Starting phenix.real_space_refine on Wed Sep 17 22:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_0712.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_0712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_0712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_0712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kln_0712/09_2025/6kln_0712.map" } 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-2.0-5805/lib/python3.9/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: 2.44, 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: 1.09 Conformation dependent library (CDL) restraints added in 554.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.53 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: 1.74 Time building geometry restraints manager: 1.41 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: 0.03 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: 1.220 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.230 Find NCS groups from input model: 0.090 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 aren 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 covalent geometry : bond 0.00940 (12004) covalent geometry : angle 0.85853 (16292) hydrogen bonds : bond 0.22575 ( 404) hydrogen bonds : angle 8.89386 ( 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 : 0.456 Fit side-chains REVERT: A 44 MET cc_start: 0.8157 (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: 0.8815 (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: 0.6957 (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: 0.8577 (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) REVERT: D 227 MET cc_start: 0.8972 (tpp) cc_final: 0.8643 (tpp) outliers start: 144 outliers final: 34 residues processed: 217 average time/residue: 0.0886 time to fit residues: 29.2619 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 : 0.394 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.035086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.028736 restraints weight = 74877.573| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 4.06 r_work: 0.2537 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12004 Z= 0.141 Angle : 0.614 6.146 16292 Z= 0.306 Chirality : 0.045 0.132 1808 Planarity : 0.004 0.032 2084 Dihedral : 8.857 65.315 1725 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.63 % Allowed : 13.61 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.20), residues: 1468 helix: -2.00 (0.20), residues: 568 sheet: -2.07 (0.29), residues: 228 loop : -1.67 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 290 TYR 0.009 0.001 TYR B 306 PHE 0.019 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 covalent geometry : bond 0.00318 (12004) covalent geometry : angle 0.61394 (16292) hydrogen bonds : bond 0.03212 ( 404) hydrogen bonds : angle 5.36607 ( 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 101 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.388 Fit side-chains REVERT: A 44 MET cc_start: 0.8199 (mmt) cc_final: 0.6692 (pmm) REVERT: A 47 MET cc_start: 0.4315 (mmt) cc_final: 0.4022 (mmm) REVERT: A 227 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8648 (mpp) REVERT: A 303 THR cc_start: 0.9624 (OUTLIER) cc_final: 0.9251 (m) REVERT: B 44 MET cc_start: 0.7899 (mmm) cc_final: 0.6384 (ptp) REVERT: B 132 MET cc_start: 0.9337 (ppp) cc_final: 0.9051 (ppp) REVERT: C 82 MET cc_start: 0.9359 (tpt) cc_final: 0.8704 (tmm) REVERT: C 176 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7843 (mtt) REVERT: C 227 MET cc_start: 0.9226 (tpp) cc_final: 0.8816 (tpp) REVERT: C 283 MET cc_start: 0.9122 (mmm) cc_final: 0.8700 (mmm) REVERT: C 305 MET cc_start: 0.9485 (mmm) cc_final: 0.9154 (mtp) REVERT: D 47 MET cc_start: 0.5714 (mtm) cc_final: 0.4940 (mpp) REVERT: D 227 MET cc_start: 0.8995 (tpp) cc_final: 0.8406 (tpp) outliers start: 33 outliers final: 15 residues processed: 95 average time/residue: 0.0778 time to fit residues: 12.0413 Evaluate side-chains 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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: 8.9990 chunk 95 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 36 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 76 optimal weight: 0.0670 chunk 15 optimal weight: 9.