Starting phenix.real_space_refine on Wed Jul 30 04:57:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kln_0712/07_2025/6kln_0712.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kln_0712/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kln_0712/07_2025/6kln_0712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kln_0712/07_2025/6kln_0712.map" model { file = "/net/cci-nas-00/data/ceres_data/6kln_0712/07_2025/6kln_0712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kln_0712/07_2025/6kln_0712.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: C, B, D Time building chain proxies: 5.70, per 1000 atoms: 0.49 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: 2.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.57 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: 3.42 Time building geometry restraints manager: 3.08 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.420 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP C 340 HIS 0.004 0.001 HIS C 101 PHE 0.009 0.002 PHE D 375 TYR 0.009 0.001 TYR A 69 ARG 0.004 0.001 ARG C 37 Details of bonding type rmsd hydrogen bonds : bond 0.22575 ( 404) hydrogen bonds : angle 8.89386 ( 1008) covalent geometry : bond 0.00940 (12004) covalent geometry : angle 0.85853 (16292) *********************** 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 : 1.372 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: 0.8814 (ppp) REVERT: B 167 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7795 (pt0) REVERT: B 249 THR cc_start: 0.9493 (OUTLIER) cc_final: 0.9288 (p) REVERT: B 351 THR cc_start: 0.9491 (OUTLIER) cc_final: 0.9074 (p) REVERT: C 44 MET cc_start: 0.7316 (mmt) cc_final: 0.6958 (tpp) REVERT: C 82 MET cc_start: 0.9121 (tpt) cc_final: 0.8469 (tmm) REVERT: C 277 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8578 (m) REVERT: C 303 THR cc_start: 0.9584 (OUTLIER) cc_final: 0.9175 (p) REVERT: C 326 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8476 (mtpp) REVERT: D 47 MET cc_start: 0.5019 (OUTLIER) cc_final: 0.4662 (mpp) REVERT: D 152 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9012 (m) outliers start: 144 outliers final: 34 residues processed: 217 average time/residue: 0.2029 time to fit residues: 66.4438 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 : 1.388 ------------------------------------------------------------------------------- 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 124 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 chunk 70 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 354 GLN ** 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 = 0.2963 r_free = 0.2963 target = 0.035681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.029361 restraints weight = 73562.768| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 4.04 r_work: 0.2566 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12004 Z= 0.113 Angle : 0.603 5.694 16292 Z= 0.299 Chirality : 0.044 0.129 1808 Planarity : 0.004 0.032 2084 Dihedral : 8.736 63.996 1725 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.55 % Allowed : 13.77 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.20), residues: 1468 helix: -2.02 (0.20), residues: 568 sheet: -2.10 (0.28), residues: 228 loop : -1.67 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 340 HIS 0.003 0.001 HIS A 87 PHE 0.020 0.001 PHE A 223 TYR 0.009 0.001 TYR B 306 ARG 0.003 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02979 ( 404) hydrogen bonds : angle 5.32134 ( 1008) covalent geometry : bond 0.00255 (12004) covalent geometry : angle 0.60251 (16292) *********************** 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: 32 poor density : 69 time to evaluate : 1.245 Fit side-chains REVERT: A 44 MET cc_start: 0.8169 (mmt) cc_final: 0.6668 (pmm) REVERT: A 47 MET cc_start: 0.4262 (mmt) cc_final: 0.3968 (mmm) REVERT: A 227 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8746 (mpp) REVERT: A 303 THR cc_start: 0.9597 (OUTLIER) cc_final: 0.9159 (p) REVERT: B 44 MET cc_start: 0.7907 (mmm) cc_final: 0.6398 (ptp) REVERT: B 132 MET cc_start: 0.9322 (ppp) cc_final: 0.9017 (ppp) REVERT: C 82 MET cc_start: 0.9312 (tpt) cc_final: 0.8662 (tmm) REVERT: C 227 MET cc_start: 0.9154 (tpp) cc_final: 0.8680 (tpp) REVERT: C 283 MET cc_start: 0.9051 (mmm) cc_final: 0.8619 (mmm) REVERT: C 303 THR cc_start: 0.9649 (OUTLIER) cc_final: 0.9446 (m) REVERT: C 305 MET cc_start: 0.9460 (mmm) cc_final: 0.9127 (mtp) REVERT: D 47 MET cc_start: 0.5713 (mtm) cc_final: 0.4971 (mpp) REVERT: D 227 MET cc_start: 0.9069 (tpp) cc_final: 0.8363 (tpp) outliers start: 32 outliers final: 15 residues processed: 95 average time/residue: 0.1907 