Starting phenix.real_space_refine on Sun Aug 24 02:42:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.map" model { file = "/net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p53_17445/08_2025/8p53_17445.cif" } resolution = 2.7 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= 0.018 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 6 5.49 5 Mg 2 5.21 5 S 76 5.16 5 C 10253 2.51 5 N 2937 2.21 5 O 3025 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16299 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2028 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2028 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 13, 'TRANS': 254} Chain: "C" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2996 Classifications: {'peptide': 378} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 361} Chain breaks: 1 Chain: "D" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2989 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 360} Chain breaks: 1 Chain: "E" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3097 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain: "F" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3097 Classifications: {'peptide': 390} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.63, per 1000 atoms: 0.22 Number of scatterers: 16299 At special positions: 0 Unit cell: (200.64, 74.58, 119.46, 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 76 16.00 P 6 15.00 Mg 2 11.99 O 3025 8.00 N 2937 7.00 C 10253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 827.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3850 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 20 sheets defined 51.4% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 23 through 39 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.517A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.578A pdb=" N VAL A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 153 through 172 Processing helix chain 'A' and resid 185 through 204 Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.955A pdb=" N ARG A 221 " --> pdb=" O ASP A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.524A pdb=" N SER A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.518A pdb=" N HIS A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 39 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 65 through 71 removed outlier: 3.536A pdb=" N VAL B 69 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.564A pdb=" N VAL B 79 " --> pdb=" O LEU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 133 through 142 Processing helix chain 'B' and resid 153 through 172 Processing helix chain 'B' and resid 185 through 204 Processing helix chain 'B' and resid 217 through 227 removed outlier: 3.970A pdb=" N ARG B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 234 Processing helix chain 'B' and resid 237 through 252 removed outlier: 3.537A pdb=" N SER B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 273 removed outlier: 3.505A pdb=" N LEU B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 27 Processing helix chain 'C' and resid 38 through 46 Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.580A pdb=" N LYS C 71 " --> pdb=" O VAL C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.504A pdb=" N LEU C 97 " --> pdb=" O PRO C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 129 Processing helix chain 'C' and resid 150 through 164 Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.590A pdb=" N VAL C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.618A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER C 213 " --> pdb=" O GLU C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 246 through 250 removed outlier: 3.639A pdb=" N ASP C 249 " --> pdb=" O GLU C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 265 Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 300 through 308 Processing helix chain 'C' and resid 316 through 322 removed outlier: 4.522A pdb=" N VAL C 321 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 322 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 339 removed outlier: 3.840A pdb=" N HIS C 337 " --> pdb=" O SER C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 360 through 376 Processing helix chain 'D' and resid 13 through 27 Processing helix chain 'D' and resid 38 through 46 Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.586A pdb=" N LYS D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.506A pdb=" N LEU D 97 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 129 Processing helix chain 'D' and resid 150 through 164 Processing helix chain 'D' and resid 179 through 190 removed outlier: 3.555A pdb=" N VAL D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.620A pdb=" N GLU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N SER D 213 " --> pdb=" O GLU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.628A pdb=" N ASP D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 265 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'D' and resid 300 through 308 Processing helix chain 'D' and resid 316 through 322 removed outlier: 4.430A pdb=" N VAL D 321 " --> pdb=" O ARG D 318 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU D 322 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 339 removed outlier: 3.818A pdb=" N HIS D 337 " --> pdb=" O SER D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 360 through 376 Processing helix chain 'E' and resid 13 through 27 Processing helix chain 'E' and resid 38 through 44 removed outlier: 3.716A pdb=" N VAL E 42 " --> pdb=" O ASP E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 65 through 77 removed outlier: 3.996A pdb=" N LEU E 69 " --> pdb=" O GLY E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 132 removed outlier: 3.596A pdb=" N MET E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 129 " --> pdb=" O ARG E 125 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N GLN E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ARG E 132 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 165 removed outlier: 4.465A pdb=" N ASP E 165 " --> pdb=" O GLN E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 removed outlier: 3.745A pdb=" N VAL E 183 " --> pdb=" O GLY E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 217 Processing helix chain 'E' and resid 232 through 237 removed outlier: 3.511A pdb=" N LEU E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 250 removed outlier: 3.612A pdb=" N ASP E 249 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 264 Processing helix chain 'E' and resid 289 through 296 Processing helix chain 'E' and resid 300 through 308 Processing helix chain 'E' and resid 316 through 322 removed outlier: 4.567A pdb=" N VAL E 321 " --> pdb=" O ARG E 318 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU E 322 " --> pdb=" O GLU E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 338 Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'E' and resid 360 through 376 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'F' and resid 13 through 28 Processing helix chain 'F' and resid 38 through 44 removed outlier: 3.718A pdb=" N VAL F 42 " --> pdb=" O ASP F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 65 through 77 removed outlier: 4.002A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 132 removed outlier: 3.542A