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.033997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.027747 restraints weight = 76075.376| |-----------------------------------------------------------------------------| r_work (start): 0.2614 rms_B_bonded: 4.06 r_work: 0.2475 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12004 Z= 0.224 Angle : 0.635 7.271 16292 Z= 0.310 Chirality : 0.046 0.162 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.487 62.653 1684 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.75 % Allowed : 14.73 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.21), residues: 1468 helix: -1.14 (0.22), residues: 564 sheet: -1.34 (0.33), residues: 228 loop : -1.10 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.011 0.001 TYR A 166 PHE 0.015 0.001 PHE A 375 TRP 0.012 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00502 (12004) covalent geometry : angle 0.63530 (16292) hydrogen bonds : bond 0.03126 ( 404) hydrogen bonds : angle 4.96306 ( 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 90 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.464 Fit side-chains REVERT: A 44 MET cc_start: 0.8344 (mmt) cc_final: 0.6802 (pmm) REVERT: A 47 MET cc_start: 0.4249 (mmt) cc_final: 0.4016 (mmm) REVERT: A 227 MET cc_start: 0.9403 (tpp) cc_final: 0.8865 (mpp) REVERT: B 44 MET cc_start: 0.7987 (mmm) cc_final: 0.6585 (ptp) REVERT: B 78 ASN cc_start: 0.9252 (OUTLIER) cc_final: 0.8479 (t0) REVERT: B 227 MET cc_start: 0.9216 (mmm) cc_final: 0.8979 (mmm) REVERT: B 283 MET cc_start: 0.9482 (tpp) cc_final: 0.9112 (tpp) REVERT: C 78 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8501 (t0) REVERT: C 82 MET cc_start: 0.9501 (tpt) cc_final: 0.8648 (tmm) REVERT: C 176 MET cc_start: 0.8601 (mtt) cc_final: 0.8167 (mtt) REVERT: C 227 MET cc_start: 0.9065 (tpp) cc_final: 0.8772 (tpp) REVERT: C 305 MET cc_start: 0.9461 (mmm) cc_final: 0.9090 (mtp) REVERT: D 47 MET cc_start: 0.5452 (mtm) cc_final: 0.4804 (mpp) REVERT: D 176 MET cc_start: 0.9202 (mtm) cc_final: 0.8844 (mtp) REVERT: D 227 MET cc_start: 0.9247 (tpp) cc_final: 0.8544 (tpp) REVERT: D 277 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8375 (t) outliers start: 22 outliers final: 14 residues processed: 87 average time/residue: 0.0890 time to fit residues: 12.4251 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 : 0.627 ------------------------------------------------------------------------------- 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 78 ASN 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 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 190 MET 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: 6.9990 chunk 129 optimal weight: 8.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 87 optimal weight: 0.1980 chunk 123 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2897 r_free = 0.2897 target = 0.034372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.028142 restraints weight = 75590.218| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 4.06 r_work: 0.2492 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.2955 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= 0.145 Angle : 0.564 7.709 16292 Z= 0.268 Chirality : 0.044 0.132 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.926 58.529 1679 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.75 % Allowed : 15.37 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.22), residues: 1468 helix: -0.58 (0.23), residues: 564 sheet: -0.89 (0.32), residues: 260 loop : -0.66 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 39 TYR 0.007 0.001 TYR B 306 PHE 0.012 0.001 PHE A 223 TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00329 (12004) covalent geometry : angle 0.56371 (16292) hydrogen bonds : bond 0.02578 ( 404) hydrogen bonds : angle 4.73162 ( 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 89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.371 Fit side-chains REVERT: A 44 MET cc_start: 0.8467 (mmt) cc_final: 0.6964 (pmm) REVERT: A 47 MET cc_start: 0.4778 (mmt) cc_final: 0.4554 (mmm) REVERT: A 227 MET cc_start: 0.9341 (tpp) cc_final: 0.8884 (mpp) REVERT: A 305 MET cc_start: 0.9413 (mtp) cc_final: 0.9086 (mtp) REVERT: B 44 MET cc_start: 0.8013 (mmm) cc_final: 0.6575 (ptp) REVERT: B 78 ASN cc_start: 0.9162 (OUTLIER) cc_final: 0.8373 (t0) REVERT: B 227 MET cc_start: 0.9208 (mmm) cc_final: 0.8970 (mmm) REVERT: C 82 MET cc_start: 0.9481 (tpt) cc_final: 0.8700 (tmm) REVERT: C 176 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8187 (mtt) REVERT: C 227 MET cc_start: 0.9086 (tpp) cc_final: 0.8709 (tpp) REVERT: C 283 MET cc_start: 0.9185 (mmm) cc_final: 0.8776 (mmm) REVERT: D 47 MET cc_start: 0.5724 (mtm) cc_final: 0.5229 (mpp) REVERT: D 176 MET cc_start: 0.9180 (mtm) cc_final: 0.8934 (mtp) REVERT: D 227 MET cc_start: 0.9262 (tpp) cc_final: 0.8741 (tpp) outliers start: 22 outliers final: 14 residues processed: 86 average time/residue: 0.0911 time to fit residues: 12.5349 Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 239 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 78 ASN 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 190 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 72 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.027092 restraints weight = 77725.934| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 3.83 r_work: 0.2455 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12004 Z= 0.326 Angle : 0.692 8.353 16292 Z= 0.336 Chirality : 0.048 0.152 1808 Planarity : 0.004 0.032 2084 Dihedral : 6.994 59.693 1676 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.83 % Allowed : 16.00 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.22), residues: 1468 helix: -0.38 (0.23), residues: 564 sheet: -1.00 (0.34), residues: 244 loop : -0.40 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.014 0.001 TYR C 166 PHE 0.013 0.001 PHE B 223 TRP 0.013 0.002 TRP C 79 HIS 0.003 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00727 (12004) covalent geometry : angle 0.69205 (16292) hydrogen bonds : bond 0.03188 ( 404) hydrogen bonds : angle 4.95867 ( 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 89 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 66 time to evaluate : 0.464 Fit side-chains REVERT: A 44 MET cc_start: 0.8399 (mmt) cc_final: 0.6907 (pmm) REVERT: A 47 MET cc_start: 0.4803 (mmt) cc_final: 0.4591 (mmm) REVERT: A 227 MET cc_start: 0.9402 (tpp) cc_final: 0.8884 (mpp) REVERT: B 44 MET cc_start: 0.8129 (mmm) cc_final: 0.6862 (ptp) REVERT: B 227 MET cc_start: 0.9241 (mmm) cc_final: 0.8983 (mmm) REVERT: B 283 MET cc_start: 0.9447 (tpp) cc_final: 0.9061 (tpp) REVERT: C 78 ASN cc_start: 0.9272 (OUTLIER) cc_final: 0.8586 (t0) REVERT: C 82 MET cc_start: 0.9551 (tpt) cc_final: 0.8517 (tmm) REVERT: C 176 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (mtt) REVERT: C 305 MET cc_start: 0.9356 (mtp) cc_final: 0.9101 (mtp) REVERT: D 47 MET cc_start: 0.6013 (mtm) cc_final: 0.5797 (mpp) REVERT: D 227 MET cc_start: 0.9361 (tpp) cc_final: 0.8911 (tpp) outliers start: 23 outliers final: 17 residues processed: 84 average time/residue: 0.0952 time to fit residues: 12.7038 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 : 0.482 ------------------------------------------------------------------------------- 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 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 149 THR Chi-restraints excluded: chain D residue 190 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 112 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 60 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2886 r_free = 0.2886 target = 0.033676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.027526 restraints weight = 76448.845| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 4.01 r_work: 0.2480 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.3341 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= 0.140 Angle : 0.554 7.812 16292 Z= 0.263 Chirality : 0.044 0.127 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.513 58.843 1676 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.51 % Allowed : 16.96 % 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 