Starting phenix.real_space_refine on Thu Sep 18 08:04:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_10364.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_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 { model { file = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_10364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_10364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_10364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t20_10364/09_2025/6t20_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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 Unresolved non-hydrogen dihedrals: 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} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} 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: 3.03, per 1000 atoms: 0.20 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: 1.50 Conformation dependent library (CDL) restraints added in 737.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.67 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: 3.01 Time building geometry restraints manager: 1.97 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: 8975 27.06 - 54.12: 140 54.12 - 81.19: 55 81.19 - 108.25: 5 108.25 - 135.31: 10 Dihedral angle restraints: 9185 sinusoidal: 3730 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 9182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 788 0.049 - 0.097: 849 0.097 - 0.146: 450 0.146 - 0.194: 168 0.194 - 0.243: 50 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA ASN B 296 " pdb=" N ASN B 296 " pdb=" C ASN B 296 " pdb=" CB ASN B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ASN D 296 " pdb=" N ASN D 296 " pdb=" C ASN D 296 " pdb=" CB ASN D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ASN E 296 " pdb=" N ASN E 296 " pdb=" C ASN E 296 " pdb=" CB ASN E 296 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (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: 1.450 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.610 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 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 : 0.089 0.243 2305 Planarity : 0.006 0.052 2625 Dihedral : 12.284 135.311 5665 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 aren 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 covalent geometry : bond 0.01855 (15240) covalent geometry : angle 1.68438 (20690) hydrogen bonds : bond 0.18648 ( 755) hydrogen bonds : angle 7.44332 ( 1890) link_TRANS : bond 0.01225 ( 10) link_TRANS : angle 3.68248 ( 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 : 0.587 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: 0.7269 (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: 0.7953 (mt0) REVERT: A 258 PRO cc_start: 0.8477 (Cg_exo) cc_final: 0.8022 (Cg_endo) REVERT: A 283 MET cc_start: 0.8871 (mmp) cc_final: 0.8642 (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: 0.7333 (tt0) REVERT: B 195 GLU cc_start: 0.8327 (tt0) cc_final: 0.8109 (tt0) REVERT: B 201 VAL cc_start: 0.9003 (m) cc_final: 0.8714 (t) REVERT: B 246 GLN cc_start: 0.7925 (mt0) cc_final: 0.7509 (tt0) REVERT: B 325 MET cc_start: 0.6907 (mmm) cc_final: 0.6437 (mmt) REVERT: B 355 MET cc_start: 0.8224 (mmm) cc_final: 0.7945 (mmt) REVERT: C 201 VAL cc_start: 0.9157 (m) cc_final: 0.8739 (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: 0.7097 (t0) REVERT: D 149 THR cc_start: 0.8139 (m) cc_final: 0.7926 (t) REVERT: D 287 ILE cc_start: 0.8354 (tt) cc_final: 0.8045 (tt) REVERT: D 349 LEU cc_start: 0.7174 (tp) cc_final: 0.6897 (mt) REVERT: E 56 ASP cc_start: 0.7163 (m-30) cc_final: 0.6786 (t0) REVERT: E 59 GLN cc_start: 0.7852 (mm-40) cc_final: 0.6921 (tp40) REVERT: E 115 ASN cc_start: 0.8438 (t0) cc_final: 0.8179 (t0) REVERT: E 173 HIS cc_start: 0.8406 (p-80) cc_final: 0.8115 (p90) REVERT: E 244 ASP cc_start: 0.7812 (p0) cc_final: 0.7062 (p0) REVERT: E 299 MET cc_start: 0.8328 (mmp) cc_final: 0.8108 (mmt) REVERT: E 371 HIS cc_start: 0.8258 (m-70) cc_final: 0.8040 (m-70) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.1457 time to fit residues: 120.3712 Evaluate side-chains 281 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3461 r_free = 0.3461 target = 0.123833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.108999 restraints weight = 22194.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112452 restraints weight = 12510.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114827 restraints weight = 7923.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116475 restraints weight = 5465.