pdb=" N MET F 127 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG F 132 " --> pdb=" O TYR F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 165 removed outlier: 4.460A pdb=" N ASP F 165 " --> pdb=" O GLN F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 190 removed outlier: 3.756A pdb=" N VAL F 183 " --> pdb=" O GLY F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 217 Processing helix chain 'F' and resid 232 through 237 removed outlier: 3.509A pdb=" N LEU F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 250 Processing helix chain 'F' and resid 251 through 265 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 300 through 308 Processing helix chain 'F' and resid 316 through 322 removed outlier: 4.549A pdb=" N VAL F 321 " --> pdb=" O ARG F 318 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU F 322 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 338 Processing helix chain 'F' and resid 346 through 355 Processing helix chain 'F' and resid 360 through 376 Processing helix chain 'F' and resid 387 through 391 Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 82 removed outlier: 6.778A pdb=" N VAL A 42 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 90 " --> pdb=" O VAL A 42 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 44 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 13 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 12 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 147 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA A 14 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL A 149 " --> pdb=" O ALA A 14 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR A 16 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL A 146 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA A 180 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 213 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N MET A 182 " --> pdb=" O VAL A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 81 through 82 removed outlier: 6.766A pdb=" N VAL B 42 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL B 90 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU B 44 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 13 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 12 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N LEU B 147 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA B 14 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL B 149 " --> pdb=" O ALA B 14 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR B 16 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL B 146 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ALA B 180 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 213 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N MET B 182 " --> pdb=" O VAL B 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 31 through 34 removed outlier: 6.654A pdb=" N LEU C 7 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS C 34 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU C 9 " --> pdb=" O CYS C 34 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS C 6 " --> pdb=" O ALA C 52 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N CYS C 54 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N LEU C 83 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 55 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ILE C 85 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 57 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 82 " --> pdb=" O ALA C 103 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU C 105 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU C 84 " --> pdb=" O LEU C 105 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 198 through 202 Processing sheet with id=AA5, first strand: chain 'C' and resid 217 through 218 removed outlier: 3.604A pdb=" N HIS C 218 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AA7, first strand: chain 'C' and resid 344 through 345 removed outlier: 7.722A pdb=" N ARG C 344 " --> pdb=" O ILE C 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 31 through 34 removed outlier: 6.664A pdb=" N LEU D 7 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS D 34 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU D 9 " --> pdb=" O CYS D 34 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS D 6 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N CYS D 54 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N LEU D 83 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL D 55 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE D 85 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU D 57 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE D 82 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LEU D 105 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU D 84 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 198 through 202 Processing sheet with id=AB1, first strand: chain 'D' and resid 217 through 218 removed outlier: 3.593A pdb=" N HIS D 218 " --> pdb=" O ARG D 230 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 266 through 268 Processing sheet with id=AB3, first strand: chain 'D' and resid 344 through 345 removed outlier: 7.752A pdb=" N ARG D 344 " --> pdb=" O ILE D 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 31 through 34 removed outlier: 6.614A pdb=" N LEU E 7 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N CYS E 34 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU E 9 " --> pdb=" O CYS E 34 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N LYS E 6 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 55 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 8 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU E 57 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE E 10 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N LEU E 83 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL E 55 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE E 85 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU E 57 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N ILE E 82 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N LEU E 105 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU E 84 " --> pdb=" O LEU E 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 198 through 202 removed outlier: 6.591A pdb=" N LEU E 242 " --> pdb=" O ILE E 283 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA E 285 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LEU E 244 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL E 170 " --> pdb=" O ALA E 284 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N THR E 286 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N ILE E 172 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 266 through 268 Processing sheet with id=AB7, first strand: chain 'E' and resid 344 through 345 removed outlier: 6.734A pdb=" N ARG E 344 " --> pdb=" O ILE E 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 31 through 34 removed outlier: 6.608A pdb=" N LEU F 7 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N CYS F 34 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU F 9 " --> pdb=" O CYS F 34 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LYS F 6 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL F 55 