Starting phenix.real_space_refine on Fri Sep 11 22:31:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.map" model { file = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2026/6kln_0712.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 8 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 7408 2.51 5 N 1980 2.21 5 O 2264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11748 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.43, per 1000 atoms: 0.21 Number of scatterers: 11748 At special positions: 0 Unit cell: (92.02, 96.3, 165.85, 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 84 16.00 P 8 15.00 Mg 4 11.99 O 2264 8.00 N 1980 7.00 C 7408 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: 0.97 Conformation dependent library (CDL) restraints added in 659.1 milliseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 20 sheets defined 43.3% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 78 through 91 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.116A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 117 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 144 removed outlier: 3.759A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 175 removed outlier: 3.579A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.930A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 275 through 283 removed outlier: 3.749A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.862A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.066A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.116A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.758A pdb=" N SER B 141 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.578A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.931A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 281 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.862A pdb=" N ARG B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 364 Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.067A pdb=" N VAL B 370 " --> pdb=" O PRO B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 78 through 91 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 144 removed outlier: 3.759A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.578A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 193 removed outlier: 3.537A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.931A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 318 removed outlier: 3.863A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 removed outlier: 3.608A pdb=" N GLY C 342 " --> pdb=" O SER C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 364 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.066A pdb=" N VAL C 370 " --> pdb=" O PRO C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.636A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.758A pdb=" N SER D 141 " --> pdb=" O GLN D 137 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.579A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.536A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.930A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.748A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 275 through 283 removed outlier: 3.750A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.633A pdb=" N TYR D 294 " --> pdb=" O ARG D 290 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.645A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 removed outlier: 3.863A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 347 removed outlier: 3.607A pdb=" N GLY D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 364 Processing helix chain 'D' and resid 366 through 370 removed outlier: 4.067A pdb=" N VAL D 370 " --> pdb=" O PRO D 367 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS A 161 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.182A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS B 161 " --> pdb=" O ASP B 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB5, first strand: chain 'C' and resid 176 through 178 removed outlier: 3.921A pdb=" N HIS C 161 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.181A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC1, first strand: chain 'D' and resid 176 through 178 removed outlier: 3.920A pdb=" N HIS D 