Starting phenix.real_space_refine on Sun May 18 01:56:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p53_17445/05_2025/8p53_17445.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p53_17445/05_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_17445/05_2025/8p53_17445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p53_17445/05_2025/8p53_17445.map" model { file = "/net/cci-nas-00/data/ceres_data/8p53_17445/05_2025/8p53_17445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p53_17445/05_2025/8p53_17445.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.10, per 1000 atoms: 0.74 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: 4.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.88 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: 5.12 Time building geometry restraints manager: 4.93 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: 0.000 Normalize map: mean=0, sd=1: 10.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 39.540 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.350 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP F 358 HIS 0.005 0.001 HIS D 287 PHE 0.016 0.001 PHE F 143 TYR 0.049 0.002 TYR E 305 ARG 0.006 0.001 ARG E 151 Details of bonding type rmsd hydrogen bonds : bond 0.15440 ( 728) hydrogen bonds : angle 6.68743 ( 2106) covalent geometry : bond 0.00399 (16577) covalent geometry : angle 0.65389 (22434) *********************** 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 : 1.679 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: 1.3672 time to fit residues: 743.1575 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 : 1.769 ------------------------------------------------------------------------------- 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 172 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 144 GLN A 227 GLN B 11 GLN B 53 ASN B 209 GLN B 227 GLN D 13 ASN E 72 GLN E 277 ASN F 72 GLN F 190 HIS F 277 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.149015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.124784 restraints weight = 22227.321| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.13 r_work: 0.3520 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 16577 Z= 0.324 Angle : 0.678 7.568 22434 Z= 0.348 Chirality : 0.048 0.170 2550 Planarity : 0.005 0.074 2927 Dihedral : 5.907 70.827 2341 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 2.46 % Allowed : 10.85 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2055 helix: 0.75 (0.17), residues: 971 sheet: -0.70 (0.30), residues: 232 loop : -0.71 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 76 HIS 0.007 0.002 HIS E 190 PHE 0.032 0.002 PHE F 143 TYR 0.036 0.002 TYR E 124 ARG 0.010 0.001 ARG E 265 Details of bonding type rmsd hydrogen bonds : bond 0.05315 ( 728) hydrogen bonds : angle 5.35211 ( 2106) covalent geometry : bond 0.00757 (16577) covalent geometry : angle 0.67799 (22434) *********************** 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 521 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 478 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8675 (mtm-85) cc_final: 0.8414 (mtm180) REVERT: A 214 ILE cc_start: 0.8956 (mm) cc_final: 0.8630 (mm) REVERT: C 113 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7764 (mtmm) REVERT: C 175 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8141 (mt-10) REVERT: C 322 GLU cc_start: 0.8297 (pm20) cc_final: 0.8092 (pm20) REVERT: C 351 MET cc_start: 0.7898 (tmm) cc_final: 0.7371 (tmm) REVERT: D 10 ILE cc_start: 0.8423 (mm) cc_final: 0.8214 (pt) REVERT: D 54 CYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8015 (t) REVERT: D 175 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 214 GLU cc_start: 0.8226 (tp30) cc_final: 0.7959 (tp30) REVERT: D 335 MET cc_start: 0.7806 (mtm) cc_final: 0.7537 (mtm) REVERT: D 351 MET cc_start: 0.7835 (tmm) cc_final: 0.7392 (tmm) REVERT: D 370 GLU cc_start: 0.7976 (tp30) cc_final: 0.7705 (tp30) REVERT: E 192 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8390 (mttp) REVERT: E 202 ASN cc_start: 0.8522 (t0) cc_final: 0.8295 (t0) REVERT: E 210 LEU cc_start: 0.8381 (tp) cc_final: 0.8085 (tp) REVERT: E 212 GLU cc_start: 0.8263 (tp30) cc_final: 0.7798 (tp30) REVERT: E 214 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7571 (tm-30) REVERT: E 230 ARG cc_start: 0.6845 (tmm-80) cc_final: 0.6552 (tmm-80) REVERT: E 295 GLU cc_start: 0.7636 (mp0) cc_final: 0.7052 (mp0) REVERT: E 322 GLU cc_start: 0.7799 (pm20) cc_final: 0.7580 (pm20) REVERT: E 336 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7780 (mt-10) REVERT: E 355 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7758 (mtp180) REVERT: E 389 LYS cc_start: 0.8854 (ptmm) cc_final: 0.8572 (ptmm) REVERT: F 106 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7522 (tm-30) REVERT: F 126 GLU cc_start: 0.7646 (tp30) cc_final: 0.7324 (tp30) REVERT: F 202 ASN cc_start: 0.8489 (t0) cc_final: 0.8209 (t0) REVERT: F 214 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7534 (tm-30) REVERT: F 230 ARG cc_start: 0.6725 (tmm-80) cc_final: 0.6365 (tmm-80) REVERT: F 245 ASP cc_start: 0.7438 (t70) cc_final: 0.7050 (t70) REVERT: F 247 ILE cc_start: 0.8246 (tt) cc_final: 0.8015 (pt) REVERT: F 322 GLU cc_start: 0.7828 (pm20) cc_final: 