 ASN C 41 GLN D 59 GLN E 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.100139 restraints weight = 23097.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.103330 restraints weight = 13106.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105524 restraints weight = 8385.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.107041 restraints weight = 5854.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108143 restraints weight = 4369.564| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15250 Z= 0.119 Angle : 0.648 10.304 20720 Z= 0.308 Chirality : 0.045 0.226 2305 Planarity : 0.004 0.037 2625 Dihedral : 9.030 160.873 2120 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.73 % Allowed : 19.81 % Favored : 77.46 % Cbeta Deviations : 0.29 % 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: 1.13 (0.20), residues: 1830 helix: 1.48 (0.19), residues: 740 sheet: 0.23 (0.30), residues: 315 loop : 0.41 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.013 0.001 TYR D 166 PHE 0.013 0.001 PHE B 124 TRP 0.015 0.002 TRP A 340 HIS 0.004 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15240) covalent geometry : angle 0.64779 / 0.31 (20690) hydrogen bonds : bond 0.03230 / 2.14 ( 755) hydrogen bonds : angle 4.55974 / 3.32 ( 1890) link_TRANS : bond 0.00085 / 0.05 ( 10) link_TRANS : angle 0.40967 / 0.24 ( 30) ********************** 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 322 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 TYR cc_start: 0.8461 (t80) cc_final: 0.8191 (t80) REVERT: A 227 MET cc_start: 0.8105 (mmm) cc_final: 0.7623 (mtp) REVERT: A 283 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: B 47 MET cc_start: 0.7171 (mmm) cc_final: 0.6652 (mmm) REVERT: B 176 MET cc_start: 0.7741 (mmt) cc_final: 0.6983 (mmm) REVERT: B 215 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8584 (mttm) REVERT: C 217 CYS cc_start: 0.8752 (m) cc_final: 0.7850 (m) REVERT: C 286 ASP cc_start: 0.5648 (OUTLIER) cc_final: 0.5389 (m-30) REVERT: C 292 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7200 (t0) REVERT: D 190 MET cc_start: 0.7545 (mtm) cc_final: 0.7253 (mtm) REVERT: D 313 MET cc_start: 0.8096 (ttm) cc_final: 0.7849 (ttp) REVERT: E 176 MET cc_start: 0.8128 (mmt) cc_final: 0.7883 (mmm) REVERT: E 222 ASP cc_start: 0.7757 (t0) cc_final: 0.7468 (t0) REVERT: E 283 MET cc_start: 0.7837 (mmp) cc_final: 0.7342 (mmp) REVERT: E 294 TYR cc_start: 0.8047 (m-10) cc_final: 0.7639 (m-80) REVERT: E 340 TRP cc_start: 0.8918 (t60) cc_final: 0.8522 (t60) outliers start: 43 outliers final: 34 residues processed: 299 average time/residue: 0.1070 time to fit residues: 51.2672 Evaluate side-chains 306 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 HIS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 138 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.108089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.093495 restraints weight = 23861.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096546 restraints weight = 13671.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.098668 restraints weight = 8844.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.100150 restraints weight = 6255.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101085 restraints weight = 4710.645| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15250 Z= 0.263 Angle : 0.774 10.101 20720 Z= 0.378 Chirality : 0.051 0.287 2305 Planarity : 0.005 0.043 2625 Dihedral : 9.686 164.314 2120 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.86 % Allowed : 20.19 % Favored : 76.95 % Cbeta Deviations : 0.29 % 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: 0.59 (0.19), residues: 1830 helix: 1.02 (0.19), residues: 745 sheet: -0.04 (0.29), residues: 325 loop : 0.12 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 116 TYR 0.017 0.002 TYR D 166 PHE 0.016 0.002 PHE D 262 TRP 0.021 0.002 TRP H 1 HIS 0.008 0.001 HIS B 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.26 (15240) covalent geometry : angle 0.77398 / 0.38 (20690) hydrogen bonds : bond 0.04660 / 3.07 ( 755) hydrogen bonds : angle 4.86289 / 3.50 ( 1890) link_TRANS : bond 0.00254 / 0.17 ( 10) link_TRANS : angle 0.71602 / 0.40 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.87 seconds wall clock time: 40 minutes 51.37 seconds (2451.37 seconds total)