time to fit residues: 29.4161 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 : 1.370 ------------------------------------------------------------------------------- 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 303 THR 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 76 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 10.0000 chunk 139 optimal weight: 0.0770 chunk 118 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 6.2146 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 296 ASN ** B 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.027491 restraints weight = 76546.558| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 4.05 r_work: 0.2463 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 12004 Z= 0.263 Angle : 0.667 7.756 16292 Z= 0.327 Chirality : 0.046 0.164 1808 Planarity : 0.004 0.033 2084 Dihedral : 7.705 66.743 1685 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.83 % Allowed : 14.09 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.21), residues: 1468 helix: -1.17 (0.22), residues: 564 sheet: -1.34 (0.33), residues: 228 loop : -1.12 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 PHE 0.013 0.002 PHE B 223 TYR 0.013 0.001 TYR A 166 ARG 0.004 0.000 ARG D 177 Details of bonding type rmsd hydrogen bonds : bond 0.03383 ( 404) hydrogen bonds : angle 5.05022 ( 1008) covalent geometry : bond 0.00584 (12004) covalent geometry : angle 0.66712 (16292) *********************** 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: 23 poor density : 67 time to evaluate : 1.529 Fit side-chains REVERT: A 44 MET cc_start: 0.8331 (mmt) cc_final: 0.6796 (pmm) REVERT: A 47 MET cc_start: 0.4258 (mmt) cc_final: 0.4020 (mmm) REVERT: A 227 MET cc_start: 0.9411 (tpp) cc_final: 0.8821 (mpp) REVERT: B 44 MET cc_start: 0.8105 (mmm) cc_final: 0.6673 (ptp) REVERT: B 78 ASN cc_start: 0.9280 (OUTLIER) cc_final: 0.8511 (t0) REVERT: B 283 MET cc_start: 0.9477 (tpp) cc_final: 0.9090 (tpp) REVERT: C 78 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8514 (t0) REVERT: C 82 MET cc_start: 0.9518 (tpt) cc_final: 0.8657 (tmm) REVERT: C 176 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: C 227 MET cc_start: 0.9114 (tpp) cc_final: 0.8651 (tpp) REVERT: D 47 MET cc_start: 0.5503 (mtm) cc_final: 0.4821 (mpp) REVERT: D 176 MET cc_start: 0.9176 (mtm) cc_final: 0.8941 (mtp) REVERT: D 277 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8622 (t) outliers start: 23 outliers final: 14 residues processed: 86 average time/residue: 0.2000 time to fit residues: 27.3574 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 : 1.415 ------------------------------------------------------------------------------- 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 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 235 SER Chi-restraints excluded: chain D residue 277 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 34 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- 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 = 0.2905 r_free = 0.2905 target = 0.034097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.027887 restraints weight = 74941.713| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.03 r_work: 0.2505 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2976 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= 0.132 Angle : 0.555 7.889 16292 Z= 0.264 Chirality : 0.044 0.125 1808 Planarity : 0.003 0.028 2084 Dihedral : 6.912 60.623 1679 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.75 % Allowed : 15.45 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.22), residues: 1468 helix: -0.60 (0.23), residues: 564 sheet: -0.91 (0.32), residues: 252 loop : -0.75 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.003 0.001 HIS B 87 PHE 0.013 0.001 PHE A 223 TYR 0.009 0.001 TYR C 133 ARG 0.002 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02522 ( 404) hydrogen bonds : angle 4.74043 ( 1008) covalent geometry : bond 0.00299 (12004) covalent geometry : angle 0.55517 (16292) *********************** 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 : 1.427 Fit side-chains REVERT: A 44 MET cc_start: 0.8465 (mmt) cc_final: 0.6967 (pmm) REVERT: A 47 MET cc_start: 0.4515 (mmt) cc_final: 0.4282 (mmm) REVERT: A 227 MET cc_start: 0.9319 (tpp) cc_final: 0.8837 (mpp) REVERT: A 305 MET cc_start: 0.9421 (mtp) cc_final: 0.9076 (mtp) REVERT: B 44 MET cc_start: 0.7992 (mmm) cc_final: 0.6556 (ptp) REVERT: B 78 ASN cc_start: 0.9152 (OUTLIER) cc_final: 0.8357 (t0) REVERT: C 78 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8451 (t0) REVERT: C 82 MET cc_start: 0.9476 (tpt) cc_final: 0.8642 (tmm) REVERT: C 176 