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU F 8 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU F 57 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ILE F 10 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LEU F 83 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL F 55 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE F 85 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU F 57 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE F 82 " --> pdb=" O ALA F 103 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LEU F 105 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 84 " --> pdb=" O LEU F 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 198 through 202 removed outlier: 6.632A pdb=" N LEU F 242 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ALA F 285 " --> pdb=" O LEU F 242 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 244 " --> pdb=" O ALA F 285 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL F 170 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR F 286 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE F 172 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU F 171 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET F 314 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU F 173 " --> pdb=" O MET F 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC2, first strand: chain 'F' and resid 344 through 345 removed outlier: 6.732A pdb=" N ARG F 344 " --> pdb=" O ILE F 381 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 728 hydrogen bonds defined for protein. 2106 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: 1.97 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5600 1.34 - 1.46: 3057 1.46 - 1.58: 7778 1.58 - 1.70: 6 1.70 - 1.82: 136 Bond restraints: 16577 Sorted by residual: bond pdb=" O3A ACP A 302 " pdb=" PB ACP A 302 " ideal model delta sigma weight residual 1.698 1.586 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O3A ACP B 302 " pdb=" PB ACP B 302 " ideal model delta sigma weight residual 1.698 1.587 0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C3B ACP A 302 " pdb=" PG ACP A 302 " ideal model delta sigma weight residual 1.875 1.791 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C3B ACP B 302 " pdb=" PG ACP B 302 " ideal model delta sigma weight residual 1.875 1.794 0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" O5' ACP A 302 " pdb=" PA ACP A 302 " ideal model delta sigma weight residual 1.659 1.601 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 16572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 21781 1.69 - 3.39: 529 3.39 - 5.08: 98 5.08 - 6.77: 15 6.77 - 8.47: 11 Bond angle restraints: 22434 Sorted by residual: angle pdb=" N ALA C 222 " pdb=" CA ALA C 222 " pdb=" C ALA C 222 " ideal model delta sigma weight residual 114.56 109.80 4.76 1.27e+00 6.20e-01 1.40e+01 angle pdb=" N ALA D 222 " pdb=" CA ALA D 222 " pdb=" C ALA D 222 " ideal model delta sigma weight residual 114.56 109.88 4.68 1.27e+00 6.20e-01 1.36e+01 angle pdb=" C3B ACP B 302 " pdb=" PB ACP B 302 " pdb=" O3A ACP B 302 " ideal model delta sigma weight residual 98.05 106.52 -8.47 3.00e+00 1.11e-01 7.96e+00 angle pdb=" CA ALA D 222 " pdb=" C ALA D 222 " pdb=" N PHE D 223 " ideal model delta sigma weight residual 119.26 116.12 3.14 1.14e+00 7.69e-01 7.61e+00 angle pdb=" CA ALA C 222 " pdb=" C ALA C 222 " pdb=" N PHE C 223 " ideal model delta sigma weight residual 119.26 116.12 3.14 1.14e+00 7.69e-01 7.59e+00 ... (remaining 22429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 9349 17.75 - 35.50: 695 35.50 - 53.25: 86 53.25 - 71.00: 29 71.00 - 88.75: 23 Dihedral angle restraints: 10182 sinusoidal: 4229 harmonic: 5953 Sorted by residual: dihedral pdb=" CA GLY F 360 " pdb=" C GLY F 360 " pdb=" N ASN F 361 " pdb=" CA ASN F 361 " ideal model delta harmonic sigma weight residual 180.00 -157.57 -22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA GLY E 360 " pdb=" C GLY E 360 " pdb=" N ASN E 361 " pdb=" CA ASN E 361 " ideal model delta harmonic sigma weight residual -180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ARG E 99 " pdb=" C ARG E 99 " pdb=" N ARG E 100 " pdb=" CA ARG E 100 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 10179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1952 0.048 - 0.095: 489 0.095 - 0.143: 104 0.143 - 0.190: 3 0.190 - 0.238: 2 Chirality restraints: 2550 Sorted by residual: chirality pdb=" C2' ACP B 302 " pdb=" C1' ACP B 302 " pdb=" C3' ACP B 302 " pdb=" O2' ACP B 302 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' ACP B 302 " pdb=" C2' ACP B 302 " pdb=" C4' ACP B 302 " pdb=" O3' ACP B 302 " both_signs ideal model delta sigma weight residual False -2.57 -2.80 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CG LEU F 24 " pdb=" CB LEU F 24 " pdb=" CD1 LEU F 24 " pdb=" CD2 LEU F 24 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 2547 not shown) Planarity restraints: 2927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 305 " -0.021 2.00e-02 2.50e+03 2.03e-02 8.27e+00 pdb=" CG TYR E 305 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR E 305 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR E 305 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR E 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR E 305 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR E 305 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 305 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 305 " -0.021 2.00e-02 2.50e+03 1.97e-02 7.78e+00 pdb=" CG TYR F 305 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR F 305 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 305 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR F 305 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR F 305 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR F 305 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 305 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 141 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" C ASN F 141 " -0.038 2.00e-02 2.50e+03 pdb=" O ASN F 141 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU F 142 " 0.013 2.00e-02 2.50e+03 ... (remaining 2924 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 95 2.53 - 3.13: 12303 3.13 - 3.72: 25283 3.72 - 4.31: 34539 4.31 - 4.90: 57784 Nonbonded interactions: 130004 Sorted by model distance: nonbonded pdb=" OG1 THR A 25 " pdb="MG MG A 301 " model vdw 1.943 2.170 nonbonded pdb=" OG1 THR B 25 " pdb="MG MG B 301 " model vdw 1.998 2.170 nonbonded pdb=" OG SER D 150 " pdb=" OD1 ASP D 323 " model vdw 2.046 3.040 nonbonded pdb=" OD2 ASP A 217 " pdb=" OG SER A 237 " model vdw 2.076 3.040 nonbonded pdb=" OD2 ASP B 217 " pdb=" OG SER B 237 " model vdw 2.077 3.040 ... (remaining 129999 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 4 through 392) selection = chain 'D' selection = (chain 'E' and (resid 4 through 129 or resid 142 through 392)) selection = (chain 'F' and (resid 4 through 129 or resid 142 through 392)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 14.