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117567 restraints weight = 4009.749| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15250 Z= 0.150 Angle : 0.690 8.156 20720 Z= 0.346 Chirality : 0.049 0.351 2305 Planarity : 0.005 0.035 2625 Dihedral : 11.373 150.242 2170 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.41 % Allowed : 10.67 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.20), residues: 1830 helix: 0.69 (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 0.005 0.001 ARG C 372 TYR 0.021 0.002 TYR D 294 PHE 0.015 0.002 PHE C 124 TRP 0.014 0.002 TRP A 340 HIS 0.003 0.001 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.00336 (15240) covalent geometry : angle 0.68854 (20690) hydrogen bonds : bond 0.04098 ( 755) hydrogen bonds : angle 5.11956 ( 1890) link_TRANS : bond 0.00214 ( 10) link_TRANS : angle 1.20962 ( 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 429 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 391 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8278 (mm) cc_final: 0.7912 (pt) REVERT: A 78 ASN cc_start: 0.6418 (t0) cc_final: 0.6146 (t0) REVERT: A 166 TYR cc_start: 0.8634 (t80) cc_final: 0.8339 (t80) REVERT: A 250 ILE cc_start: 0.7381 (mm) cc_final: 0.7091 (mm) REVERT: A 258 PRO cc_start: 0.8571 (Cg_exo) cc_final: 0.8300 (Cg_endo) REVERT: A 315 LYS cc_start: 0.8125 (tttt) cc_final: 0.7767 (ttmm) REVERT: A 329 ILE cc_start: 0.8638 (mm) cc_final: 0.8422 (mm) REVERT: B 113 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7283 (mmtt) REVERT: B 176 MET cc_start: 0.7811 (mmt) cc_final: 0.7008 (mmm) REVERT: B 201 VAL cc_start: 0.8962 (m) cc_final: 0.8657 (t) REVERT: B 221 LEU cc_start: 0.8061 (mm) cc_final: 0.7802 (pt) REVERT: B 226 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 246 GLN cc_start: 0.7924 (mt0) cc_final: 0.7437 (tt0) REVERT: B 349 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6602 (tt) REVERT: B 364 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7826 (tm-30) REVERT: C 75 ILE cc_start: 0.8579 (mt) cc_final: 0.8221 (tt) REVERT: C 92 ASN cc_start: 0.8337 (t0) cc_final: 0.8041 (m-40) REVERT: C 201 VAL cc_start: 0.8850 (m) cc_final: 0.8486 (p) REVERT: C 211 ASP cc_start: 0.7580 (t70) cc_final: 0.7142 (m-30) REVERT: C 259 GLU cc_start: 0.7639 (tp30) cc_final: 0.7327 (tp30) REVERT: D 78 ASN cc_start: 0.7877 (t0) cc_final: 0.7321 (m-40) REVERT: D 152 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8786 (m) REVERT: D 214 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: D 292 ASP cc_start: 0.7321 (t0) cc_final: 0.6925 (t0) REVERT: D 364 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 50 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7631 (mtmt) REVERT: E 87 HIS cc_start: 0.8076 (t70) cc_final: 0.7855 (t-90) REVERT: E 169 TYR cc_start: 0.8254 (m-80) cc_final: 0.7798 (m-80) REVERT: E 269 MET cc_start: 0.6790 (ttm) cc_final: 0.6574 (ttm) REVERT: E 271 SER cc_start: 0.8644 (t) cc_final: 0.8382 (m) REVERT: E 299 MET cc_start: 0.8079 (mmp) cc_final: 0.7839 (mmt) REVERT: E 305 MET cc_start: 0.8272 (mmm) cc_final: 0.8067 (mmm) outliers start: 38 outliers final: 23 residues processed: 415 average time/residue: 0.1093 time to fit residues: 70.6646 Evaluate side-chains 307 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 280 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 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 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 214 GLU 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 Chi-restraints excluded: chain E residue 370 VAL 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: 7.9990 chunk 61 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 162 ASN B 111 ASN ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 111 ASN D 162 ASN D 371 HIS E 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092917 restraints weight = 23946.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095947 restraints weight = 13835.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.098108 restraints weight = 9091.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099616 restraints weight = 6489.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100664 restraints weight = 4944.161| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15250 Z= 0.293 Angle : 0.806 9.767 20720 Z= 0.403 Chirality : 0.052 0.302 2305 Planarity : 0.005 0.041 2625 Dihedral : 11.585 147.723 2170 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.51 % Allowed : 12.95 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1830 helix: 0.89 (0.19), residues: 740 sheet: 0.17 (0.29), residues: 315 loop : 0.12 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 196 TYR 0.028 0.002 TYR D 294 PHE 0.023 0.003 PHE D 262 TRP 0.018 0.003 TRP A 79 HIS 0.009 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00692 (15240) covalent geometry : angle 0.80570 (20690) hydrogen bonds : bond 0.05513 ( 755) hydrogen bonds : angle 5.16005 ( 1890) link_TRANS : bond 0.00131 ( 10) link_TRANS : angle 0.90419 ( 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 368 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 297 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8554 (mm) cc_final: 0.8269 (pt) REVERT: A 166 TYR cc_start: 0.8634 (t80) cc_final: 0.8277 (t80) REVERT: A 217 CYS cc_start: 0.9187 (m) cc_final: 0.8949 (m) REVERT: A 246 GLN cc_start: 0.8104 (mt0) cc_final: 0.7826 (mt0) REVERT: A 258 PRO cc_start: 0.8929 (Cg_exo) cc_final: 0.8660 (Cg_endo) REVERT: A 270 GLU cc_start: 0.5365 (mm-30) cc_final: 0.4851 (mp0) REVERT: A 329 ILE cc_start: 0.8824 (mm) cc_final: 0.8499 (tt) REVERT: B 14 SER cc_start: 0.7585 (t) cc_final: 0.7316 (p) REVERT: B 201 VAL cc_start: 0.8841 (m) cc_final: 0.8456 (t) REVERT: B 227 MET cc_start: 0.8599 (mmm) cc_final: 0.8390 (mmm) REVERT: B 296 ASN cc_start: 0.8399 (m-40) cc_final: 0.8118 (m110) REVERT: B 354 GLN cc_start: 0.8140 (mm110) cc_final: 0.7831 (mm-40) REVERT: C 201 VAL cc_start: 0.8795 (m) cc_final: 0.8416 (p) REVERT: C 259 GLU cc_start: 0.7758 (tp30) cc_final: 0.7295 (tp30) REVERT: D 311 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7946 (m-30) REVERT: E 269 MET cc_start: 0.6722 (ttm) cc_final: 0.6403 (ttm) REVERT: E 271 SER cc_start: 0.8865 (t) cc_final: 0.8514 (m) REVERT: E 283 MET cc_start: 0.7773 (mmp) cc_final: 0.7505 (mmm) REVERT: E 305 MET cc_start: 0.8331 (mmm) cc_final: 0.8044 (mmm) REVERT: E 327 ILE cc_start: 0.8703 (mm) cc_final: 0.8179 (tp) REVERT: F 5 CYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6763 (p) outliers start: 71 outliers final: 47 residues processed: 339 average time/residue: 0.1036 time to fit residues: 55.6170 Evaluate side-chains 287 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 238 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU 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 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 141 SER 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 216 LEU Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain D residue 260 THR 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 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 267 ILE Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 43 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 89 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 12 ASN B 111 ASN C 41 GLN D 49 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096755 restraints weight = 23456.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.099944 restraints weight = 13393.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.102180 restraints weight = 8657.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103728 restraints weight = 6093.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.104829 restraints weight = 4595.049| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15250 Z= 0.170 Angle : 0.664 7.421 20720 Z= 0.324 Chirality : 0.047 0.251 2305 Planarity : 0.005 0.038 2625 Dihedral : 11.332 153.409 2170 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.56 % Allowed : 14.60 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.20), residues: 1830 helix: 1.17 (0.19), residues: 740 sheet: 0.19 (0.29), residues: 315 loop : 0.21 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.017 0.001 TYR D 294 PHE 0.015 0.001 PHE B 375 TRP 0.015 0.002 TRP D 340 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00397 (15240) covalent geometry : angle 0.66308 (20690) hydrogen bonds : bond 0.04101 ( 755) hydrogen bonds : angle 4.84318 ( 1890) link_TRANS : bond 0.00078 ( 10) link_TRANS : angle 0.90842 ( 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 332 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 276 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ILE cc_start: 0.8545 (mm) cc_final: 0.8274 (pt) REVERT: A 166 TYR cc_start: 0.8615 (t80) cc_final: 0.8209 (t80) REVERT: A 217 CYS cc_start: 0.8997 (m) cc_final: 0.8732 (m) REVERT: A 246 GLN cc_start: 0.8084 (mt0) cc_final: 0.7733 (mt0) REVERT: A 258 PRO cc_start: 0.8931 (Cg_exo) cc_final: 0.8630 (Cg_endo) REVERT: A 270 GLU cc_start: 0.5431 (mm-30) cc_final: 0.5171 (mm-30) REVERT: A 283 MET cc_start: 0.8716 (mmm) cc_final: 0.8484 (mmm) REVERT: A 329 ILE cc_start: 0.8814 (mm) cc_final: 0.8524 (tt) REVERT: B 14 SER cc_start: 0.7676 (t) cc_final: 0.7422 (p) REVERT: B 201 VAL cc_start: 0.8772 (m) cc_final: 0.8440 (t) REVERT: B 215 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8349 (mttm) REVERT: B 364 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7832 (tm-30) REVERT: C 157 ASP cc_start: 0.7967 (t0) cc_final: 0.7747 (t0) REVERT: C 192 ILE cc_start: 0.7953 (tp) cc_final: 0.7696 (tt) REVERT: C 201 VAL cc_start: 0.8666 (m) cc_final: 0.8313 (p) REVERT: C 217 CYS cc_start: 0.8925 (m) cc_final: 0.8002 (m) REVERT: C 256 ARG cc_start: 0.7493 (ttp80) cc_final: 0.7273 (ttp-110) REVERT: C 259 GLU cc_start: 0.7805 (tp30) cc_final: 0.7268 (tp30) REVERT: D 166 TYR cc_start: 0.7881 (t80) cc_final: 0.7671 (t80) REVERT: E 269 MET cc_start: 0.6729 (ttm) cc_final: 0.6484 (mtp) REVERT: E 271 SER cc_start: 0.8884 (t) cc_final: 0.8520 (m) REVERT: E 283 MET cc_start: 0.7694 (mmp) cc_final: 0.7478 (mmm) REVERT: E 305 MET cc_start: 0.8211 (mmm) cc_final: 0.7917 (mmm) REVERT: E 327 ILE cc_start: 0.8534 (mm) cc_final: 0.8240 (tp) outliers start: 56 outliers final: 45 residues processed: 311 average time/residue: 0.1010 time to fit residues: 49.8379 Evaluate side-chains 306 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 260 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 142 LEU 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 282 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 269 MET Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 303 THR 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 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 141 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 186 THR 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 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 5 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 115 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 371 HIS C 41 GLN D 101 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095318 restraints weight = 23810.