0.7597 (pm20) REVERT: F 336 GLU cc_start: 0.8560 (mt-10) cc_final: 0.7578 (tt0) outliers start: 43 outliers final: 17 residues processed: 484 average time/residue: 1.3368 time to fit residues: 710.4085 Evaluate side-chains 486 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 467 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 54 CYS Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 182 VAL 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 147 VAL Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 182 VAL 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 140 optimal weight: 0.1980 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 169 optimal weight: 0.0470 chunk 184 optimal weight: 2.9990 chunk 125 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN D 13 ASN D 255 GLN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN F 72 GLN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4016 r_free = 0.4016 target = 0.151936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.127543 restraints weight = 22209.138| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.17 r_work: 0.3559 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16577 Z= 0.130 Angle : 0.542 6.331 22434 Z= 0.275 Chirality : 0.041 0.156 2550 Planarity : 0.004 0.045 2927 Dihedral : 5.279 64.814 2337 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.57 % Allowed : 13.93 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2055 helix: 1.13 (0.17), residues: 973 sheet: -0.77 (0.29), residues: 242 loop : -0.56 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 PHE 0.015 0.001 PHE D 223 TYR 0.027 0.001 TYR E 124 ARG 0.009 0.001 ARG E 194 Details of bonding type rmsd hydrogen bonds : bond 0.03705 ( 728) hydrogen bonds : angle 4.92254 ( 2106) covalent geometry : bond 0.00292 (16577) covalent geometry : angle 0.54241 (22434) *********************** 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 519 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 474 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8365 (mtm180) REVERT: A 202 ARG cc_start: 0.7616 (ttp-170) cc_final: 0.7340 (ttp-170) REVERT: A 214 ILE cc_start: 0.8930 (mm) cc_final: 0.8602 (mm) REVERT: A 217 ASP cc_start: 0.8179 (t0) cc_final: 0.7978 (t70) REVERT: C 7 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.8022 (tt) REVERT: C 175 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8283 (mt-10) REVERT: C 178 THR cc_start: 0.8732 (t) cc_final: 0.8470 (m) REVERT: C 322 GLU cc_start: 0.8188 (pm20) cc_final: 0.7958 (pm20) REVERT: D 8 LEU cc_start: 0.8061 (mt) cc_final: 0.7731 (mt) REVERT: D 175 GLU cc_start: 0.8548 (mt-10) cc_final: 0.7856 (mm-30) REVERT: D 351 MET cc_start: 0.7744 (tmm) cc_final: 0.7322 (tmm) REVERT: D 370 GLU cc_start: 0.7960 (tp30) cc_final: 0.7694 (tp30) REVERT: E 202 ASN cc_start: 0.8557 (t0) cc_final: 0.8313 (t0) REVERT: E 210 LEU cc_start: 0.8358 (tp) cc_final: 0.8005 (tp) REVERT: E 212 GLU cc_start: 0.8289 (tp30) cc_final: 0.7689 (tp30) REVERT: E 214 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7551 (tm-30) REVERT: E 230 ARG cc_start: 0.6801 (tmm-80) cc_final: 0.6364 (tmm-80) REVERT: E 257 LYS cc_start: 0.8714 (mttm) cc_final: 0.8478 (mttt) REVERT: E 295 GLU cc_start: 0.7631 (mp0) cc_final: 0.7084 (mp0) REVERT: E 336 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7677 (mt-10) REVERT: F 106 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7493 (tm-30) REVERT: F 107 MET cc_start: 0.7851 (tpt) cc_final: 0.7378 (mmm) REVERT: F 202 ASN cc_start: 0.8542 (t0) cc_final: 0.8194 (t0) REVERT: F 212 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7881 (mm-30) REVERT: F 214 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7471 (tm-30) REVERT: F 230 ARG cc_start: 0.6784 (tmm-80) cc_final: 0.6350 (tmm-80) REVERT: F 241 THR cc_start: 0.8365 (m) cc_final: 0.8116 (m) REVERT: F 245 ASP cc_start: 0.7386 (t0) cc_final: 0.7070 (t70) REVERT: F 247 ILE cc_start: 0.8262 (tt) cc_final: 0.7967 (pt) REVERT: F 314 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7870 (mtm) REVERT: F 336 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7605 (tt0) REVERT: F 385 GLU cc_start: 0.8101 (mp0) cc_final: 0.7285 (mp0) outliers start: 45 outliers final: 18 residues processed: 482 average time/residue: 1.3407 time to fit residues: 709.0204 Evaluate side-chains 474 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 454 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain D residue 72 GLN Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 236 LEU 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 151 ARG Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 246 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 186 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 163 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 17 optimal weight: 0.1980 chunk 64 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 164 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 141 ASN F 186 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN F 367 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.127558 restraints weight = 22273.055| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.19 r_work: 0.3564 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2089 