161 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 404 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.27 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: 3840 1.34 - 1.46: 2624 1.46 - 1.58: 5380 1.58 - 1.70: 12 1.70 - 1.82: 148 Bond restraints: 12004 Sorted by residual: bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.80e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.75e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.399 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.398 -0.051 2.00e-02 2.50e+03 6.59e+00 bond pdb=" CG HIC D 73 " pdb=" CD2 HIC D 73 " ideal model delta sigma weight residual 1.369 1.407 -0.038 2.00e-02 2.50e+03 3.61e+00 ... (remaining 11999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 15354 1.64 - 3.27: 802 3.27 - 4.91: 108 4.91 - 6.55: 24 6.55 - 8.18: 4 Bond angle restraints: 16292 Sorted by residual: angle pdb=" N ILE A 267 " pdb=" CA ILE A 267 " pdb=" C ILE A 267 " ideal model delta sigma weight residual 111.91 108.86 3.05 8.90e-01 1.26e+00 1.18e+01 angle pdb=" N ILE C 267 " pdb=" CA ILE C 267 " pdb=" C ILE C 267 " ideal model delta sigma weight residual 111.91 108.89 3.02 8.90e-01 1.26e+00 1.15e+01 angle pdb=" N ILE B 267 " pdb=" CA ILE B 267 " pdb=" C ILE B 267 " ideal model delta sigma weight residual 111.91 108.91 3.00 8.90e-01 1.26e+00 1.14e+01 angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 111.91 108.92 2.99 8.90e-01 1.26e+00 1.13e+01 angle pdb=" C ALA C 22 " pdb=" N GLY C 23 " pdb=" CA GLY C 23 " ideal model delta sigma weight residual 123.30 120.24 3.06 1.06e+00 8.90e-01 8.34e+00 ... (remaining 16287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 6296 17.74 - 35.48: 736 35.48 - 53.21: 128 53.21 - 70.95: 48 70.95 - 88.69: 12 Dihedral angle restraints: 7220 sinusoidal: 2920 harmonic: 4300 Sorted by residual: dihedral pdb=" CA SER D 232 " pdb=" C SER D 232 " pdb=" N SER D 233 " pdb=" CA SER D 233 " ideal model delta harmonic sigma weight residual -180.00 -156.53 -23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER A 232 " pdb=" C SER A 232 " pdb=" N SER A 233 " pdb=" CA SER A 233 " ideal model delta harmonic sigma weight residual -180.00 -156.56 -23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA SER C 232 " pdb=" C SER C 232 " pdb=" N SER C 233 " pdb=" CA SER C 233 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 7217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 853 0.035 - 0.070: 612 0.070 - 0.105: 246 0.105 - 0.140: 93 0.140 - 0.175: 4 Chirality restraints: 1808 Sorted by residual: chirality pdb=" CB VAL D 152 " pdb=" CA VAL D 152 " pdb=" CG1 VAL D 152 " pdb=" CG2 VAL D 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CB VAL B 152 " pdb=" CA VAL B 152 " pdb=" CG1 VAL B 152 " pdb=" CG2 VAL B 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.57e-01 chirality pdb=" CB VAL A 152 " pdb=" CA VAL A 152 " pdb=" CG1 VAL A 152 " pdb=" CG2 VAL A 152 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1805 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.36e+00 pdb=" C GLU B 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU B 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER B 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 270 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C GLU A 270 " -0.027 2.00e-02 2.50e+03 pdb=" O GLU A 270 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 271 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 242 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 243 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 8514 3.10 - 3.70: 17100 3.70 - 4.30: 25426 4.30 - 4.90: 43623 Nonbonded interactions: 94774 Sorted by model distance: nonbonded pdb="MG MG D 801 " pdb=" O1B ADP D 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG B 801 " pdb=" O1B ADP B 802 " model vdw 1.903 2.170 nonbonded pdb="MG MG A 801 " pdb=" O1B ADP A 802 " model vdw 1.904 2.170 nonbonded pdb="MG MG C 801 " pdb=" O1B ADP C 802 " model vdw 1.904 2.170 nonbonded pdb=" O SER A 33 " pdb=" OG SER A 33 " model vdw 2.168 3.040 ... (remaining 94769 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.720 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.470 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.009 0.058 12004 Z= 0.416 Angle : 