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 16577 Z= 0.182 Angle : 0.654 8.466 22434 Z= 0.329 Chirality : 0.043 0.238 2550 Planarity : 0.004 0.033 2927 Dihedral : 13.216 88.751 6332 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.11 % Allowed : 0.06 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.24 (0.18), residues: 2055 helix: 0.59 (0.17), residues: 995 sheet: -0.89 (0.31), residues: 235 loop : -0.74 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 151 TYR 0.049 0.002 TYR E 305 PHE 0.016 0.001 PHE F 143 TRP 0.009 0.001 TRP F 358 HIS 0.005 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00399 (16577) covalent geometry : angle 0.65389 (22434) hydrogen bonds : bond 0.15440 ( 728) hydrogen bonds : angle 6.68743 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 496 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 THR cc_start: 0.8536 (p) cc_final: 0.8041 (p) REVERT: C 10 ILE cc_start: 0.8162 (mm) cc_final: 0.7904 (pt) REVERT: C 19 ASP cc_start: 0.7383 (t0) cc_final: 0.7040 (t0) REVERT: C 57 LEU cc_start: 0.7694 (tp) cc_final: 0.7302 (tp) REVERT: C 113 LYS cc_start: 0.7731 (mtmm) cc_final: 0.7470 (mtmm) REVERT: D 8 LEU cc_start: 0.8010 (mt) cc_final: 0.7803 (mt) REVERT: D 233 ARG cc_start: 0.8278 (mtp85) cc_final: 0.7927 (mtp85) REVERT: D 351 MET cc_start: 0.7451 (tmm) cc_final: 0.7086 (tmm) REVERT: D 370 GLU cc_start: 0.7423 (tp30) cc_final: 0.7063 (tp30) REVERT: E 212 GLU cc_start: 0.8041 (tp30) cc_final: 0.7772 (tp30) REVERT: E 259 LEU cc_start: 0.8900 (tp) cc_final: 0.8674 (tt) REVERT: E 295 GLU cc_start: 0.7273 (mp0) cc_final: 0.6735 (mp0) REVERT: E 336 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7612 (tt0) REVERT: F 106 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7385 (tm-30) REVERT: F 202 ASN cc_start: 0.8335 (t0) cc_final: 0.7923 (t0) REVERT: F 246 GLU cc_start: 0.7381 (pt0) cc_final: 0.7148 (pt0) REVERT: F 385 GLU cc_start: 0.8093 (mp0) cc_final: 0.7580 (mp0) outliers start: 2 outliers final: 2 residues processed: 496 average time/residue: 0.5935 time to fit residues: 322.1736 Evaluate side-chains 455 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 ILE Chi-restraints excluded: chain E residue 141 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 0.0870 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN A 227 GLN B 11 GLN B 209 GLN B 227 GLN D 13 ASN D 277 ASN E 72 GLN E 277 ASN F 72 GLN F 190 HIS F 277 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.152674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.128922 restraints weight = 22202.070| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.12 r_work: 0.3578 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16577 Z= 0.178 Angle : 0.590 6.967 22434 Z= 0.300 Chirality : 0.043 0.157 2550 Planarity : 0.005 0.062 2927 Dihedral : 5.611 67.365 2341 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.00 % Allowed : 10.39 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.13 (0.18), residues: 2055 helix: 0.95 (0.17), residues: 989 sheet: -0.66 (0.32), residues: 228 loop : -0.64 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 265 TYR 0.031 0.002 TYR E 124 PHE 0.020 0.001 PHE F 143 TRP 0.013 0.001 TRP C 76 HIS 0.006 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00409 (16577) covalent geometry : angle 0.58966 (22434) hydrogen bonds : bond 0.04179 ( 728) hydrogen bonds : angle 5.09487 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 472 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8347 (mtm180) REVERT: A 214 ILE cc_start: 0.8937 (mm) cc_final: 0.8609 (mm) REVERT: C 57 LEU cc_start: 0.7945 (tp) cc_final: 0.7657 (tp) REVERT: C 113 LYS cc_start: 0.7990 (mtmm) cc_final: 0.7759 (mtmm) REVERT: C 175 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 178 THR cc_start: 0.8713 (t) cc_final: 0.8461 (m) REVERT: C 288 LYS cc_start: 0.8972 (mtpm) cc_final: 0.8711 (mtpm) REVERT: D 8 LEU cc_start: 0.8062 (mt) cc_final: 0.7795 (mt) REVERT: D 10 ILE cc_start: 0.8375 (mm) cc_final: 0.8170 (pt) REVERT: D 19 ASP cc_start: 0.7372 (t0) cc_final: 0.7125 (t0) REVERT: D 54 CYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7952 (t) REVERT: D 175 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7846 (mm-30) REVERT: D 214 GLU cc_start: 0.8208 (tp30) cc_final: 0.7925 (tp30) REVERT: D 335 MET cc_start: 0.7790 (mtm) cc_final: 0.7580 (mtm) REVERT: D 351 MET cc_start: 0.7750 (tmm) cc_final: 0.7351 (tmm) REVERT: D 370 GLU cc_start: 0.7936 (tp30) cc_final: 0.7652 (tp30) REVERT: D 385 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7470 (mm-30) REVERT: E 192 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8325 (mttp) REVERT: E 202 ASN cc_start: 0.8540 (t0) cc_final: 0.8305 (t0) REVERT: E 210 LEU cc_start: 0.8384 (tp) cc_final: 0.8131 (tp) REVERT: E 212 GLU cc_start: 0.8234 (tp30) cc_final: 0.7696 (tp30) REVERT: E 230 ARG cc_start: 0.6799 (tmm-80) cc_final: 0.6497 (tmm-80) REVERT: E 295 GLU cc_start: 0.7599 (mp0) cc_final: 0.7014 (mp0) REVERT: E 322 GLU cc_start: 0.7706 (pm20) cc_final: 0.7469 (pm20) REVERT: E 336 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7688 (tt0) REVERT: F 106 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7451 (tm-30) REVERT: F 202 ASN cc_start: 0.8485 (t0) cc_final: 0.7798 (t0) REVERT: F 214 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7469 (tm-30) REVERT: F 230 ARG cc_start: 0.6758 (tmm-80) cc_final: 0.6444 (tmm-80) REVERT: F 245 ASP cc_start: 0.7403 (t70) cc_final: 0.6984 (t70) REVERT: F 322 GLU cc_start: 0.7683 (pm20) cc_final: 0.7449 (pm20) REVERT: F 336 GLU cc_start: 0.8461 (mt-10) cc_final: 0.7755 (tt0) outliers start: 35 outliers final: 13 residues processed: 478 average time/residue: 0.5486 time to fit residues: 288.7437 Evaluate side-chains 465 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 450 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 192 LYS Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 119 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 164 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 199 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN D 13 ASN D 255 GLN D 277 ASN E 263 GLN E 277 ASN F 141 ASN F 190 HIS F 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.128098 restraints weight = 22592.152| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.20 r_work: 0.3566 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16577 Z= 0.153 Angle : 0.551 6.993 22434 Z= 0.278 Chirality : 0.041 0.158 2550 Planarity : 0.004 0.063 2927 Dihedral : 5.199 64.493 2337 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.34 % Allowed : 13.88 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.32 (0.19), residues: 2055 helix: 1.15 (0.17), residues: 979 sheet: -0.62 (0.31), residues: 232 loop : -0.58 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 16 TYR 0.030 0.001 TYR E 124 PHE 0.019 0.001 PHE F 143 TRP 0.015 0.001 TRP C 76 HIS 0.007 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00350 (16577) covalent geometry : angle 0.55146 (22434) hydrogen bonds : bond 0.03848 ( 728) hydrogen bonds : angle 4.88585 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 465 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8308 (mtm180) REVERT: A 214 ILE cc_start: 0.8936 (mm) cc_final: 0.8614 (mm) REVERT: B 73 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8453 (mtm180) REVERT: B 166 LEU cc_start: 0.8699 (tt) cc_final: 0.8483 (tp) REVERT: C 7 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8059 (tt) REVERT: C 113 LYS cc_start: 0.7951 (mtmm) cc_final: 0.7741 (mtmm) REVERT: C 175 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7871 (mm-30) REVERT: C 178 THR cc_start: 0.8727 (t) cc_final: 