aren not related in a simple way. whole: -0.48 (0.23), residues: 1468 helix: -0.03 (0.23), residues: 564 sheet: -0.74 (0.32), residues: 268 loop : -0.18 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.007 0.001 TYR B 306 PHE 0.012 0.001 PHE C 223 TRP 0.010 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.00317 (12004) covalent geometry : angle 0.55426 (16292) hydrogen bonds : bond 0.02544 ( 404) hydrogen bonds : angle 4.63221 ( 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 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.402 Fit side-chains REVERT: A 44 MET cc_start: 0.8462 (mmt) cc_final: 0.7012 (pmm) REVERT: A 227 MET cc_start: 0.9305 (tpp) cc_final: 0.8943 (mpp) REVERT: B 44 MET cc_start: 0.7946 (mmm) cc_final: 0.6577 (ptp) REVERT: B 227 MET cc_start: 0.9182 (mmm) cc_final: 0.8917 (mmm) REVERT: C 78 ASN cc_start: 0.9173 (OUTLIER) cc_final: 0.8453 (t0) REVERT: C 82 MET cc_start: 0.9518 (tpt) cc_final: 0.8714 (tmm) REVERT: C 176 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8475 (mtt) REVERT: C 283 MET cc_start: 0.9163 (mmm) cc_final: 0.8814 (mmm) REVERT: C 305 MET cc_start: 0.9315 (mtp) cc_final: 0.8990 (mtp) REVERT: D 82 MET cc_start: 0.9475 (tpt) cc_final: 0.8869 (mmm) REVERT: D 227 MET cc_start: 0.9307 (tpp) cc_final: 0.8836 (tpp) outliers start: 19 outliers final: 13 residues processed: 82 average time/residue: 0.0889 time to fit residues: 11.5518 Evaluate side-chains 83 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 355 MET 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 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 190 MET 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: 9.9990 chunk 112 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 142 optimal weight: 6.9990 overall best weight: 4.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2871 r_free = 0.2871 target = 0.033235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.027127 restraints weight = 76714.296| |-----------------------------------------------------------------------------| r_work (start): 0.2606 rms_B_bonded: 3.99 r_work: 0.2468 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12004 Z= 0.176 Angle : 0.570 7.902 16292 Z= 0.271 Chirality : 0.044 0.126 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.298 58.685 1673 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.43 % Allowed : 17.04 % 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 aren not related in a simple way. whole: -0.28 (0.23), residues: 1468 helix: 0.14 (0.23), residues: 568 sheet: -0.69 (0.32), residues: 268 loop : -0.04 (0.26), residues: 632 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 0.016 0.001 PHE C 223 TRP 0.010 0.001 TRP C 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00398 (12004) covalent geometry : angle 0.57029 (16292) hydrogen bonds : bond 0.02653 ( 404) hydrogen bonds : angle 4.57513 ( 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 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 68 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8362 (mmt) cc_final: 0.7122 (pmm) REVERT: A 47 MET cc_start: 0.5253 (mmt) cc_final: 0.4785 (mmm) REVERT: A 227 MET cc_start: 0.9302 (tpp) cc_final: 0.8884 (mpp) REVERT: B 44 MET cc_start: 0.7961 (mmm) cc_final: 0.6655 (ptp) REVERT: B 227 MET cc_start: 0.9188 (mmm) cc_final: 0.8937 (mmm) REVERT: B 283 MET cc_start: 0.9385 (tpp) cc_final: 0.9053 (tpp) REVERT: C 78 ASN cc_start: 0.9174 (OUTLIER) cc_final: 0.8418 (t0) REVERT: C 176 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8429 (mtt) REVERT: C 283 MET cc_start: 0.9165 (mmm) cc_final: 0.8774 (mmm) REVERT: C 305 MET cc_start: 0.9298 (mtp) cc_final: 0.8940 (mtp) REVERT: D 82 MET cc_start: 0.9475 (tpt) cc_final: 0.8822 (mmm) REVERT: D 227 MET cc_start: 0.9342 (tpp) cc_final: 0.8849 (tpp) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.0946 time to fit residues: 12.4053 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 : 0.472 ------------------------------------------------------------------------------- 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 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 190 MET Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 0.0060 chunk 47 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 chunk 141 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 overall best weight: 2.