0.859 8.181 16292 Z= 0.486 Chirality : 0.053 0.175 1808 Planarity : 0.004 0.038 2084 Dihedral : 16.338 88.687 4468 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 11.46 % Allowed : 9.71 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.65 (0.17), residues: 1468 helix: -3.50 (0.15), residues: 580 sheet: -2.92 (0.28), residues: 220 loop : -2.59 (0.19), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 37 TYR 0.009 0.001 TYR A 69 PHE 0.009 0.002 PHE D 375 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00940 / 0.42 (12004) covalent geometry : angle 0.85853 / 0.49 (16292) hydrogen bonds : bond 0.22575 / 15.79 ( 404) hydrogen bonds : angle 8.89386 / 6.09 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 80 time to evaluate : 0.472 Fit side-chains REVERT: A 44 MET cc_start: 0.8158 (mmt) cc_final: 0.7043 (pmm) REVERT: A 152 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8761 (p) REVERT: B 66 THR cc_start: 0.9648 (OUTLIER) cc_final: 0.9425 (t) REVERT: B 132 MET cc_start: 0.9097 (ppp) cc_final: 0.8814 (ppp) REVERT: B 167 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: B 249 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9288 (p) REVERT: B 351 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 44 MET cc_start: 0.7316 (mmt) cc_final: 0.6958 (tpp) REVERT: C 82 MET cc_start: 0.9121 (tpt) cc_final: 0.8469 (tmm) REVERT: C 277 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 303 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9175 (p) REVERT: C 326 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: D 47 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4662 (mpp) REVERT: D 152 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9012 (m) outliers start: 144 outliers final: 34 residues processed: 217 average time/residue: 0.0864 time to fit residues: 28.8057 Evaluate side-chains 111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 67 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 167 GLU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 298 VAL Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 326 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 47 MET Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN A 161 HIS A 162 ASN B 78 ASN B 92 ASN B 161 HIS ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 ASN C 92 ASN C 161 HIS C 162 ASN D 78 ASN D 92 ASN D 161 HIS D 162 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028779 restraints weight = 74766.033| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 4.06 r_work: 0.2536 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12004 Z= 0.139 Angle : 0.612 5.902 16292 Z= 0.305 Chirality : 0.044 0.137 1808 Planarity : 0.004 0.032 2084 Dihedral : 8.753 63.963 1725 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.63 % Allowed : 13.54 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.20), residues: 1468 helix: -1.99 (0.20), residues: 568 sheet: -2.06 (0.29), residues: 228 loop : -1.65 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.009 0.001 TYR B 306 PHE 0.021 0.001 PHE A 223 TRP 0.011 0.002 TRP A 340 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (12004) covalent geometry : angle 0.61168 / 0.30 (16292) hydrogen bonds : bond 0.03017 / 2.03 ( 404) hydrogen bonds : angle 5.30281 / 3.80 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.440 Fit side-chains REVERT: A 44 MET cc_start: 0.8202 (mmt) cc_final: 0.6688 (pmm) REVERT: A 47 MET cc_start: 0.4294 (mmt) cc_final: 0.4004 (mmm) REVERT: A 227 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8808 (mpp) REVERT: A 303 THR cc_start: 0.9603 (OUTLIER) cc_final: 0.9220 (m) REVERT: B 44 MET cc_start: 0.7894 (mmm) cc_final: 0.6376 (ptp) REVERT: B 132 MET cc_start: 0.9314 (ppp) cc_final: 0.9022 (ppp) REVERT: C 82 MET cc_start: 0.9363 (tpt) cc_final: 0.8683 (tmm) REVERT: C 176 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7911 (mtt) REVERT: C 283 MET cc_start: 0.9130 (mmm) cc_final: 0.8702 (mmm) REVERT: C 305 MET cc_start: 0.9473 (mmm) cc_final: 0.9169 (mtp) REVERT: D 47 MET cc_start: 0.5717 (mtm) cc_final: 0.4932 (mpp) REVERT: D 227 MET cc_start: 0.9114 (tpp) cc_final: 0.8402 (tpp) outliers start: 33 outliers final: 16 residues processed: 97 average time/residue: 0.0751 time to fit residues: 11.9861 Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 25 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 15 optimal weight: 20.0000 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN B 162 ASN B 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.027359 restraints weight = 76616.012| |-----------------------------------------------------------------------------| r_work (start): 0.2596 rms_B_bonded: 4.05 r_work: 0.2458 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12004 Z= 0.267 Angle : 0.669 7.147 16292 Z= 0.328 Chirality : 0.047 0.163 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.706 64.061 1684 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.67 % Allowed : 14.65 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.21), residues: 1468 helix: -1.16 (0.22), residues: 564 sheet: -1.34 (0.33), residues: 228 loop : -1.11 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 177 TYR 0.012 0.001 TYR A 166 PHE 0.013 0.002 PHE A 223 TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (12004) covalent geometry : angle 0.66918 / 0.33 (16292) hydrogen bonds : bond 0.03307 / 2.22 ( 404) hydrogen bonds : angle 5.06709 / 3.62 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.428 Fit side-chains REVERT: A 44 MET cc_start: 0.8330 (mmt) cc_final: 0.6793 (pmm) REVERT: A 47 MET cc_start: 0.4408 (mmt) cc_final: 0.4159 (mmm) REVERT: A 227 MET cc_start: 0.9400 (tpp) cc_final: 0.8807 (mpp) REVERT: B 44 MET cc_start: 0.8051 (mmm) cc_final: 0.6605 (ptp) REVERT: B 283 MET cc_start: 0.9478 (tpp) cc_final: 0.9092 (tpp) REVERT: C 78 ASN cc_start: 0.9248 (OUTLIER) cc_final: 0.8514 (t0) REVERT: C 82 MET cc_start: 0.9519 (tpt) cc_final: 0.8665 (tmm) REVERT: C 176 MET cc_start: 0.8612 (mtt) cc_final: 0.8183 (mtt) REVERT: C 227 MET cc_start: 0.9358 (tpp) cc_final: 0.9062 (tpp) REVERT: C 305 MET cc_start: 0.9449 (mmm) cc_final: 0.9062 (mtp) REVERT: D 47 MET cc_start: 0.5505 (mtm) cc_final: 0.4885 (mpp) REVERT: D 277 THR cc_start: 0.9073 (OUTLIER) cc_final: 0.8788 (t) outliers start: 21 outliers final: 15 residues processed: 85 average time/residue: 0.0806 time to fit residues: 11.0997 Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 10 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.033874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.027704 restraints weight = 76243.539| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 4.03 r_work: 0.2471 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12004 Z= 0.199 Angle : 0.596 7.582 16292 Z= 0.287 Chirality : 0.045 0.130 1808 Planarity : 0.003 0.029 2084 Dihedral : 7.080 58.863 1679 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.75 % Allowed : 15.53 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.22), residues: 1468 helix: -0.61 (0.23), residues: 564 sheet: -1.12 (0.34), residues: 244 loop : -0.67 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.008 0.001 TYR A 166 PHE 0.011 0.001 PHE A 223 TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (12004) covalent geometry : angle 0.59607 / 0.29 (16292) hydrogen bonds : bond 0.02783 / 1.85 ( 404) hydrogen bonds : angle 4.84691 / 3.46 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.513 Fit side-chains REVERT: A 44 MET cc_start: 0.8485 (mmt) cc_final: 0.7004 (pmm) REVERT: A 47 MET cc_start: 0.4833 (mmt) cc_final: 0.4588 (mmm) REVERT: A 227 MET cc_start: 0.9356 (tpp) cc_final: 0.8864 (mpp) REVERT: A 305 MET cc_start: 0.9415 (mtp) cc_final: 0.9072 (mtp) REVERT: B 44 MET cc_start: 0.7993 (mmm) cc_final: 0.6543 (ptp) REVERT: B 283 MET cc_start: 0.9446 (tpp) cc_final: 0.9062 (tpp) REVERT: C 82 MET cc_start: 0.9506 (tpt) cc_final: 0.8727 (tmm) REVERT: C 176 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8181 (mtt) REVERT: C 283 MET cc_start: 0.9208 (mmm) cc_final: 0.8797 (mmm) REVERT: D 47 MET cc_start: 0.5749 (mtm) cc_final: 0.5336 (mpp) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.0778 time to fit residues: 10.7999 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 overall best weight: 5.