0.8478 (m) REVERT: C 288 LYS cc_start: 0.8951 (mtpm) cc_final: 0.8740 (mtpm) REVERT: C 329 ASN cc_start: 0.8605 (m-40) cc_final: 0.8396 (m110) REVERT: D 8 LEU cc_start: 0.8066 (mt) cc_final: 0.7774 (mt) REVERT: D 19 ASP cc_start: 0.7435 (t0) cc_final: 0.7187 (t0) REVERT: D 175 GLU cc_start: 0.8601 (mt-10) cc_final: 0.7913 (mm-30) REVERT: D 214 GLU cc_start: 0.8240 (tp30) cc_final: 0.7973 (tp30) REVERT: D 351 MET cc_start: 0.7788 (tmm) cc_final: 0.7367 (tmm) REVERT: D 370 GLU cc_start: 0.7968 (tp30) cc_final: 0.7708 (tp30) REVERT: D 385 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7459 (mm-30) REVERT: E 202 ASN cc_start: 0.8574 (t0) cc_final: 0.8336 (t0) REVERT: E 210 LEU cc_start: 0.8373 (tp) cc_final: 0.8088 (tp) REVERT: E 212 GLU cc_start: 0.8233 (tp30) cc_final: 0.7702 (tp30) REVERT: E 230 ARG cc_start: 0.6830 (tmm-80) cc_final: 0.6528 (tmm-80) REVERT: E 295 GLU cc_start: 0.7651 (mp0) cc_final: 0.7099 (mp0) REVERT: E 336 GLU cc_start: 0.8368 (mt-10) cc_final: 0.7618 (tt0) REVERT: E 355 ARG cc_start: 0.8276 (mtp180) cc_final: 0.7752 (mtp180) REVERT: F 106 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7495 (tm-30) REVERT: F 214 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7465 (tm-30) REVERT: F 230 ARG cc_start: 0.6836 (tmm-80) cc_final: 0.6432 (tmm-80) REVERT: F 241 THR cc_start: 0.8378 (m) cc_final: 0.8120 (m) REVERT: F 336 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7623 (tt0) outliers start: 41 outliers final: 21 residues processed: 475 average time/residue: 0.5825 time to fit residues: 302.8535 Evaluate side-chains 473 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 451 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 103 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 chunk 8 optimal weight: 0.0370 chunk 19 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.2980 chunk 149 optimal weight: 0.6980 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 106 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN E 277 ASN F 141 ASN F 190 HIS F 277 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.152326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127705 restraints weight = 22331.358| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.19 r_work: 0.3567 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16577 Z= 0.138 Angle : 0.534 6.198 22434 Z= 0.271 Chirality : 0.041 0.163 2550 Planarity : 0.004 0.042 2927 Dihedral : 5.106 64.397 2337 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.51 % Allowed : 15.08 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.41 (0.19), residues: 2055 helix: 1.26 (0.17), residues: 979 sheet: -0.70 (0.31), residues: 222 loop : -0.54 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 64 TYR 0.029 0.001 TYR E 124 PHE 0.011 0.001 PHE A 114 TRP 0.017 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00316 (16577) covalent geometry : angle 0.53424 (22434) hydrogen bonds : bond 0.03629 ( 728) hydrogen bonds : angle 4.77766 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 447 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8289 (mtm180) REVERT: A 81 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8426 (mp) REVERT: A 202 ARG cc_start: 0.7619 (ttp-170) cc_final: 0.7357 (ttp-170) REVERT: A 214 ILE cc_start: 0.8922 (mm) cc_final: 0.8576 (mm) REVERT: B 73 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8467 (mtm180) REVERT: B 105 MET cc_start: 0.8289 (mtp) cc_final: 0.8084 (mtp) REVERT: C 175 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 178 THR cc_start: 0.8718 (t) cc_final: 0.8475 (m) REVERT: C 288 LYS cc_start: 0.8930 (mtpm) cc_final: 0.8705 (mtpm) REVERT: C 385 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 8 LEU cc_start: 0.7957 (mt) cc_final: 0.7715 (mt) REVERT: D 19 ASP cc_start: 0.7414 (t0) cc_final: 0.7176 (t0) REVERT: D 175 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8121 (tt0) REVERT: D 351 MET cc_start: 0.7791 (tmm) cc_final: 0.7346 (tmm) REVERT: D 370 GLU cc_start: 0.7899 (tp30) cc_final: 0.7607 (tp30) REVERT: D 385 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7457 (mm-30) REVERT: E 107 MET cc_start: 0.7937 (tpt) cc_final: 0.7651 (mmm) REVERT: E 202 ASN cc_start: 0.8576 (t0) cc_final: 0.8334 (t0) REVERT: E 210 LEU cc_start: 0.8365 (tp) cc_final: 0.8024 (tp) REVERT: E 212 GLU cc_start: 0.8257 (tp30) cc_final: 0.7660 (tp30) REVERT: E 230 ARG cc_start: 0.6866 (tmm-80) cc_final: 0.6426 (tmm-80) REVERT: E 295 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7091 (mp0) REVERT: E 336 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7554 (tt0) REVERT: E 355 ARG cc_start: 0.8268 (mtp180) cc_final: 0.7710 (mtp180) REVERT: F 106 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7527 (tm-30) REVERT: F 107 MET cc_start: 0.7854 (tpt) cc_final: 0.7306 (mmm) REVERT: F 214 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7461 (tm-30) REVERT: F 230 ARG cc_start: 0.6884 (tmm-80) cc_final: 0.6450 (tmm-80) REVERT: F 314 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8120 (mtm) REVERT: F 336 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7681 (tt0) outliers start: 44 outliers final: 26 residues processed: 456 average time/residue: 0.5768 time to fit residues: 288.2548 Evaluate side-chains 474 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 445 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 127 MET Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 370 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 123 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 170 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 137 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 277 ASN E 277 ASN F 190 HIS F 277 ASN F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.127771 restraints weight = 22408.709| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.18 r_work: 0.3566 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16577 Z= 0.141 Angle : 0.539 6.836 22434 Z= 0.272 Chirality : 0.041 0.171 2550 Planarity : 0.004 0.050 2927 Dihedral : 5.086 64.521 2337 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.80 % Allowed : 16.50 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.47 (0.19), residues: 2055 helix: 1.40 (0.17), residues: 968 sheet: -0.73 (0.31), residues: 222 loop : -0.59 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 64 TYR 0.029 0.001 TYR E 124 PHE 0.014 0.001 PHE A 114 TRP 0.018 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00322 (16577) covalent geometry : angle 0.53888 (22434) hydrogen bonds : bond 0.03624 ( 728) hydrogen bonds : angle 4.74142 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 457 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8620 (mtm-85) cc_final: 0.8287 (mtm180) REVERT: A 81 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 202 ARG cc_start: 0.7654 (ttp-170) cc_final: 0.7405 (ttp-170) REVERT: B 73 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8478 (mtm180) REVERT: B 105 MET cc_start: 0.8281 (mtp) cc_final: 0.8071 (mtp) REVERT: C 175 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8306 (mt-10) REVERT: C 178 THR cc_start: 0.8717 (t) cc_final: 0.8476 (m) REVERT: C 351 MET cc_start: 0.7786 (tmm) cc_final: 0.7299 (tmm) REVERT: C 370 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7597 (tm-30) REVERT: D 8 LEU cc_start: 0.7941 (mt) cc_final: 0.7716 (mt) REVERT: D 19 ASP cc_start: 0.7359 (t0) cc_final: 0.7153 (t0) REVERT: D 107 MET cc_start: 0.7187 (tmm) cc_final: 0.6905 (tmm) REVERT: D 175 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8153 (tt0) REVERT: D 351 MET cc_start: 0.7810 (tmm) cc_final: 0.7339 (tmm) REVERT: D 370 GLU cc_start: 0.7922 (tp30) cc_final: 0.7636 (tp30) REVERT: E 160 MET cc_start: 0.8798 (ttm) cc_final: 0.8577 (mtp) REVERT: E 202 ASN cc_start: 0.8592 (t0) cc_final: 0.8348 (t0) REVERT: E 210 LEU cc_start: 0.8351 (tp) cc_final: 0.7989 (tp) REVERT: E 212 GLU cc_start: 0.8299 (tp30) cc_final: 0.7834 (tp30) REVERT: E 230 ARG cc_start: 0.6879 (tmm-80) cc_final: 0.6423 (tmm-80) REVERT: E 254 MET cc_start: 0.8147 (mmm) cc_final: 0.7699 (mmm) REVERT: E 295 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: E 336 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 355 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7679 (mtp180) REVERT: F 214 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7452 (tm-30) REVERT: F 230 ARG cc_start: 0.6899 (tmm-80) cc_final: 0.6507 (tmm-80) REVERT: F 314 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8094 (mtm) REVERT: F 336 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7657 (tt0) outliers start: 49 outliers final: 29 residues processed: 471 average time/residue: 0.5775 time to fit residues: 298.2581 Evaluate side-chains 480 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 447 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 30 optimal weight: 1.9990 chunk 105 optimal weight: 0.0470 chunk 40 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 202 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN D 329 ASN E 277 ASN E 356 HIS ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 308 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.127235 restraints weight = 22347.825| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.17 r_work: 0.3560 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16577 Z= 0.159 Angle : 0.556 6.878 22434 Z= 0.283 Chirality : 0.042 0.180 2550 Planarity : 0.004 0.060 2927 Dihedral : 5.118 65.173 2337 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.14 % Allowed : 17.30 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.43 (0.19), residues: 2055 helix: 1.38 (0.17), residues: 968 sheet: -0.83 (0.31), residues: 222 loop : -0.60 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 194 TYR 0.029 0.001 TYR E 124 PHE 0.016 0.001 PHE A 114 TRP 0.020 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 Details of bonding type rmsd covalent geometry : bond 0.00367 (16577) covalent geometry : angle 0.55608 (22434) hydrogen bonds : bond 0.03770 ( 728) hydrogen bonds : angle 4.78324 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 461 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8631 (mtm-85) cc_final: 0.8290 (mtm180) REVERT: A 81 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8413 (mp) REVERT: A 202 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7463 (ttp-170) REVERT: B 73 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8489 (mtm180) REVERT: B 105 MET cc_start: 0.8303 (mtp) cc_final: 0.8091 (mtp) REVERT: C 6 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8316 (mmmm) REVERT: C 113 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7723 (mtmm) REVERT: C 175 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8305 (mt-10) REVERT: C 178 THR cc_start: 0.8727 (t) cc_final: 0.8480 (m) REVERT: C 288 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8663 (mtpp) REVERT: C 351 MET cc_start: 0.7804 (tmm) cc_final: 0.7303 (tmm) REVERT: C 370 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: D 8 LEU cc_start: 0.7858 (mt) cc_final: 0.7625 (mt) REVERT: D 19 ASP cc_start: 0.7391 (t0) cc_final: 0.7189 (t0) REVERT: D 107 MET cc_start: 0.7228 (tmm) cc_final: 0.6911 (tmm) REVERT: D 175 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8154 (tt0) REVERT: D 319 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 335 MET cc_start: 0.7740 (mtm) cc_final: 0.7523 (ttm) REVERT: D 351 MET cc_start: 0.7809 (tmm) cc_final: 0.7323 (tmm) REVERT: D 370 GLU cc_start: 0.7984 (tp30) cc_final: 0.7706 (tp30) REVERT: E 202 ASN cc_start: 0.8578 (t0) cc_final: 0.8327 (t0) REVERT: E 210 LEU cc_start: 0.8364 (tp) cc_final: 0.7976 (tp) REVERT: E 212 GLU cc_start: 0.8347 (tp30) cc_final: 0.7679 (tp30) REVERT: E 230 ARG cc_start: 0.6891 (tmm-80) cc_final: 0.6423 (tmm-80) REVERT: E 257 LYS cc_start: 0.8766 (mttm) cc_final: 0.8489 (mttp) REVERT: E 291 GLU cc_start: 0.7819 (mt-10) cc_final: 0.6877 (mt-10) REVERT: E 295 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7057 (mp0) REVERT: E 336 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7674 (mt-10) REVERT: E 355 ARG cc_start: 0.8240 (mtp180) cc_final: 0.7653 (mtp180) REVERT: F 214 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7473 (tm-30) REVERT: F 230 ARG cc_start: 0.6898 (tmm-80) cc_final: 0.6504 (tmm-80) REVERT: F 245 ASP cc_start: 0.7563 (t0) cc_final: 0.7346 (m-30) REVERT: F 301 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7579 (tm-30) REVERT: F 336 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7577 (tt0) REVERT: F 385 GLU cc_start: 0.8136 (mp0) cc_final: 0.7392 (mp0) outliers start: 55 outliers final: 33 residues processed: 474 average time/residue: 0.5584 time to fit residues: 290.5010 Evaluate side-chains 492 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 456 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain E residue 364 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 53 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 277 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 308 ASN F 356 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.150840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.126533 restraints weight = 22315.259| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.16 r_work: 0.3550 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16577 Z= 0.190 Angle : 0.581 8.001 22434 Z= 0.295 Chirality : 0.043 0.190 2550 Planarity : 0.004 0.062 2927 Dihedral : 5.243 66.504 2337 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.20 % Allowed : 18.16 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.36 (0.19), residues: 2055 helix: 1.33 (0.17), residues: 966 sheet: -0.89 (0.29), residues: 232 loop : -0.63 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 41 TYR 0.029 0.001 TYR E 124 PHE 0.019 0.001 PHE A 114 TRP 0.021 0.002 TRP C 76 HIS 0.004 0.001 HIS D 287 Details of bonding type rmsd covalent geometry : bond 0.00442 (16577) covalent geometry : angle 0.58071 (22434) hydrogen bonds : bond 0.04074 ( 728) hydrogen bonds : angle 4.88184 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8623 (mtm-85) cc_final: 0.8326 (mtm180) REVERT: A 81 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 202 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7459 (ttp-170) REVERT: A 251 ASP cc_start: 0.8331 (t70) cc_final: 0.8112 (t0) REVERT: B 73 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8493 (mtm180) REVERT: C 6 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8311 (mmmm) REVERT: C 175 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7768 (mt-10) REVERT: C 178 THR cc_start: 0.8747 (t) cc_final: 0.8481 (m) REVERT: C 288 LYS cc_start: 0.8911 (mtpt) cc_final: 0.8682 (mtpp) REVERT: C 351 MET cc_start: 