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.098516 restraints weight = 13492.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100728 restraints weight = 8685.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.102308 restraints weight = 6120.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.103403 restraints weight = 4603.935| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15250 Z= 0.234 Angle : 0.718 8.075 20720 Z= 0.352 Chirality : 0.050 0.270 2305 Planarity : 0.005 0.045 2625 Dihedral : 11.416 164.835 2170 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 4.57 % Allowed : 15.05 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.20), residues: 1830 helix: 0.82 (0.19), residues: 770 sheet: 0.04 (0.28), residues: 315 loop : 0.11 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 196 TYR 0.017 0.002 TYR D 294 PHE 0.017 0.002 PHE D 262 TRP 0.015 0.002 TRP D 340 HIS 0.009 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00555 (15240) covalent geometry : angle 0.71753 (20690) hydrogen bonds : bond 0.04655 ( 755) hydrogen bonds : angle 4.89170 ( 1890) link_TRANS : bond 0.00090 ( 10) link_TRANS : angle 0.94239 ( 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 341 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 269 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6574 (mtt-85) REVERT: A 166 TYR cc_start: 0.8669 (t80) cc_final: 0.8243 (t80) REVERT: A 217 CYS cc_start: 0.9195 (m) cc_final: 0.8873 (m) REVERT: A 246 GLN cc_start: 0.8181 (mt0) cc_final: 0.7790 (mt0) REVERT: A 258 PRO cc_start: 0.9029 (Cg_exo) cc_final: 0.8785 (Cg_endo) REVERT: A 270 GLU cc_start: 0.5786 (OUTLIER) cc_final: 0.5497 (mm-30) REVERT: B 201 VAL cc_start: 0.8823 (m) cc_final: 0.8411 (t) REVERT: B 215 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8389 (mttm) REVERT: B 364 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7901 (tm-30) REVERT: C 157 ASP cc_start: 0.8002 (t70) cc_final: 0.7691 (t0) REVERT: C 201 VAL cc_start: 0.8730 (m) cc_final: 0.8394 (p) REVERT: C 292 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7234 (t0) REVERT: D 166 TYR cc_start: 0.7847 (t80) cc_final: 0.7637 (t80) REVERT: D 346 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8325 (tt) REVERT: E 143 TYR cc_start: 0.7969 (m-80) cc_final: 0.7321 (m-80) REVERT: E 269 MET cc_start: 0.6622 (ttm) cc_final: 0.6397 (mtp) REVERT: E 271 SER cc_start: 0.8915 (t) cc_final: 0.8549 (m) REVERT: E 283 MET cc_start: 0.7820 (mmp) cc_final: 0.7428 (mmp) REVERT: E 305 MET cc_start: 0.8195 (mmm) cc_final: 0.7908 (mmm) REVERT: E 327 ILE cc_start: 0.8592 (mm) cc_final: 0.8383 (tp) outliers start: 72 outliers final: 56 residues processed: 312 average time/residue: 0.1051 time to fit residues: 52.2053 Evaluate side-chains 311 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 250 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 94 LEU 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 147 ARG Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 14 SER 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 180 LEU 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 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 349 LEU 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 202 THR Chi-restraints excluded: chain C residue 214 GLU 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 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 141 SER 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 186 THR 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 257 CYS Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 346 LEU Chi-restraints excluded: chain E residue 52 SER 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 318 THR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain F residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 41 optimal weight: 0.2980 chunk 157 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 97 optimal weight: 0.4980 chunk 173 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 173 HIS B 59 GLN C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.099422 restraints weight = 23145.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102593 restraints weight = 13092.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.104802 restraints weight = 8386.