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= 0.135 Angle : 0.532 6.616 22434 Z= 0.270 Chirality : 0.041 0.167 2550 Planarity : 0.004 0.047 2927 Dihedral : 5.159 64.816 2337 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.46 % Allowed : 16.79 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 2055 helix: 1.28 (0.17), residues: 973 sheet: -0.77 (0.29), residues: 242 loop : -0.49 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 76 HIS 0.006 0.001 HIS E 190 PHE 0.011 0.001 PHE D 223 TYR 0.029 0.001 TYR E 124 ARG 0.009 0.000 ARG E 194 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 728) hydrogen bonds : angle 4.78218 ( 2106) covalent geometry : bond 0.00305 (16577) covalent geometry : angle 0.53194 (22434) *********************** 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 507 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 464 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7409 (tt0) REVERT: A 73 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8344 (mtm180) REVERT: A 81 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (mp) REVERT: A 202 ARG cc_start: 0.7661 (ttp-170) cc_final: 0.7406 (ttp-170) REVERT: A 214 ILE cc_start: 0.8935 (mm) cc_final: 0.8605 (mm) REVERT: C 6 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8359 (mmmm) REVERT: C 175 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8079 (mt-10) REVERT: C 178 THR cc_start: 0.8738 (t) cc_final: 0.8493 (m) REVERT: D 8 LEU cc_start: 0.7935 (mt) cc_final: 0.7697 (mt) REVERT: D 175 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7719 (mm-30) REVERT: D 178 THR cc_start: 0.8686 (t) cc_final: 0.8405 (m) REVERT: D 351 MET cc_start: 0.7777 (tmm) cc_final: 0.7319 (tmm) REVERT: D 370 GLU cc_start: 0.7895 (tp30) cc_final: 0.7611 (tp30) REVERT: E 107 MET cc_start: 0.8017 (tpt) cc_final: 0.7690 (mmm) REVERT: E 202 ASN cc_start: 0.8563 (t0) cc_final: 0.8328 (t0) REVERT: E 210 LEU cc_start: 0.8362 (tp) cc_final: 0.7997 (tp) REVERT: E 212 GLU cc_start: 0.8299 (tp30) cc_final: 0.7756 (tp30) REVERT: E 214 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7555 (tm-30) REVERT: E 230 ARG cc_start: 0.6855 (tmm-80) cc_final: 0.6408 (tmm-80) REVERT: E 295 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: E 336 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7733 (mt-10) REVERT: E 355 ARG cc_start: 0.8232 (mtp180) cc_final: 0.7707 (mtp180) REVERT: F 106 GLU cc_start: 0.7772 (tm-30) cc_final: 0.7568 (tm-30) REVERT: F 214 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7500 (tm-30) REVERT: F 230 ARG cc_start: 0.6865 (tmm-80) cc_final: 0.6441 (tmm-80) REVERT: F 241 THR cc_start: 0.8339 (m) cc_final: 0.8088 (m) REVERT: F 247 ILE cc_start: 0.8263 (tt) cc_final: 0.7978 (pt) REVERT: F 314 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8105 (mtm) REVERT: F 336 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7470 (tt0) REVERT: F 385 GLU cc_start: 0.8149 (mp0) cc_final: 0.7366 (mp0) outliers start: 43 outliers final: 24 residues processed: 475 average time/residue: 1.3603 time to fit residues: 708.5130 Evaluate side-chains 486 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 458 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN 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 B residue 76 LEU Chi-restraints excluded: chain C residue 165 ASP 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 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 147 VAL 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 213 SER 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 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 22 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 164 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 176 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN D 289 ASN D 329 ASN E 31 GLN E 277 ASN E 356 HIS ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 202 ASN F 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.150431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.125906 restraints weight = 22515.774| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.17 r_work: 0.3543 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2237 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= 0.185 Angle : 0.561 6.807 22434 Z= 0.286 Chirality : 0.042 0.178 2550 Planarity : 0.004 0.057 2927 Dihedral : 5.280 66.806 2337 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 17.53 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 2055 helix: 1.25 (0.17), residues: 971 sheet: -0.79 (0.30), residues: 220 loop : -0.60 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 76 HIS 0.005 0.001 HIS E 190 PHE 0.018 0.001 PHE A 114 TYR 0.030 0.001 TYR E 124 ARG 0.010 0.001 ARG E 194 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 728) hydrogen bonds : angle 4.85282 ( 2106) covalent geometry : bond 0.00429 (16577) covalent geometry : angle 0.56086 (22434) *********************** 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 527 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 472 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: A 73 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8362 (mtm180) REVERT: A 202 ARG cc_start: 0.7691 (ttp-170) cc_final: 0.7438 (ttp-170) REVERT: A 214 ILE cc_start: 0.8936 (mm) cc_final: 0.8593 (mm) REVERT: A 217 ASP cc_start: 0.8177 (t70) cc_final: 0.7973 (t0) REVERT: B 260 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7155 (mtp180) REVERT: C 6 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8365 (mmmm) REVERT: C 175 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8319 (mt-10) REVERT: C 178 THR cc_start: 0.8765 (t) cc_final: 0.8508 (m) REVERT: C 329 ASN cc_start: 0.8599 (m-40) cc_final: 0.8376 (m110) REVERT: C 351 MET cc_start: 0.7848 (tmm) cc_final: 0.7345 (tmm) REVERT: C 370 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: D 8 LEU cc_start: 0.7941 (mt) cc_final: 0.7707 (mt) REVERT: D 107 MET cc_start: 0.7265 (tmm) cc_final: 0.7008 (tmm) REVERT: D 175 GLU cc_start: 0.8563 (mt-10) cc_final: 0.7992 (mt-10) REVERT: D 351 MET cc_start: 0.7820 (tmm) cc_final: 0.7319 (tmm) REVERT: D 370 GLU cc_start: 0.7996 (tp30) cc_final: 0.7726 (tp30) REVERT: E 210 LEU cc_start: 0.8365 (tp) cc_final: 0.7966 (tp) REVERT: E 212 GLU cc_start: 0.8258 (tp30) cc_final: 0.7729 (tp30) REVERT: E 214 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7536 (tm-30) REVERT: E 230 ARG cc_start: 0.6846 (tmm-80) cc_final: 0.6442 (tmm-80) REVERT: E 291 GLU cc_start: 0.7845 (mt-10) cc_final: 0.6894 (mt-10) REVERT: E 295 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: E 336 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7746 (mt-10) REVERT: E 355 ARG cc_start: 0.8266 (mtp180) cc_final: 0.7697 (mtp180) REVERT: F 107 MET cc_start: 0.7926 (tpt) cc_final: 0.7522 (mmm) REVERT: F 202 ASN cc_start: 0.8566 (t0) cc_final: 0.8286 (t0) REVERT: F 214 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 230 ARG cc_start: 0.6841 (tmm-80) cc_final: 0.6447 (tmm-80) REVERT: F 245 ASP cc_start: 0.7390 (t0) cc_final: 0.7136 (t70) REVERT: F 247 ILE cc_start: 0.8304 (tt) cc_final: 0.7990 (pt) REVERT: F 336 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7552 (tt0) outliers start: 55 outliers final: 34 residues processed: 488 average time/residue: 1.3719 time to fit residues: 732.5650 Evaluate side-chains 499 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 64 ARG 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 B residue 76 LEU Chi-restraints excluded: chain B residue 260 ARG 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 213 SER Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 322 GLU 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 191 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 147 VAL 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 213 SER 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 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 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 180 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 184 optimal weight: 0.6980 chunk 151 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN D 255 GLN D 329 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126213 restraints weight = 22305.566| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.16 r_work: 0.3542 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16577 Z= 0.174 Angle : 0.563 7.274 22434 Z= 0.287 Chirality : 0.042 0.177 2550 Planarity : 0.004 0.052 2927 Dihedral : 5.248 66.033 2337 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.14 % Allowed : 18.62 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 2055 helix: 1.37 (0.17), residues: 959 sheet: -0.86 (0.30), residues: 230 loop : -0.64 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 76 HIS 0.005 0.001 HIS E 190 PHE 0.017 0.001 PHE A 114 TYR 0.029 0.001 TYR E 124 ARG 0.012 0.001 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.03923 ( 728) hydrogen bonds : angle 4.83097 ( 2106) covalent geometry : bond 0.00402 (16577) covalent geometry : angle 0.56332 (22434) *********************** 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 522 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 467 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: A 73 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8377 (mtm180) REVERT: A 202 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7446 (ttp-170) REVERT: A 214 ILE cc_start: 0.8930 (mm) cc_final: 0.8587 (mm) REVERT: C 6 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8343 (mmmm) REVERT: C 10 ILE cc_start: 0.8555 (pt) cc_final: 0.8355 (pp) REVERT: C 175 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8336 (mt-10) REVERT: C 178 THR cc_start: 0.8742 (t) cc_final: 0.8497 (m) REVERT: C 329 ASN cc_start: 0.8571 (m-40) cc_final: 0.8342 (m110) REVERT: C 351 MET cc_start: 0.7873 (tmm) cc_final: 0.7372 (tmm) REVERT: D 8 LEU cc_start: 0.7875 (mt) cc_final: 0.7628 (mt) REVERT: D 107 MET cc_start: 0.7266 (tmm) cc_final: 0.6987 (tmm) REVERT: D 175 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8002 (mt-10) REVERT: D 351 MET cc_start: 0.7856 (tmm) cc_final: 0.7352 (tmm) REVERT: D 370 GLU cc_start: 0.7932 (tp30) cc_final: 0.7655 (tp30) REVERT: E 210 LEU cc_start: 0.8358 (tp) cc_final: 0.7974 (tp) REVERT: E 212 GLU cc_start: 0.8251 (tp30) cc_final: 0.7701 (tp30) REVERT: E 214 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7553 (tm-30) REVERT: E 230 ARG cc_start: 0.6844 (tmm-80) cc_final: 0.6553 (tmm-80) REVERT: E 