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.033594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.027424 restraints weight = 76670.688| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 4.08 r_work: 0.2459 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 12004 Z= 0.217 Angle : 0.604 7.997 16292 Z= 0.290 Chirality : 0.045 0.133 1808 Planarity : 0.004 0.030 2084 Dihedral : 6.752 59.435 1676 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.67 % Allowed : 17.04 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1468 helix: -0.31 (0.23), residues: 564 sheet: -0.97 (0.34), residues: 244 loop : -0.35 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.009 0.001 TYR A 166 PHE 0.009 0.001 PHE C 255 TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (12004) covalent geometry : angle 0.60449 / 0.29 (16292) hydrogen bonds : bond 0.02817 / 1.87 ( 404) hydrogen bonds : angle 4.76103 / 3.38 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 0.479 Fit side-chains REVERT: A 44 MET cc_start: 0.8413 (mmt) cc_final: 0.6963 (pmm) REVERT: A 227 MET cc_start: 0.9362 (tpp) cc_final: 0.8871 (mpp) REVERT: A 325 MET cc_start: 0.7765 (ptt) cc_final: 0.7486 (ppp) REVERT: B 44 MET cc_start: 0.7972 (mmm) cc_final: 0.6592 (ptp) REVERT: B 283 MET cc_start: 0.9429 (tpp) cc_final: 0.9054 (tpp) REVERT: C 78 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8504 (t0) REVERT: C 82 MET cc_start: 0.9526 (tpt) cc_final: 0.8717 (tmm) REVERT: C 176 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8248 (mtt) REVERT: D 47 MET cc_start: 0.6125 (mtm) cc_final: 0.5769 (mpp) REVERT: D 82 MET cc_start: 0.9407 (tpt) cc_final: 0.8832 (mmm) REVERT: D 227 MET cc_start: 0.9254 (tpp) cc_final: 0.8485 (mpp) outliers start: 21 outliers final: 15 residues processed: 86 average time/residue: 0.0913 time to fit residues: 12.6502 Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.033424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.027284 restraints weight = 76566.729| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 4.03 r_work: 0.2476 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12004 Z= 0.160 Angle : 0.565 8.093 16292 Z= 0.268 Chirality : 0.044 0.126 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.466 59.321 1674 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.27 % Allowed : 17.20 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1468 helix: 0.01 (0.23), residues: 564 sheet: -0.74 (0.32), residues: 268 loop : -0.15 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.007 0.001 TYR A 166 PHE 0.009 0.001 PHE C 255 TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (12004) covalent geometry : angle 0.56500 / 0.27 (16292) hydrogen bonds : bond 0.02603 / 1.72 ( 404) hydrogen bonds : angle 4.63337 / 3.29 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.525 Fit side-chains REVERT: A 44 MET cc_start: 0.8276 (mmt) cc_final: 0.7179 (pmm) REVERT: A 227 MET cc_start: 0.9288 (tpp) cc_final: 0.8894 (mpp) REVERT: A 305 MET cc_start: 0.9418 (mtp) cc_final: 0.9062 (mtp) REVERT: A 325 MET cc_start: 0.7913 (ptt) cc_final: 0.7302 (ppp) REVERT: B 44 MET cc_start: 0.7954 (mmm) cc_final: 0.6585 (ptp) REVERT: B 283 MET cc_start: 0.9405 (tpp) cc_final: 0.9003 (tpp) REVERT: C 78 ASN cc_start: 0.9186 (OUTLIER) cc_final: 0.8426 (t0) REVERT: C 82 MET cc_start: 0.9518 (tpt) cc_final: 0.9303 (mmm) REVERT: C 176 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8231 (mtt) REVERT: C 283 MET cc_start: 0.9177 (mmm) cc_final: 0.8826 (mmm) REVERT: D 47 MET cc_start: 0.5907 (mtm) cc_final: 0.5687 (mpp) REVERT: D 82 MET cc_start: 0.9389 (tpt) cc_final: 0.8584 (tmm) REVERT: D 227 MET cc_start: 0.9295 (tpp) cc_final: 0.8537 (tpp) outliers start: 16 outliers final: 10 residues processed: 83 average time/residue: 0.0934 time to fit residues: 12.2271 Evaluate side-chains 79 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.0770 chunk 81 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 overall best weight: 7.