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.033628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.027552 restraints weight = 76180.388| |-----------------------------------------------------------------------------| r_work (start): 0.2628 rms_B_bonded: 3.99 r_work: 0.2490 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.3558 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= 0.131 Angle : 0.538 7.518 16292 Z= 0.253 Chirality : 0.043 0.127 1808 Planarity : 0.003 0.028 2084 Dihedral : 5.973 58.678 1673 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.35 % Allowed : 17.20 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.23), residues: 1468 helix: 0.26 (0.23), residues: 568 sheet: -0.64 (0.32), residues: 268 loop : 0.06 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.006 0.001 TYR B 306 PHE 0.015 0.001 PHE C 223 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00299 (12004) covalent geometry : angle 0.53772 (16292) hydrogen bonds : bond 0.02475 ( 404) hydrogen bonds : angle 4.44813 ( 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 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8396 (mmt) cc_final: 0.7124 (pmm) REVERT: A 47 MET cc_start: 0.4887 (mmt) cc_final: 0.4393 (mmm) REVERT: A 227 MET cc_start: 0.9211 (tpp) cc_final: 0.8873 (mpp) REVERT: A 305 MET cc_start: 0.9429 (mtp) cc_final: 0.9096 (mtp) REVERT: B 44 MET cc_start: 0.7969 (mmm) cc_final: 0.6594 (ptp) REVERT: B 227 MET cc_start: 0.9196 (mmm) cc_final: 0.8961 (mmm) REVERT: B 283 MET cc_start: 0.9410 (tpp) cc_final: 0.9000 (mpp) REVERT: C 78 ASN cc_start: 0.9091 (OUTLIER) cc_final: 0.8431 (t0) REVERT: C 82 MET cc_start: 0.9357 (mmm) cc_final: 0.8567 (tmm) REVERT: C 283 MET cc_start: 0.9119 (mmm) cc_final: 0.8721 (mmm) REVERT: C 305 MET cc_start: 0.9282 (mtp) cc_final: 0.8914 (mtp) REVERT: D 82 MET cc_start: 0.9454 (tpt) cc_final: 0.8788 (mmm) REVERT: D 227 MET cc_start: 0.9335 (tpp) cc_final: 0.8939 (tpp) outliers start: 17 outliers final: 15 residues processed: 82 average time/residue: 0.1019 time to fit residues: 13.1487 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 : 0.552 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 190 MET 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: 9.9990 chunk 17 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.034005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.027948 restraints weight = 75204.576| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.96 r_work: 0.2510 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12004 Z= 0.106 Angle : 0.525 7.670 16292 Z= 0.245 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.673 57.803 1673 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.19 % Allowed : 17.60 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.23), residues: 1468 helix: 0.42 (0.23), residues: 568 sheet: -0.63 (0.32), residues: 268 loop : 0.15 (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 B 306 PHE 0.016 0.001 PHE C 223 TRP 0.008 0.001 TRP C 340 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00245 (12004) covalent geometry : angle 0.52452 (16292) hydrogen bonds : bond 0.02395 ( 404) hydrogen bonds : angle 4.33901 ( 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: 15 poor density : 66 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8445 (mmt) cc_final: 0.7189 (pmm) REVERT: A 47 MET cc_start: 0.5063 (mmt) cc_final: 0.4576 (mmm) REVERT: A 227 MET cc_start: 0.9189 (tpp) cc_final: 0.8950 (mpp) REVERT: A 305 MET cc_start: 0.9406 (mtp) cc_final: 0.9057 (mtp) REVERT: B 44 MET cc_start: 0.7947 (mmm) cc_final: 0.6633 (ptp) REVERT: B 227 MET cc_start: 0.9187 (mmm) cc_final: 0.8959 (mmm) REVERT: B 283 MET cc_start: 0.9409 (tpp) cc_final: 0.9018 (mpp) REVERT: C 78 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8437 (t0) REVERT: C 82 MET cc_start: 0.9353 (mmm) cc_final: 0.8576 (tmm) REVERT: C 283 MET cc_start: 0.9105 (mmm) cc_final: 0.8702 (mmm) REVERT: C 305 