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.106336 restraints weight = 5863.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107307 restraints weight = 4372.902| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15250 Z= 0.117 Angle : 0.622 8.914 20720 Z= 0.296 Chirality : 0.046 0.233 2305 Planarity : 0.004 0.036 2625 Dihedral : 11.052 160.259 2170 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.11 % Allowed : 17.21 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.20), residues: 1830 helix: 1.39 (0.19), residues: 740 sheet: 0.16 (0.28), residues: 315 loop : 0.35 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.008 0.001 TYR E 306 PHE 0.011 0.001 PHE B 375 TRP 0.014 0.001 TRP D 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00263 (15240) covalent geometry : angle 0.62175 (20690) hydrogen bonds : bond 0.03380 ( 755) hydrogen bonds : angle 4.63968 ( 1890) link_TRANS : bond 0.00186 ( 10) link_TRANS : angle 0.98119 ( 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 330 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 281 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7477 (t0) REVERT: A 166 TYR cc_start: 0.8636 (t80) cc_final: 0.8241 (t80) REVERT: A 217 CYS cc_start: 0.8830 (m) cc_final: 0.8580 (m) REVERT: A 227 MET cc_start: 0.8078 (mmm) cc_final: 0.7673 (mtp) REVERT: A 246 GLN cc_start: 0.8112 (mt0) cc_final: 0.7741 (mt0) REVERT: A 258 PRO cc_start: 0.8933 (Cg_exo) cc_final: 0.8724 (Cg_endo) REVERT: A 270 GLU cc_start: 0.5530 (mm-30) cc_final: 0.4986 (mm-30) REVERT: B 116 ARG cc_start: 0.7840 (mmm-85) cc_final: 0.7515 (mtp85) REVERT: B 176 MET cc_start: 0.7685 (mmt) cc_final: 0.7002 (mmm) REVERT: B 215 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8399 (mttm) REVERT: B 349 LEU cc_start: 0.7098 (tp) cc_final: 0.6876 (tt) REVERT: B 364 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7733 (tm-30) REVERT: C 201 VAL cc_start: 0.8589 (m) cc_final: 0.8279 (p) REVERT: C 217 CYS cc_start: 0.8785 (m) cc_final: 0.7911 (m) REVERT: C 249 THR cc_start: 0.8967 (m) cc_final: 0.8763 (p) REVERT: C 355 MET cc_start: 0.7618 (mmm) cc_final: 0.7250 (mmt) REVERT: D 152 VAL cc_start: 0.8977 (m) cc_final: 0.8620 (p) REVERT: E 271 SER cc_start: 0.8846 (t) cc_final: 0.8435 (m) REVERT: E 283 MET cc_start: 0.7757 (mmp) cc_final: 0.7110 (mmp) REVERT: E 305 MET cc_start: 0.8110 (mmm) cc_final: 0.7832 (mtp) REVERT: E 340 TRP cc_start: 0.8955 (t60) cc_final: 0.8426 (t60) REVERT: E 353 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6808 (mp10) outliers start: 49 outliers final: 34 residues processed: 307 average time/residue: 0.1052 time to fit residues: 50.6572 Evaluate side-chains 304 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 142 LEU 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 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 215 LYS 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 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 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 141 SER 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 106 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain F residue 5 CYS Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 154 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 137 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.106950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.092223 restraints weight = 23848.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.095210 restraints weight = 13795.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097292 restraints weight = 9022.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.098794 restraints weight = 6428.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.099820 restraints weight = 4871.504| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15250 Z= 0.280 Angle : 0.780 9.284 20720 Z= 0.381 Chirality : 0.051 0.273 2305 Planarity : 0.005 0.041 2625 Dihedral : 11.221 148.726 2170 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.38 % Allowed : 17.40 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.19), residues: 1830 helix: 0.94 (0.19), residues: 745 sheet: 0.01 (0.28), residues: 315 loop : 0.07 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 196 TYR 0.014 0.002 TYR B 362 PHE 0.019 0.002 PHE D 262 TRP 0.014 0.002 TRP A 86 HIS 0.009 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00665 (15240) covalent geometry : angle 0.77977 (20690) hydrogen bonds : bond 0.04956 ( 755) hydrogen bonds : angle 4.93403 ( 1890) link_TRANS : bond 0.00156 ( 10) link_TRANS : angle 0.97724 ( 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 322 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 253 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.7308 (t0) cc_final: 0.7031 (m110) REVERT: A 166 TYR cc_start: 0.8614 (t80) cc_final: 0.8139 (t80) REVERT: A 217 CYS cc_start: 0.9208 (m) cc_final: 0.8946 (m) REVERT: A 227 MET cc_start: 0.8092 (mmm) cc_final: 0.7723 (mtp) REVERT: A 246 GLN cc_start: 0.8243 (mt0) cc_final: 0.7771 (mt0) REVERT: A 258 PRO cc_start: 0.8900 (Cg_exo) cc_final: 0.8693 (Cg_endo) REVERT: A 270 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5043 (mp0) REVERT: B 176 MET cc_start: 0.7757 (mmt) cc_final: 0.7456 (mmt) REVERT: B 201 VAL cc_start: 0.8829 (m) cc_final: 0.8401 (t) REVERT: B 215 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8383 (mttm) REVERT: C 157 ASP cc_start: 0.8064 (t70) cc_final: 0.7706 (t0) REVERT: C 201 VAL cc_start: 0.8756 (m) cc_final: 0.8447 (p) REVERT: C 211 ASP cc_start: 0.7857 (t0) cc_final: 0.7111 (m-30) REVERT: C 292 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7229 (t0) REVERT: D 313 MET cc_start: 0.7802 (ttm) cc_final: 0.7558 (ttm) REVERT: E 176 MET cc_start: 0.8092 (mmt) cc_final: 0.7859 (mmm) REVERT: E 271 SER cc_start: 0.8777 (t) cc_final: 0.8308 (m) REVERT: E 283 MET cc_start: 0.7768 (mmp) cc_final: 0.7422 (mmp) REVERT: E 286 ASP cc_start: 0.6467 (OUTLIER) cc_final: 0.6128 (m-30) REVERT: E 305 MET cc_start: 0.8229 (mmm) cc_final: 0.7965 (mtp) outliers start: 69 outliers final: 52 residues processed: 294 average time/residue: 0.1007 time to fit residues: 46.7285 Evaluate side-chains 299 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 243 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 12 ASN 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 151 ILE Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 14 SER 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 180 LEU 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 269 MET Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 360 GLN 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 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 289 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 141 SER 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 257 CYS Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 MET 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 286 ASP 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: 0.6980 chunk 35 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 chunk 130 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 162 ASN ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN E 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.113291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098668 restraints weight = 23422.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101853 restraints weight = 13317.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104052 restraints weight = 8548.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105590 restraints weight = 5974.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106665 restraints weight = 4464.398| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5990 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= 0.122 Angle : 0.651 12.211 20720 Z= 0.308 Chirality : 0.046 0.235 2305 Planarity : 0.004 0.035 2625 Dihedral : 10.781 165.284 2170 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.11 % Allowed : 18.92 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.20), residues: 1830 helix: 1.29 (0.19), residues: 740 sheet: 0.32 (0.29), residues: 310 loop : 0.23 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 116 TYR 0.013 0.001 TYR D 306 PHE 0.014 0.001 PHE A 31 TRP 0.015 0.002 TRP A 340 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00276 (15240) covalent geometry : angle 0.65013 (20690) hydrogen bonds : bond 0.03411 ( 755) hydrogen bonds : angle 4.64604 ( 1890) link_TRANS : bond 0.00181 ( 10) link_TRANS : angle 0.97758 ( 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 313 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8354 (OUTLIER) cc_final: 0.7825 (t0) REVERT: A 166 TYR cc_start: 0.8636 (t80) cc_final: 0.8255 (t80) REVERT: A 217 CYS cc_start: 0.8810 (m) cc_final: 0.8535 (m) REVERT: A 227 MET cc_start: 0.8029 (mmm) cc_final: 0.7626 (mtp) REVERT: A 270 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.5069 (mm-30) REVERT: A 283 MET cc_start: 0.8362 (mmm) cc_final: 0.8080 (mmm) REVERT: B 176 MET cc_start: 0.7744 (mmt) cc_final: 0.7014 (mmm) REVERT: B 201 VAL cc_start: 0.8715 (m) cc_final: 0.8391 (t) REVERT: B 215 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8541 (mttm) REVERT: C 201 VAL cc_start: 0.8678 (m) cc_final: 0.8337 (p) REVERT: C 217 CYS cc_start: 0.8777 (m) cc_final: 0.7854 (m) REVERT: C 249 THR cc_start: 0.8925 (m) cc_final: 0.8696 (p) REVERT: D 116 ARG cc_start: 0.7358 (mtt-85) cc_final: 0.6986 (mtt180) REVERT: D 152 VAL cc_start: 0.8866 (m) cc_final: 0.8527 (p) REVERT: D 313 MET cc_start: 0.7657 (ttm) cc_final: 0.7409 (ttm) REVERT: E 176 MET cc_start: 0.8088 (mmt) cc_final: 0.7848 (mmm) REVERT: E 271 SER cc_start: 0.8997 (t) cc_final: 0.8536 (m) REVERT: E 283 MET cc_start: 0.7787 (mmp) cc_final: 0.7264 (mmp) REVERT: E 305 MET cc_start: 0.8142 (mmm) cc_final: 0.7853 (mtp) outliers start: 49 outliers final: 38 residues processed: 290 average time/residue: 0.0986 time to fit residues: 45.7491 Evaluate side-chains 297 