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.027310 restraints weight = 77395.865| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 3.83 r_work: 0.2473 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12004 Z= 0.280 Angle : 0.643 7.865 16292 Z= 0.310 Chirality : 0.046 0.145 1808 Planarity : 0.004 0.031 2084 Dihedral : 6.612 60.319 1673 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.51 % Allowed : 17.12 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.23), residues: 1468 helix: 0.04 (0.23), residues: 568 sheet: -0.90 (0.35), residues: 244 loop : -0.09 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.010 0.001 TYR A 166 PHE 0.010 0.001 PHE B 223 TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.28 (12004) covalent geometry : angle 0.64319 / 0.31 (16292) hydrogen bonds : bond 0.02982 / 1.98 ( 404) hydrogen bonds : angle 4.80045 / 3.41 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.474 Fit side-chains REVERT: A 44 MET cc_start: 0.8284 (mmt) cc_final: 0.7211 (pmm) REVERT: A 227 MET cc_start: 0.9312 (tpp) cc_final: 0.8911 (mpp) REVERT: A 325 MET cc_start: 0.8050 (ptt) cc_final: 0.7512 (ppp) REVERT: B 44 MET cc_start: 0.8132 (mmm) cc_final: 0.6883 (ptp) REVERT: B 283 MET cc_start: 0.9414 (tpp) cc_final: 0.9029 (tpp) REVERT: C 78 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8610 (t0) REVERT: C 82 MET cc_start: 0.9556 (tpt) cc_final: 0.8908 (tmm) REVERT: C 176 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8321 (mtt) REVERT: C 205 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8457 (mp0) REVERT: C 283 MET cc_start: 0.9239 (mmm) cc_final: 0.8850 (mmm) REVERT: D 82 MET cc_start: 0.9468 (tpt) cc_final: 0.8709 (tmm) REVERT: D 227 MET cc_start: 0.9363 (tpp) cc_final: 0.8731 (tpp) outliers start: 19 outliers final: 14 residues processed: 82 average time/residue: 0.0923 time to fit residues: 11.9483 Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 21 optimal weight: 8.9990 chunk 109 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.033899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.027834 restraints weight = 75999.955| |-----------------------------------------------------------------------------| r_work (start): 0.2618 rms_B_bonded: 4.02 r_work: 0.2478 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12004 Z= 0.147 Angle : 0.553 7.624 16292 Z= 0.261 Chirality : 0.044 0.127 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.247 59.744 1673 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.27 % Allowed : 17.60 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.23), residues: 1468 helix: 0.19 (0.23), residues: 568 sheet: -0.67 (0.32), residues: 268 loop : 0.07 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.006 0.001 TYR C 133 PHE 0.008 0.001 PHE D 255 TRP 0.010 0.002 TRP A 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (12004) covalent geometry : angle 0.55322 / 0.26 (16292) hydrogen bonds : bond 0.02535 / 1.67 ( 404) hydrogen bonds : angle 4.54823 / 3.23 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8330 (mmt) cc_final: 0.7202 (pmm) REVERT: A 227 MET cc_start: 0.9211 (tpp) cc_final: 0.8876 (mpp) REVERT: A 325 MET cc_start: 0.8046 (ptm) cc_final: 0.7242 (ppp) REVERT: B 44 MET cc_start: 0.8023 (mmm) cc_final: 0.6735 (ptp) REVERT: B 283 MET cc_start: 0.9392 (tpp) cc_final: 0.9112 (tpp) REVERT: C 78 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8440 (t0) REVERT: C 82 MET cc_start: 0.9538 (tpt) cc_final: 0.9336 (mmm) REVERT: C 176 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8453 (mtt) REVERT: C 283 MET cc_start: 0.9179 (mmm) cc_final: 0.8764 (mmm) REVERT: D 82 MET cc_start: 0.9390 (tpt) cc_final: 0.8572 (tmm) REVERT: D 227 MET cc_start: 0.9355 (tpp) cc_final: 0.8727 (tpp) outliers start: 16 outliers final: 13 residues processed: 81 average time/residue: 0.0924 time to fit residues: 11.9427 Evaluate side-chains 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.0050 chunk 26 optimal weight: 0.0870 chunk 88 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 2.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.027931 restraints weight = 75312.167| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 4.00 r_work: 0.2508 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8950 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 12004 Z= 0.106 Angle : 0.528 7.869 16292 Z= 0.246 Chirality : 0.043 0.127 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.811 58.320 1673 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.11 % Allowed : 17.75 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1468 helix: 0.43 (0.23), residues: 568 sheet: -0.63 (0.32), residues: 268 loop : 0.14 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.006 0.001 TYR C 133 PHE 0.008 0.001 PHE D 255 TRP 0.009 0.001 TRP C 340 