0.7827 (tmm) cc_final: 0.7323 (tmm) REVERT: C 370 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7540 (mm-30) REVERT: C 385 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7494 (mm-30) REVERT: D 8 LEU cc_start: 0.7841 (mt) cc_final: 0.7623 (mt) REVERT: D 19 ASP cc_start: 0.7380 (t0) cc_final: 0.7178 (t0) REVERT: D 107 MET cc_start: 0.7279 (tmm) cc_final: 0.6943 (tmm) REVERT: D 175 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8196 (tt0) REVERT: D 351 MET cc_start: 0.7821 (tmm) cc_final: 0.7304 (tmm) REVERT: D 370 GLU cc_start: 0.8012 (tp30) cc_final: 0.7758 (tp30) REVERT: E 202 ASN cc_start: 0.8566 (t0) cc_final: 0.8319 (t0) REVERT: E 210 LEU cc_start: 0.8338 (tp) cc_final: 0.7967 (tp) REVERT: E 212 GLU cc_start: 0.8329 (tp30) cc_final: 0.7807 (tp30) REVERT: E 230 ARG cc_start: 0.6891 (tmm-80) cc_final: 0.6434 (tmm-80) REVERT: E 291 GLU cc_start: 0.7832 (mt-10) cc_final: 0.6890 (mt-10) REVERT: E 295 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: E 313 GLU cc_start: 0.7601 (mp0) cc_final: 0.7369 (mp0) REVERT: E 336 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7720 (mt-10) REVERT: E 355 ARG cc_start: 0.8251 (mtp180) cc_final: 0.7642 (mtp180) REVERT: F 214 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7428 (tm-30) REVERT: F 230 ARG cc_start: 0.6878 (tmm-80) cc_final: 0.6477 (tmm-80) REVERT: F 245 ASP cc_start: 0.7561 (t0) cc_final: 0.7353 (m-30) REVERT: F 301 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7555 (tm-30) REVERT: F 385 GLU cc_start: 0.8129 (mp0) cc_final: 0.7379 (mp0) outliers start: 56 outliers final: 32 residues processed: 481 average time/residue: 0.5830 time to fit residues: 307.5513 Evaluate side-chains 492 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 457 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 65 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 170 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 0.0670 chunk 159 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 277 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.151635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127176 restraints weight = 22314.761| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.16 r_work: 0.3556 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16577 Z= 0.157 Angle : 0.575 7.858 22434 Z= 0.292 Chirality : 0.042 0.198 2550 Planarity : 0.004 0.071 2927 Dihedral : 5.178 65.429 2337 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.74 % Allowed : 19.07 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.40 (0.19), residues: 2055 helix: 1.37 (0.17), residues: 968 sheet: -0.94 (0.30), residues: 222 loop : -0.60 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 41 TYR 0.027 0.001 TYR E 124 PHE 0.018 0.001 PHE A 114 TRP 0.023 0.002 TRP C 76 HIS 0.004 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00364 (16577) covalent geometry : angle 0.57498 (22434) hydrogen bonds : bond 0.03804 ( 728) hydrogen bonds : angle 4.82850 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 459 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8630 (mtm-85) cc_final: 0.8339 (mtm180) REVERT: A 202 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7483 (ttp-170) REVERT: C 6 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8318 (mmmm) REVERT: C 175 GLU cc_start: 0.8515 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 178 THR cc_start: 0.8740 (t) cc_final: 0.8494 (m) REVERT: C 351 MET cc_start: 0.7846 (tmm) cc_final: 0.7345 (tmm) REVERT: C 370 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: C 385 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7480 (mm-30) REVERT: D 8 LEU cc_start: 0.7792 (mt) cc_final: 0.7572 (mt) REVERT: D 107 MET cc_start: 0.7252 (tmm) cc_final: 0.6888 (tmm) REVERT: D 175 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8189 (tt0) REVERT: D 329 ASN cc_start: 0.8627 (m110) cc_final: 0.8417 (m-40) REVERT: D 351 MET cc_start: 0.7831 (tmm) cc_final: 0.7323 (tmm) REVERT: E 24 LEU cc_start: 0.7863 (mm) cc_final: 0.7641 (mp) REVERT: E 105 LEU cc_start: 0.7853 (mt) cc_final: 0.7515 (mp) REVERT: E 202 ASN cc_start: 0.8522 (t0) cc_final: 0.8267 (t0) REVERT: E 210 LEU cc_start: 0.8365 (tp) cc_final: 0.8000 (tp) REVERT: E 212 GLU cc_start: 0.8280 (tp30) cc_final: 0.7653 (tp30) REVERT: E 230 ARG cc_start: 0.6876 (tmm-80) cc_final: 0.6425 (tmm-80) REVERT: E 257 LYS cc_start: 0.8735 (mttm) cc_final: 0.8504 (mttp) REVERT: E 265 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8106 (ttp80) REVERT: E 291 GLU cc_start: 0.7824 (mt-10) cc_final: 0.6902 (mt-10) REVERT: E 295 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: E 313 GLU cc_start: 0.7551 (mp0) cc_final: 0.7325 (mp0) REVERT: E 336 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7635 (mt-10) REVERT: E 355 ARG cc_start: 0.8236 (mtp180) cc_final: 0.7638 (mtp180) REVERT: F 106 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7333 (tm-30) REVERT: F 214 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7408 (tm-30) REVERT: F 230 ARG cc_start: 0.6860 (tmm-80) cc_final: 0.6466 (tmm-80) REVERT: F 245 ASP cc_start: 0.7503 (t0) cc_final: 0.7302 (m-30) REVERT: F 301 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7520 (tm-30) REVERT: F 336 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7500 (tt0) REVERT: F 385 GLU cc_start: 0.8141 (mp0) cc_final: 0.7388 (mp0) outliers start: 48 outliers final: 34 residues processed: 474 average time/residue: 0.5793 time to fit residues: 301.5619 Evaluate side-chains 490 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 454 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 53 LEU Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 206 ILE Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 59 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 308 ASN F 361 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.125098 restraints weight = 22229.796| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.14 r_work: 0.3528 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16577 Z= 0.234 Angle : 0.633 8.214 22434 Z= 0.322 Chirality : 0.044 0.217 2550 Planarity : 0.005 0.078 2927 Dihedral : 5.434 68.062 2337 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.80 % Allowed : 19.19 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.24 (0.19), residues: 2055 helix: 1.22 (0.17), residues: 967 sheet: -0.98 (0.29), residues: 232 loop : -0.66 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 41 TYR 0.030 0.002 TYR E 124 PHE 0.021 0.002 PHE A 114 TRP 0.025 0.002 TRP C 76 HIS 0.005 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00548 (16577) covalent geometry : angle 0.63334 (22434) hydrogen bonds : bond 0.04438 ( 728) hydrogen bonds : angle 5.02051 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 474 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8638 (mtm-85) cc_final: 0.8333 (mtm180) REVERT: A 202 ARG cc_start: 0.7681 (ttp-170) cc_final: 0.7462 (ttp-170) REVERT: A 251 ASP cc_start: 0.8340 (t70) cc_final: 0.8126 (t0) REVERT: B 73 ARG cc_start: 0.8748 (mtm-85) cc_final: 0.8444 (mtm180) REVERT: B 260 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7235 (mtp180) REVERT: B 263 LEU cc_start: 0.8792 (tp) cc_final: 0.8517 (tp) REVERT: C 6 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8278 (mmmm) REVERT: C 113 LYS cc_start: 0.7907 (mtmm) cc_final: 0.7661 (mtmm) REVERT: C 178 