291 GLU cc_start: 0.7889 (mt-10) cc_final: 0.6941 (mt-10) REVERT: E 295 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: E 336 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7670 (mt-10) REVERT: F 202 ASN cc_start: 0.8499 (t0) cc_final: 0.8282 (t0) REVERT: F 214 GLU cc_start: 0.7708 (tm-30) cc_final: 0.7391 (tm-30) REVERT: F 230 ARG cc_start: 0.6842 (tmm-80) cc_final: 0.6467 (tmm-80) REVERT: F 245 ASP cc_start: 0.7385 (t0) cc_final: 0.7048 (t70) REVERT: F 247 ILE cc_start: 0.8323 (tt) cc_final: 0.8003 (pt) REVERT: F 336 GLU cc_start: 0.8498 (mt-10) cc_final: 0.7803 (mt-10) REVERT: F 385 GLU cc_start: 0.8128 (mp0) cc_final: 0.7844 (mp0) outliers start: 55 outliers final: 35 residues processed: 487 average time/residue: 1.3489 time to fit residues: 722.6977 Evaluate side-chains 497 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 460 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN 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 76 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 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 117 SER Chi-restraints excluded: chain D residue 191 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 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 213 SER 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 57 LEU 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 364 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 184 optimal weight: 0.0060 chunk 151 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 81 optimal weight: 0.0470 chunk 17 optimal weight: 0.8980 chunk 186 optimal weight: 0.9990 chunk 88 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 overall best weight: 0.4094 ------------------------------------------------------------------------------- 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 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 329 ASN ** E 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.151674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127235 restraints weight = 22469.187| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.18 r_work: 0.3559 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16577 Z= 0.131 Angle : 0.552 7.483 22434 Z= 0.279 Chirality : 0.041 0.180 2550 Planarity : 0.004 0.058 2927 Dihedral : 5.105 64.478 2337 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.08 % Allowed : 19.19 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 2055 helix: 1.53 (0.17), residues: 956 sheet: -0.85 (0.32), residues: 210 loop : -0.59 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 76 HIS 0.004 0.001 HIS F 190 PHE 0.011 0.001 PHE A 114 TYR 0.026 0.001 TYR E 124 ARG 0.012 0.001 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 728) hydrogen bonds : angle 4.71202 ( 2106) covalent geometry : bond 0.00300 (16577) covalent geometry : angle 0.55197 (22434) *********************** 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 509 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 455 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: A 73 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8350 (mtm180) REVERT: A 202 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7445 (ttp-170) REVERT: A 214 ILE cc_start: 0.8911 (mm) cc_final: 0.8561 (mm) REVERT: A 236 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7765 (mpp80) REVERT: B 260 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7052 (mtp180) REVERT: C 6 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8281 (mmmm) REVERT: C 175 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8290 (mt-10) REVERT: C 178 THR cc_start: 0.8739 (t) cc_final: 0.8496 (m) REVERT: C 351 MET cc_start: 0.7856 (tmm) cc_final: 0.7348 (tmm) REVERT: C 370 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: D 8 LEU cc_start: 0.7777 (mt) cc_final: 0.7548 (mt) REVERT: D 107 MET cc_start: 0.7226 (tmm) cc_final: 0.6943 (tmm) REVERT: D 175 GLU cc_start: 0.8552 (mt-10) cc_final: 0.7999 (mt-10) REVERT: D 329 ASN cc_start: 0.8580 (m110) cc_final: 0.8364 (m-40) REVERT: D 351 MET cc_start: 0.7830 (tmm) cc_final: 0.7314 (tmm) REVERT: D 370 GLU cc_start: 0.7976 (tp30) cc_final: 0.7713 (tp30) REVERT: E 210 LEU cc_start: 0.8371 (tp) cc_final: 0.7970 (tp) REVERT: E 212 GLU cc_start: 0.8275 (tp30) cc_final: 0.7722 (tp30) REVERT: E 214 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 230 ARG cc_start: 0.6910 (tmm-80) cc_final: 0.6587 (tmm-80) REVERT: E 291 GLU cc_start: 0.7829 (mt-10) cc_final: 0.6870 (mt-10) REVERT: E 295 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: E 336 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7792 (mt-10) REVERT: E 355 ARG cc_start: 0.8215 (mtp180) cc_final: 0.7743 (mtp180) REVERT: F 106 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7394 (tm-30) REVERT: F 107 MET cc_start: 0.8023 (tpt) cc_final: 0.7625 (mmm) REVERT: F 214 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7397 (tm-30) REVERT: F 230 ARG cc_start: 0.6875 (tmm-80) cc_final: 0.6468 (tmm-80) REVERT: F 241 THR cc_start: 0.8353 (m) cc_final: 0.8065 (m) REVERT: F 247 ILE cc_start: 0.8314 (tt) cc_final: 0.8000 (pt) REVERT: F 305 TYR cc_start: 0.7568 (m-10) cc_final: 0.7342 (m-10) REVERT: F 314 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: F 336 GLU