MET cc_start: 0.9293 (mtp) cc_final: 0.8902 (mtp) REVERT: D 82 MET cc_start: 0.9449 (tpt) cc_final: 0.8785 (mmm) REVERT: D 227 MET cc_start: 0.9331 (tpp) cc_final: 0.8973 (tpp) outliers start: 15 outliers final: 14 residues processed: 80 average time/residue: 0.0898 time to fit residues: 11.4375 Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 205 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 190 MET 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: 3.9990 chunk 51 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.033894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.027834 restraints weight = 76247.519| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 4.01 r_work: 0.2501 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3687 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= 0.125 Angle : 0.533 7.645 16292 Z= 0.249 Chirality : 0.043 0.125 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.604 57.504 1673 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.19 % Allowed : 17.68 % 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 aren not related in a simple way. whole: 0.14 (0.23), residues: 1468 helix: 0.55 (0.23), residues: 568 sheet: -0.61 (0.32), residues: 268 loop : 0.21 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 177 TYR 0.006 0.001 TYR A 166 PHE 0.017 0.001 PHE C 223 TRP 0.008 0.001 TRP D 79 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00286 (12004) covalent geometry : angle 0.53315 (16292) hydrogen bonds : bond 0.02458 ( 404) hydrogen bonds : angle 4.31157 ( 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 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 44 MET cc_start: 0.8476 (mmt) cc_final: 0.7230 (pmm) REVERT: A 47 MET cc_start: 0.5010 (mmt) cc_final: 0.4547 (mmm) REVERT: A 227 MET cc_start: 0.9199 (tpp) cc_final: 0.8914 (mpp) REVERT: A 305 MET cc_start: 0.9411 (mtp) cc_final: 0.9050 (mtp) REVERT: B 44 MET cc_start: 0.7946 (mmm) cc_final: 0.6656 (ptp) REVERT: B 227 MET cc_start: 0.9183 (mmm) cc_final: 0.8954 (mmm) REVERT: B 283 MET cc_start: 0.9394 (tpp) cc_final: 0.8990 (mpp) REVERT: C 47 MET cc_start: 0.6487 (mpp) cc_final: 0.4842 (mtp) REVERT: C 78 ASN cc_start: 0.9107 (OUTLIER) cc_final: 0.8443 (t0) REVERT: C 82 MET cc_start: 0.9352 (mmm) cc_final: 0.8578 (tmm) REVERT: C 305 MET cc_start: 0.9301 (mtp) cc_final: 0.8903 (mtp) REVERT: D 82 MET cc_start: 0.9451 (tpt) cc_final: 0.8779 (mmm) REVERT: D 227 MET cc_start: 0.9355 (tpp) cc_final: 0.9006 (tpp) outliers start: 15 outliers final: 13 residues processed: 79 average time/residue: 0.0885 time to fit residues: 11.2902 Evaluate side-chains 80 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.472 ------------------------------------------------------------------------------- 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 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 205 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 190 MET 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: 0.5980 chunk 123 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 43 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.034450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.028365 restraints weight = 75735.360| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 4.03 r_work: 0.2527 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12004 Z= 0.092 Angle : 0.514 7.302 16292 Z= 0.238 Chirality : 0.043 0.127 1808 Planarity : 0.003 0.026 2084 Dihedral : 5.371 57.361 1672 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.80 % Allowed : 18.23 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.23), residues: 1468 helix: 0.70 (0.24), residues: 568 sheet: -0.56 (0.32), residues: 268 loop : 0.28 (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 0.016 0.001 PHE C 223 TRP 0.008 0.001 TRP B 356 HIS 0.004 0.001 HIS B 87 Details of bonding type rmsd covalent geometry : bond 0.00215 (12004) covalent geometry : angle 0.51352 (16292) hydrogen bonds : bond 0.02303 ( 404) hydrogen bonds : angle 4.21799 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2051.64 seconds wall clock time: 36 minutes 12.80 seconds (2172.80 seconds total)