THR cc_start: 0.8739 (t) cc_final: 0.8464 (m) REVERT: C 351 MET cc_start: 0.7842 (tmm) cc_final: 0.7309 (tmm) REVERT: C 370 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: D 8 LEU cc_start: 0.7748 (mt) cc_final: 0.7529 (mt) REVERT: D 107 MET cc_start: 0.7288 (tmm) cc_final: 0.6970 (tmm) REVERT: D 175 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8208 (tt0) REVERT: D 322 GLU cc_start: 0.8233 (pm20) cc_final: 0.7936 (pm20) REVERT: D 351 MET cc_start: 0.7852 (tmm) cc_final: 0.7320 (tmm) REVERT: D 370 GLU cc_start: 0.7829 (tp30) cc_final: 0.7404 (tp30) REVERT: E 202 ASN cc_start: 0.8534 (t0) cc_final: 0.8286 (t0) REVERT: E 210 LEU cc_start: 0.8349 (tp) cc_final: 0.7993 (tp) REVERT: E 212 GLU cc_start: 0.8323 (tp30) cc_final: 0.7775 (tp30) REVERT: E 230 ARG cc_start: 0.6863 (tmm-80) cc_final: 0.6430 (tmm-80) REVERT: E 291 GLU cc_start: 0.7812 (mt-10) cc_final: 0.6888 (mt-10) REVERT: E 295 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: E 313 GLU cc_start: 0.7578 (mp0) cc_final: 0.7352 (mp0) REVERT: E 336 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7758 (mt-10) REVERT: E 355 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7646 (mtp180) REVERT: F 106 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7337 (tm-30) REVERT: F 214 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7457 (tm-30) REVERT: F 230 ARG cc_start: 0.6818 (tmm-80) cc_final: 0.6457 (tmm-80) REVERT: F 245 ASP cc_start: 0.7518 (t0) cc_final: 0.7311 (m-30) REVERT: F 301 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7538 (tm-30) REVERT: F 336 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7576 (tt0) REVERT: F 385 GLU cc_start: 0.8162 (mp0) cc_final: 0.7836 (mp0) outliers start: 49 outliers final: 32 residues processed: 488 average time/residue: 0.5596 time to fit residues: 300.7120 Evaluate side-chains 505 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 470 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 86 optimal weight: 0.0070 chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 173 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 31 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 277 ASN F 308 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.150885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126863 restraints weight = 22142.268| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.14 r_work: 0.3554 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16577 Z= 0.153 Angle : 0.607 9.725 22434 Z= 0.308 Chirality : 0.042 0.202 2550 Planarity : 0.005 0.083 2927 Dihedral : 5.256 65.756 2337 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.11 % Allowed : 20.45 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.35 (0.19), residues: 2055 helix: 1.37 (0.17), residues: 960 sheet: -1.09 (0.32), residues: 206 loop : -0.66 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 41 TYR 0.025 0.001 TYR E 124 PHE 0.015 0.001 PHE A 114 TRP 0.028 0.002 TRP C 76 HIS 0.003 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00353 (16577) covalent geometry : angle 0.60672 (22434) hydrogen bonds : bond 0.03808 ( 728) hydrogen bonds : angle 4.86576 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 451 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8355 (mtm180) REVERT: A 202 ARG cc_start: 0.7729 (ttp-170) cc_final: 0.7497 (ttp-170) REVERT: B 73 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.8451 (mtm180) REVERT: B 260 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7145 (mtp180) REVERT: C 6 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8285 (mmmm) REVERT: C 178 THR cc_start: 0.8731 (t) cc_final: 0.8492 (m) REVERT: C 351 MET cc_start: 0.7832 (tmm) cc_final: 0.7323 (tmm) REVERT: C 370 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7524 (mm-30) REVERT: D 8 LEU cc_start: 0.7706 (mt) cc_final: 0.7485 (mt) REVERT: D 107 MET cc_start: 0.7246 (tmm) cc_final: 0.6932 (tmm) REVERT: D 175 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8190 (tt0) REVERT: D 322 GLU cc_start: 0.8221 (pm20) cc_final: 0.7909 (pm20) REVERT: D 329 ASN cc_start: 0.8610 (m110) cc_final: 0.8405 (m-40) REVERT: D 351 MET cc_start: 0.7806 (tmm) cc_final: 0.7274 (tmm) REVERT: D 370 GLU cc_start: 0.7721 (tp30) cc_final: 0.7292 (tp30) REVERT: E 33 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8129 (m) REVERT: E 105 LEU cc_start: 0.7810 (mt) cc_final: 0.7513 (mp) REVERT: E 210 LEU cc_start: 0.8356 (tp) cc_final: 0.8009 (tp) REVERT: E 212 GLU cc_start: 0.8336 (tp30) cc_final: 0.7689 (tp30) REVERT: E 230 ARG cc_start: 0.6874 (tmm-80) cc_final: 0.6433 (tmm-80) REVERT: E 257 LYS cc_start: 0.8756 (mttm) cc_final: 0.8525 (mttp) REVERT: E 291 GLU cc_start: 0.7801 (mt-10) cc_final: 0.6875 (mt-10) REVERT: E 295 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: E 313 GLU cc_start: 0.7563 (mp0) cc_final: 0.7335 (mp0) REVERT: E 336 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7693 (mt-10) REVERT: F 106 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7285 (tm-30) REVERT: F 214 GLU cc_start: 0.7770 (tm-30) cc_final: 0.7457 (tm-30) REVERT: F 230 ARG cc_start: 0.6830 (tmm-80) cc_final: 0.6430 (tmm-80) REVERT: F 245 ASP cc_start: 0.7487 (t0) cc_final: 0.7286 (m-30) REVERT: F 301 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7525 (tm-30) REVERT: F 336 GLU cc_start: 0.8489 (mt-10) cc_final: 0.7928 (mt-10) REVERT: F 385 GLU cc_start: 0.8114 (mp0) cc_final: 0.7751 (mp0) outliers start: 37 outliers final: 29 residues processed: 460 average time/residue: 0.5680 time to fit residues: 287.5782 Evaluate side-chains 482 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 449 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 370 GLU Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 246 GLU Chi-restraints excluded: chain E residue 295 GLU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 127 MET Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 181 GLU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 213 SER Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 314 MET Chi-restraints excluded: chain F residue 321 VAL Chi-restraints excluded: chain F residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 107 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN D 13 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 277 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126169 restraints weight = 22373.248| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 2.15 r_work: 0.3545 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16577 Z= 0.198 Angle : 0.632 9.026 22434 Z= 0.321 Chirality : 0.043 0.203 2550 Planarity : 0.005 0.077 2927 Dihedral : 5.340 66.945 2337 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.28 % Allowed : 20.56 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.24 (0.19), residues: 2055 helix: 1.28 (0.17), residues: 961 sheet: -1.07 (0.30), residues: 232 loop : -0.71 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 41 TYR 0.027 0.001 TYR E 124 PHE 0.020 0.002 PHE A 114 TRP 0.028 0.002 TRP C 76 HIS 0.004 0.001 HIS F 356 Details of bonding type rmsd covalent geometry : bond 0.00464 (16577) covalent geometry : angle 0.63224 (22434) hydrogen bonds : bond 0.04154 ( 728) hydrogen bonds : angle 4.94397 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7473.44 seconds wall clock time: 127 minutes 7.78 seconds (7627.78 seconds total)