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 256 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 142 LEU 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 270 GLU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 14 SER 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 269 MET 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 214 GLU Chi-restraints excluded: chain C residue 260 THR 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 141 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 257 CYS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain I residue 5 CYS 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: 0.6980 chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN C 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.096186 restraints weight = 23645.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099330 restraints weight = 13456.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.101505 restraints weight = 8646.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.103013 restraints weight = 6069.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.104081 restraints weight = 4539.975| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.6078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15250 Z= 0.153 Angle : 0.678 12.180 20720 Z= 0.321 Chirality : 0.047 0.239 2305 Planarity : 0.004 0.037 2625 Dihedral : 10.788 174.695 2170 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.24 % Allowed : 19.30 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.20), residues: 1830 helix: 1.23 (0.19), residues: 745 sheet: 0.21 (0.29), residues: 315 loop : 0.31 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.016 0.001 TYR D 166 PHE 0.011 0.001 PHE B 375 TRP 0.016 0.002 TRP A 86 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00357 (15240) covalent geometry : angle 0.67751 (20690) hydrogen bonds : bond 0.03785 ( 755) hydrogen bonds : angle 4.62648 ( 1890) link_TRANS : bond 0.00111 ( 10) link_TRANS : angle 0.96157 ( 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 307 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8288 (t0) REVERT: A 166 TYR cc_start: 0.8645 (t80) cc_final: 0.8252 (t80) REVERT: A 217 CYS cc_start: 0.8921 (m) cc_final: 0.8611 (m) REVERT: A 227 MET cc_start: 0.8048 (mmm) cc_final: 0.7701 (mtp) REVERT: A 270 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5197 (mm-30) REVERT: A 283 MET cc_start: 0.8313 (mmm) cc_final: 0.8020 (mmm) REVERT: A 329 ILE cc_start: 0.8883 (mt) cc_final: 0.8543 (tt) REVERT: B 176 MET cc_start: 0.7712 (mmt) cc_final: 0.7022 (mmm) REVERT: B 201 VAL cc_start: 0.8788 (m) cc_final: 0.8452 (t) REVERT: B 215 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8549 (mttm) REVERT: C 201 VAL cc_start: 0.8718 (m) cc_final: 0.8386 (p) REVERT: C 217 CYS cc_start: 0.8835 (m) cc_final: 0.8164 (m) REVERT: C 249 THR cc_start: 0.8954 (m) cc_final: 0.8716 (p) REVERT: C 286 ASP cc_start: 0.5530 (OUTLIER) cc_final: 0.5202 (m-30) REVERT: C 292 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7197 (t0) REVERT: D 116 ARG cc_start: 0.7417 (mtt-85) cc_final: 0.7205 (mtt180) REVERT: D 152 VAL cc_start: 0.8970 (m) cc_final: 0.8590 (p) REVERT: D 190 MET cc_start: 0.7591 (mtm) cc_final: 0.7307 (mtm) REVERT: D 313 MET cc_start: 0.7670 (ttm) cc_final: 0.7435 (ttm) REVERT: E 176 MET cc_start: 0.8097 (mmt) cc_final: 0.7864 (mmm) REVERT: E 283 MET cc_start: 0.7803 (mmp) cc_final: 0.7309 (mmp) REVERT: E 294 TYR cc_start: 0.8042 (m-10) cc_final: 0.7684 (m-10) REVERT: E 305 MET cc_start: 0.8134 (mmm) cc_final: 0.7838 (mtp) REVERT: E 353 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6641 (mp10) outliers start: 51 outliers final: 41 residues processed: 286 average time/residue: 0.1013 time to fit residues: 46.1264 Evaluate side-chains 296 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 142 LEU 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 270 GLU Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 14 SER 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 269 MET 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 214 GLU Chi-restraints excluded: chain C residue 260 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 45 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 HIS Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 219 VAL 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 106 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 176 optimal weight: 0.0060 chunk 129 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 48 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 168 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN B 173 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 HIS C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.099928 restraints weight = 23141.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.103137 restraints weight = 13107.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105348 restraints weight = 8366.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.106866 restraints weight = 5826.