cc_start: 0.8482 (mt-10) cc_final: 0.7452 (tt0) REVERT: F 339 LYS cc_start: 0.8729 (mmmt) cc_final: 0.8501 (mmtt) REVERT: F 385 GLU cc_start: 0.8107 (mp0) cc_final: 0.7348 (mp0) outliers start: 54 outliers final: 34 residues processed: 472 average time/residue: 1.3522 time to fit residues: 700.3374 Evaluate side-chains 487 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 448 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 64 ARG 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 B residue 76 LEU Chi-restraints excluded: chain B residue 260 ARG 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 213 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 117 SER Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 191 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 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 213 SER 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 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 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 7 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 22 optimal weight: 0.0000 chunk 95 optimal weight: 0.0020 chunk 191 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 overall best weight: 0.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 191 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 25 ASN ** E 31 GLN ** 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 = 0.4022 r_free = 0.4022 target = 0.152147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.127681 restraints weight = 22346.888| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.19 r_work: 0.3567 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16577 Z= 0.121 Angle : 0.557 7.703 22434 Z= 0.281 Chirality : 0.040 0.190 2550 Planarity : 0.004 0.055 2927 Dihedral : 5.036 63.739 2337 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.08 % Allowed : 19.99 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 2055 helix: 1.60 (0.17), residues: 956 sheet: -0.84 (0.33), residues: 206 loop : -0.57 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 76 HIS 0.004 0.001 HIS F 188 PHE 0.012 0.001 PHE C 223 TYR 0.025 0.001 TYR E 124 ARG 0.013 0.001 ARG E 194 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 728) hydrogen bonds : angle 4.65377 ( 2106) covalent geometry : bond 0.00276 (16577) covalent geometry : angle 0.55651 (22434) *********************** 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 504 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 450 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8610 (mtm-85) cc_final: 0.8340 (mtm180) REVERT: A 202 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7450 (ttp-170) REVERT: B 260 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: C 72 GLN cc_start: 0.7913 (pm20) cc_final: 0.7713 (mp10) REVERT: C 175 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8264 (mt-10) REVERT: C 178 THR cc_start: 0.8742 (t) cc_final: 0.8507 (m) REVERT: C 351 MET cc_start: 0.7850 (tmm) cc_final: 0.7341 (tmm) REVERT: C 370 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: D 8 LEU cc_start: 0.7777 (mt) cc_final: 0.7560 (mt) REVERT: D 107 MET cc_start: 0.7245 (tmm) cc_final: 0.6960 (tmm) REVERT: D 175 GLU cc_start: 0.8546 (mt-10) cc_final: 0.7934 (mt-10) REVERT: D 319 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7665 (mt-10) REVERT: D 351 MET cc_start: 0.7829 (tmm) cc_final: 0.7308 (tmm) REVERT: E 105 LEU cc_start: 0.7813 (mt) cc_final: 0.7469 (mp) REVERT: E 160 MET cc_start: 0.8717 (ttm) cc_final: 0.8505 (mtp) REVERT: E 210 LEU cc_start: 0.8390 (tp) cc_final: 0.7994 (tp) REVERT: E 212 GLU cc_start: 0.8255 (tp30) cc_final: 0.7643 (tp30) REVERT: E 214 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 230 ARG cc_start: 0.6910 (tmm-80) cc_final: 0.6482 (tmm-80) REVERT: E 291 GLU cc_start: 0.7835 (mt-10) cc_final: 0.6898 (mt-10) REVERT: E 295 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: E 336 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7752 (mt-10) REVERT: E 355 ARG cc_start: 0.8224 (mtp180) cc_final: 0.7745 (mtp180) REVERT: F 106 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7353 (tm-30) REVERT: F 151 ARG cc_start: 0.6563 (mmp-170) cc_final: 0.6305 (mmp-170) REVERT: F 214 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 230 ARG cc_start: 0.6918 (tmm-80) cc_final: 0.6519 (tmm-80) REVERT: F 241 THR cc_start: 0.8328 (m) cc_final: 0.8038 (m) REVERT: F 247 ILE cc_start: 0.8302 (tt) cc_final: 0.8002 (pt) REVERT: F 305 TYR cc_start: 0.7566 (m-10) cc_final: 0.7319 (m-10) REVERT: F 314 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7850 (mtm) REVERT: F 336 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7433 (tt0) REVERT: F 339 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8513 (mmmt) REVERT: F 385 GLU cc_start: 0.8105 (mp0) cc_final: 0.7354 (mp0) outliers start: 54 outliers final: 29 residues processed: 467 average time/residue: 1.3230 time to fit residues: 677.8521 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 : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 114 PHE Chi-restraints excluded: chain B residue 260 ARG Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 213 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 191 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 