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12004) covalent geometry : angle 0.52774 / 0.25 (16292) hydrogen bonds : bond 0.02395 / 1.58 ( 404) hydrogen bonds : angle 4.36174 / 3.09 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8371 (mmt) cc_final: 0.7281 (pmm) REVERT: A 227 MET cc_start: 0.9143 (tpp) cc_final: 0.8902 (mpp) REVERT: A 305 MET cc_start: 0.9408 (mtp) cc_final: 0.9095 (mtp) REVERT: A 325 MET cc_start: 0.7865 (ptm) cc_final: 0.6962 (ppp) REVERT: B 44 MET cc_start: 0.7952 (mmm) cc_final: 0.6711 (ptp) REVERT: B 283 MET cc_start: 0.9385 (tpp) cc_final: 0.9111 (tpp) REVERT: C 78 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8371 (t0) REVERT: C 283 MET cc_start: 0.9131 (mmm) cc_final: 0.8713 (mmm) REVERT: D 82 MET cc_start: 0.9347 (tpt) cc_final: 0.8516 (tmm) REVERT: D 227 MET cc_start: 0.9406 (tpp) cc_final: 0.8887 (tpp) outliers start: 14 outliers final: 12 residues processed: 80 average time/residue: 0.0979 time to fit residues: 12.3528 Evaluate side-chains 79 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 0.0770 chunk 51 optimal weight: 0.0570 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.034597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028533 restraints weight = 75644.532| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 4.03 r_work: 0.2535 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12004 Z= 0.083 Angle : 0.517 7.739 16292 Z= 0.239 Chirality : 0.042 0.127 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.432 56.961 1673 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.96 % Allowed : 18.23 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1468 helix: 0.57 (0.23), residues: 568 sheet: -0.52 (0.32), residues: 268 loop : 0.24 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 177 TYR 0.006 0.001 TYR C 133 PHE 0.008 0.001 PHE D 255 TRP 0.009 0.001 TRP C 340 HIS 0.005 0.001 HIS C 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.08 (12004) covalent geometry : angle 0.51687 / 0.24 (16292) hydrogen bonds : bond 0.02273 / 1.50 ( 404) hydrogen bonds : angle 4.23391 / 2.99 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.438 Fit side-chains REVERT: A 44 MET cc_start: 0.8447 (mmt) cc_final: 0.7222 (pmm) REVERT: A 47 MET cc_start: 0.5385 (mmm) cc_final: 0.5182 (mmm) REVERT: A 305 MET cc_start: 0.9385 (mtp) cc_final: 0.9035 (mtp) REVERT: B 44 MET cc_start: 0.7936 (mmm) cc_final: 0.6671 (ptp) REVERT: B 283 MET cc_start: 0.9382 (tpp) cc_final: 0.9129 (tpp) REVERT: C 78 ASN cc_start: 0.9104 (OUTLIER) cc_final: 0.8437 (t0) REVERT: C 82 MET cc_start: 0.9275 (mmm) cc_final: 0.8646 (tmm) REVERT: C 283 MET cc_start: 0.9071 (mmm) cc_final: 0.8664 (mmm) REVERT: C 305 MET cc_start: 0.9377 (mmm) cc_final: 0.9129 (mtp) REVERT: D 82 MET cc_start: 0.9334 (tpt) cc_final: 0.8504 (tmm) REVERT: D 176 MET cc_start: 0.8422 (mtp) cc_final: 0.8157 (mtp) REVERT: D 227 MET cc_start: 0.9416 (tpp) cc_final: 0.8934 (tpp) outliers start: 12 outliers final: 9 residues processed: 79 average time/residue: 0.0941 time to fit residues: 11.8035 Evaluate side-chains 77 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 130 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 123 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.034522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.028482 restraints weight = 75825.541| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 4.01 r_work: 0.2528 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12004 Z= 0.107 Angle : 0.529 7.792 16292 Z= 0.246 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.379 56.770 1673 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.64 % Allowed : 18.47 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.23), residues: 1468 helix: 0.73 (0.24), residues: 568 sheet: -0.50 (0.32), residues: 268 loop : 0.31 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.007 0.001 TYR A 294 PHE 0.024 0.001 PHE A 223 TRP 0.008 0.001 TRP D 79 HIS 0.005 0.001 HIS B 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (12004) covalent geometry : angle 0.52928 / 0.25 (16292) hydrogen bonds : bond 0.02357 / 1.56 ( 404) hydrogen bonds : angle 4.19918 / 2.98 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2067.04 seconds wall clock time: 36 minutes 41.25 seconds (2201.25 seconds total)