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107946 restraints weight = 4337.951| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15250 Z= 0.111 Angle : 0.638 10.471 20720 Z= 0.300 Chirality : 0.045 0.218 2305 Planarity : 0.004 0.038 2625 Dihedral : 10.109 172.496 2170 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.73 % Allowed : 20.44 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.20), residues: 1830 helix: 1.45 (0.19), residues: 740 sheet: 0.47 (0.29), residues: 310 loop : 0.41 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.010 0.001 TYR D 306 PHE 0.013 0.001 PHE A 31 TRP 0.015 0.002 TRP A 340 HIS 0.005 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00247 (15240) covalent geometry : angle 0.63716 (20690) hydrogen bonds : bond 0.03133 ( 755) hydrogen bonds : angle 4.53204 ( 1890) link_TRANS : bond 0.00199 ( 10) link_TRANS : angle 0.98185 ( 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 327 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8118 (t0) REVERT: A 83 GLU cc_start: 0.8296 (tt0) cc_final: 0.8055 (tm-30) REVERT: A 166 TYR cc_start: 0.8591 (t80) cc_final: 0.8246 (t80) REVERT: A 217 CYS cc_start: 0.8614 (m) cc_final: 0.8384 (m) REVERT: A 227 MET cc_start: 0.8049 (mmm) cc_final: 0.7668 (mtp) REVERT: A 270 GLU cc_start: 0.5611 (OUTLIER) cc_final: 0.5114 (mm-30) REVERT: A 329 ILE cc_start: 0.8874 (mt) cc_final: 0.8551 (tt) REVERT: B 176 MET cc_start: 0.7726 (mmt) cc_final: 0.6962 (mmm) REVERT: B 215 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8581 (mttm) REVERT: B 313 MET cc_start: 0.8227 (tpp) cc_final: 0.7958 (ttm) REVERT: C 201 VAL cc_start: 0.8647 (m) cc_final: 0.8311 (p) REVERT: C 217 CYS cc_start: 0.8693 (m) cc_final: 0.7802 (m) REVERT: C 249 THR cc_start: 0.8850 (m) cc_final: 0.8639 (p) REVERT: C 286 ASP cc_start: 0.5393 (OUTLIER) cc_final: 0.5160 (m-30) REVERT: D 152 VAL cc_start: 0.8786 (m) cc_final: 0.8457 (p) REVERT: D 190 MET cc_start: 0.7522 (mtm) cc_final: 0.7220 (mtm) REVERT: D 313 MET cc_start: 0.7599 (ttm) cc_final: 0.7375 (ttm) REVERT: E 283 MET cc_start: 0.7743 (mmp) cc_final: 0.7274 (mmp) REVERT: E 294 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7595 (m-80) REVERT: E 305 MET cc_start: 0.8015 (mmm) cc_final: 0.7712 (mtp) REVERT: E 340 TRP cc_start: 0.8936 (t60) cc_final: 0.8424 (t60) outliers start: 43 outliers final: 35 residues processed: 303 average time/residue: 0.1041 time to fit residues: 49.9870 Evaluate side-chains 306 residues out of total 1575 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 266 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 106 THR Chi-restraints excluded: chain A residue 142 LEU 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 270 GLU Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain B residue 14 SER 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 202 THR Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain B residue 269 MET 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 152 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 214 GLU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 287 ILE 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 141 SER Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 294 TYR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 353 GLN Chi-restraints excluded: chain I residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 138 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 77 optimal weight: 0.0570 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 121 GLN B 40 HIS ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.110604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095884 restraints weight = 23581.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.099002 restraints weight = 13430.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.101225 restraints weight = 8649.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102735 restraints weight = 6053.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.103833 restraints weight = 4533.717| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15250 Z= 0.143 Angle : 0.677 10.662 20720 Z= 0.319 Chirality : 0.047 0.231 2305 Planarity : 0.004 0.037 2625 Dihedral : 9.684 153.316 2170 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.05 % Allowed : 20.70 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.20), residues: 1830 helix: 1.38 (0.19), residues: 745 sheet: 0.25 (0.29), residues: 325 loop : 0.43 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 116 TYR 0.012 0.001 TYR D 306 PHE 0.010 0.001 PHE B 375 TRP 0.015 0.002 TRP E 86 HIS 0.006 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00333 (15240) covalent geometry : angle 0.67604 (20690) hydrogen bonds : bond 0.03547 ( 755) hydrogen bonds : angle 4.52821 ( 1890) link_TRANS : bond 0.00120 ( 10) link_TRANS : angle 0.96072 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.08 seconds wall clock time: 41 minutes 58.82 seconds (2518.82 seconds total)