42 VAL Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 151 ARG Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 213 SER 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 178 THR Chi-restraints excluded: chain F residue 201 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 33 optimal weight: 0.0170 chunk 158 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 110 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 129 optimal weight: 0.0270 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** 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 329 ASN ** E 31 GLN ** 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 = 0.4028 r_free = 0.4028 target = 0.152579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128160 restraints weight = 22474.703| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.20 r_work: 0.3575 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16577 Z= 0.117 Angle : 0.559 8.911 22434 Z= 0.281 Chirality : 0.040 0.206 2550 Planarity : 0.004 0.056 2927 Dihedral : 4.968 63.236 2337 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.63 % Allowed : 20.33 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2055 helix: 1.59 (0.17), residues: 961 sheet: -1.00 (0.35), residues: 182 loop : -0.58 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 76 HIS 0.003 0.001 HIS F 376 PHE 0.012 0.001 PHE C 223 TYR 0.024 0.001 TYR E 124 ARG 0.013 0.000 ARG C 194 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 728) hydrogen bonds : angle 4.60287 ( 2106) covalent geometry : bond 0.00266 (16577) covalent geometry : angle 0.55910 (22434) *********************** 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 491 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 445 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 73 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.8322 (mtm180) REVERT: A 202 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7439 (ttp-170) REVERT: B 41 ARG cc_start: 0.8415 (mpp-170) cc_final: 0.8155 (mpp-170) REVERT: B 260 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7026 (mtp180) REVERT: B 263 LEU cc_start: 0.8677 (tp) cc_final: 0.8461 (tp) REVERT: C 351 MET cc_start: 0.7824 (tmm) cc_final: 0.7310 (tmm) REVERT: C 370 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: D 8 LEU cc_start: 0.7763 (mt) cc_final: 0.7545 (mt) REVERT: D 107 MET cc_start: 0.7211 (tmm) cc_final: 0.6926 (tmm) REVERT: D 175 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7877 (mm-30) REVERT: D 351 MET cc_start: 0.7816 (tmm) cc_final: 0.7296 (tmm) REVERT: E 33 THR cc_start: 0.8344 (OUTLIER) cc_final: 0.8039 (m) REVERT: E 105 LEU cc_start: 0.7814 (mt) cc_final: 0.7474 (mp) REVERT: E 210 LEU cc_start: 0.8385 (tp) cc_final: 0.7984 (tp) REVERT: E 212 GLU cc_start: 0.8296 (tp30) cc_final: 0.7789 (tp30) REVERT: E 214 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7533 (tm-30) REVERT: E 230 ARG cc_start: 0.6945 (tmm-80) cc_final: 0.6500 (tmm-80) REVERT: E 291 GLU cc_start: 0.7796 (mt-10) cc_final: 0.6893 (mt-10) REVERT: E 295 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: E 301 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 336 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 355 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7754 (mtp180) REVERT: F 106 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7291 (tm-30) REVERT: F 214 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 230 ARG cc_start: 0.6914 (tmm-80) cc_final: 0.6519 (tmm-80) REVERT: F 241 THR cc_start: 0.8315 (m) cc_final: 0.8023 (m) REVERT: F 247 ILE cc_start: 0.8318 (tt) cc_final: 0.7966 (pt) REVERT: F 305 TYR cc_start: 0.7562 (m-10) cc_final: 0.7333 (m-10) REVERT: F 314 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7864 (mtm) REVERT: F 336 GLU cc_start: 0.8481 (mt-10) cc_final: 0.7485 (tt0) REVERT: F 339 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8511 (mmmt) REVERT: F 385 GLU cc_start: 0.8105 (mp0) cc_final: 0.7373 (mp0) outliers start: 46 outliers final: 29 residues processed: 459 average time/residue: 1.3832 time to fit residues: 707.8326 Evaluate side-chains 476 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 441 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLN Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 114 PHE 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 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 166 THR Chi-restraints excluded: chain D residue 191 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 147 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 5 THR 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 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 55 optimal weight: 0.0970 chunk 5 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 191 optimal weight: 0.2980 chunk 54 optimal weight: 0.0010 chunk 97 optimal weight: 10.0000 chunk 35 optimal weight: 0.0470 chunk 137 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 191 ASN B 11 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 HIS C 329 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 31 GLN ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.153511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.129037 restraints weight = 22539.054| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.22 r_work: 0.3587 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16577 Z= 0.108 Angle : 0.575 10.276 22434 Z= 0.286 Chirality : 0.040 0.232 2550 Planarity : 0.004 0.057 2927 Dihedral : 4.886 62.297 2337 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 21.25 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 2055 helix: 1.68 (0.17), residues: 955 sheet: -1.02 (0.34), residues: 192 loop : -0.57 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 76 HIS 0.003 0.001 HIS E 188 PHE 0.013 0.001 PHE C 223 TYR 0.023 0.001 TYR E 124 ARG 0.013 0.000 ARG E 194 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 728) hydrogen bonds : angle 4.54578 ( 2106) covalent geometry : bond 0.00243 (16577) covalent geometry : angle 0.57485 (22434) ********************** 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 494 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 455 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8314 (mtm180) REVERT: A 202 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7405 (ttp-170) REVERT: B 41 ARG cc_start: 0.8406 (mpp-170) cc_final: 0.8193 (mpp-170) REVERT: B 260 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6952 (mtp180) REVERT: C 6 LYS cc_start: 0.8661 (mmtt) cc_final: 0.8233 (mmmm) REVERT: C 175 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8068 (mt-10) REVERT: C 370 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7523 (mm-30) REVERT: D 8 LEU cc_start: 0.7738 (mt) cc_final: 0.7512 (mt) REVERT: D 107 MET cc_start: 0.7153 (tmm) cc_final: 0.6891 (tmm) REVERT: D 175 GLU cc_start: 0.8517 (mt-10) cc_final: 0.7889 (mm-30) REVERT: D 351 MET cc_start: 0.7806 (tmm) cc_final: 0.7287 (tmm) REVERT: D 370 GLU cc_start: 0.7754 (tp30) cc_final: 0.7329 (tp30) REVERT: E 33 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7957 (m) REVERT: E 105 LEU cc_start: 0.7795 (mt) cc_final: 0.7450 (mp) REVERT: E 210 LEU cc_start: 0.8389 (tp) cc_final: 0.8000 (tp) REVERT: E 214 GLU cc_start: 0.7809 (tm-30) cc_final: 0.7525 (tm-30) REVERT: E 230 ARG cc_start: 0.6937 (tmm-80) cc_final: 0.6499 (tmm-80) REVERT: E 295 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: E 301 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7601 (tm-30) REVERT: E 336 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7813 (mt-10) REVERT: E 364 GLU cc_start: 0.8225 (tt0) cc_final: 0.8021 (mt-10) REVERT: F 106 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7300 (tm-30) REVERT: F 151 ARG cc_start: 0.6541 (mmp-170) cc_final: 0.6243 (mmp-170) REVERT: F 210 LEU cc_start: 0.8271 (tp) cc_final: 0.8069 (tp) REVERT: F 214 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7463 (tm-30) REVERT: F 230 ARG cc_start: 0.6964 (tmm-80) cc_final: 0.6565 (tmm-80) REVERT: F 241 THR cc_start: 0.8303 (m) cc_final: 0.8012 (m) REVERT: F 247 ILE cc_start: 0.8310 (tt) cc_final: 0.7987 (pt) REVERT: F 314 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7802 (mtm) REVERT: F 336 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7434 (tt0) REVERT: F 339 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8503 (mmmt) REVERT: F 385 GLU cc_start: 0.8076 (mp0) cc_final: 0.7357 (mp0) outliers start: 39 outliers final: 27 residues processed: 468 average time/residue: 1.2860 time to fit residues: 662.3486 Evaluate side-chains 475 residues out of total 1751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 443 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 114 PHE 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 191 SER 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 166 THR Chi-restraints excluded: chain D residue 191 SER Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 33 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 147 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 5 THR 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 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 123 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 152 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 188 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN D 329 ASN E 277 ASN ** F 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.150958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.126504 restraints weight = 22333.258| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.18 r_work: 0.3550 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16577 Z= 0.175 Angle : 0.605 9.052 22434 Z= 0.304 Chirality : 0.043 0.248 2550 Planarity : 0.005 0.075 2927 Dihedral : 5.140 65.775 2337 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.11 % Allowed : 21.47 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 2055 helix: 1.41 (0.17), residues: 978 sheet: -0.87 (0.33), residues: 206 loop : -0.63 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 76 HIS 0.004 0.001 HIS D 287 PHE 0.014 0.001 PHE C 223 TYR 0.026 0.001 TYR E 124 ARG 0.015 0.001 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 728) hydrogen bonds : angle 4.75961 ( 2106) covalent geometry : bond 0.00410 (16577) covalent geometry : angle 0.60517 (22434) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16384.83 seconds wall clock time: 281 minutes 38.94 seconds (16898.94 seconds total)