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8204 (mtt) REVERT: C 227 MET cc_start: 0.9070 (tpp) cc_final: 0.8846 (tpp) REVERT: C 283 MET cc_start: 0.9148 (mmm) cc_final: 0.8739 (mmm) REVERT: D 47 MET cc_start: 0.5644 (mtm) cc_final: 0.5156 (mpp) outliers start: 22 outliers final: 11 residues processed: 86 average time/residue: 0.1984 time to fit residues: 27.4024 Evaluate side-chains 79 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 103 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 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 149 THR Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 110 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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** B 78 ASN C 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.033016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.027187 restraints weight = 77604.637| |-----------------------------------------------------------------------------| r_work (start): 0.2593 rms_B_bonded: 3.83 r_work: 0.2457 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 12004 Z= 0.329 Angle : 0.698 7.964 16292 Z= 0.339 Chirality : 0.048 0.151 1808 Planarity : 0.004 0.032 2084 Dihedral : 7.022 59.949 1676 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.67 % Allowed : 16.08 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.22), residues: 1468 helix: -0.42 (0.23), residues: 564 sheet: -1.03 (0.34), residues: 244 loop : -0.45 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 79 HIS 0.004 0.001 HIS B 40 PHE 0.014 0.001 PHE B 223 TYR 0.014 0.001 TYR C 166 ARG 0.003 0.000 ARG D 39 Details of bonding type rmsd hydrogen bonds : bond 0.03243 ( 404) hydrogen bonds : angle 4.96839 ( 1008) covalent geometry : bond 0.00729 (12004) covalent geometry : angle 0.69753 (16292) *********************** 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 87 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.205 Fit side-chains REVERT: A 44 MET cc_start: 0.8389 (mmt) cc_final: 0.6976 (pmm) REVERT: A 227 MET cc_start: 0.9405 (tpp) cc_final: 0.8878 (mpp) REVERT: B 44 MET cc_start: 0.8089 (mmm) cc_final: 0.6803 (ptp) REVERT: B 283 MET cc_start: 0.9449 (tpp) cc_final: 0.9063 (tpp) REVERT: C 78 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8599 (t0) REVERT: C 82 MET cc_start: 0.9554 (tpt) cc_final: 0.8516 (tmm) REVERT: C 176 MET cc_start: 0.8701 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: C 227 MET cc_start: 0.9103 (tpp) cc_final: 0.8734 (tpp) REVERT: D 47 MET cc_start: 0.6116 (mtm) cc_final: 0.5806 (mpp) REVERT: D 176 MET cc_start: 0.8953 (mtm) cc_final: 0.8707 (mtt) REVERT: D 227 MET cc_start: 0.9309 (tpp) cc_final: 0.8548 (mpp) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 0.1893 time to fit residues: 25.1724 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 : 1.235 ------------------------------------------------------------------------------- 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 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 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 137 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 42 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- 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 = 0.2867 r_free = 0.2867 target = 0.033622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.027547 restraints weight = 76274.539| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 4.00 r_work: 0.2470 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12004 Z= 0.184 Angle : 0.583 7.763 16292 Z= 0.278 Chirality : 0.045 0.129 1808 Planarity : 0.003 0.030 2084 Dihedral : 6.659 59.750 1676 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.51 % Allowed : 16.72 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1468 helix: -0.09 (0.23), residues: 564 sheet: -0.95 (0.34), residues: 244 loop : -0.26 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 79 HIS 0.004 0.001 HIS A 87 PHE 0.009 0.001 PHE C 255 TYR 0.008 0.001 TYR C 133 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 404) hydrogen bonds : angle 4.71623 ( 1008) covalent geometry : bond 0.00413 (12004) covalent geometry : angle 0.58339 (16292) *********************** 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 86 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.384 Fit side-chains REVERT: A 44 MET cc_start: 0.8219 (mmt) cc_final: 0.7133 (pmm) REVERT: A 227 MET cc_start: 0.9329 (tpp) cc_final: 0.8893 (mpp) REVERT: B 44 MET cc_start: 0.7961 (mmm) cc_final: 0.6599 (ptp) REVERT: B 283 MET cc_start: 0.9434 (tpp) cc_final: 0.9008 (tpp) REVERT: C 78 ASN cc_start: 0.9203 (OUTLIER) cc_final: 0.8512 (t0) REVERT: C 82 MET cc_start: 0.9536 (tpt) cc_final: 0.8829 (tmm) REVERT: C 132 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8828 (ptm) REVERT: C 176 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: C 227 MET cc_start: 0.9079 (tpp) cc_final: 0.8782 (tpp) REVERT: C 283 MET cc_start: 0.9167 (mmm) cc_final: 0.8812 (mmm) REVERT: D 82 MET cc_start: 0.9498 (tpt) cc_final: 0.8896 (mmm) REVERT: D 227 MET cc_start: 0.9329 (tpp) cc_final: 0.8641 (tpp) outliers start: 19 outliers final: 13 residues processed: 84 average time/residue: 0.2256 time to fit residues: 30.0015 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 : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 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 132 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 0.6980 chunk 123 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.033705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.027577 restraints weight = 76413.045| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.03 r_work: 0.2490 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3475 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= 0.125 Angle : 0.539 7.690 16292 Z= 0.254 Chirality : 0.044 0.128 1808 Planarity : 0.003 0.029 2084 Dihedral : 6.155 58.892 1673 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.27 % Allowed : 17.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1468 helix: 0.16 (0.23), residues: 568 sheet: -0.68 (0.32), residues: 268 loop : -0.04 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 79 HIS 0.004 0.001 HIS B 87 PHE 0.008 0.001 PHE C 255 TYR 0.006 0.001 TYR C 133 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02460 ( 404) hydrogen bonds : angle 4.51221 ( 1008) covalent geometry : bond 0.00286 (12004) covalent geometry : angle 0.53947 (16292) *********************** 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 84 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.547 Fit side-chains REVERT: A 44 MET cc_start: 0.8335 (mmt) cc_final: 0.7234 (pmm) REVERT: A 227 MET cc_start: 0.9251 (tpp) cc_final: 0.8924 (mpp) REVERT: A 305 MET cc_start: 0.9414 (mtp) cc_final: 0.9060 (mtp) REVERT: A 325 MET cc_start: 0.8023 (ptm) cc_final: 0.7438 (ppp) REVERT: B 44 MET cc_start: 0.7980 (mmm) cc_final: 0.6613 (ptp) REVERT: B 283 MET cc_start: 0.9419 (tpp) cc_final: 0.9140 (tpp) REVERT: C 78 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8388 (t0) REVERT: C 132 MET cc_start: 0.8983 (ttp) cc_final: 0.8773 (ptm) REVERT: C 176 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8266 (mtt) REVERT: C 205 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8768 (mt-10) REVERT: C 283 MET cc_start: 0.9132 (mmm) cc_final: 0.8738 (mmm) REVERT: D 82 MET cc_start: 0.9458 (tpt) cc_final: 0.8818 (mmm) REVERT: D 227 MET cc_start: 0.9358 (tpp) cc_final: 0.8749 (tpp) outliers start: 16 outliers final: 12 residues processed: 83 average time/residue: 0.1929 time to fit residues: 25.4444 Evaluate side-chains 82 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 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 73 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 76 optimal weight: 0.3980 chunk 116 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- 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 = 0.2890 r_free = 0.2890 target = 0.033653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.027570 restraints weight = 76481.368| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 4.02 r_work: 0.2488 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.3561 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= 0.136 Angle : 0.544 7.711 16292 Z= 0.256 Chirality : 0.044 0.127 1808 Planarity : 0.003 0.028 2084 Dihedral : 5.933 58.683 1673 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.11 % Allowed : 17.28 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1468 helix: 0.34 (0.23), residues: 568 sheet: -0.61 (0.32), residues: 268 loop : 0.02 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 79 HIS 0.004 0.001 HIS B 87 PHE 0.008 0.001 PHE C 255 TYR 0.007 0.001 TYR A 166 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02503 ( 404) hydrogen bonds : angle 4.44094 ( 1008) covalent geometry : bond 0.00311 (12004) covalent geometry : angle 0.54357 (16292) *********************** 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 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.369 Fit side-chains REVERT: A 44 MET cc_start: 0.8329 (mmt) cc_final: 0.7219 (pmm) REVERT: A 82 MET cc_start: 0.9103 (tpt) cc_final: 0.8867 (tpt) REVERT: A 227 MET cc_start: 0.9219 (tpp) cc_final: 0.8867 (mpp) REVERT: B 44 MET cc_start: 0.8021 (mmm) cc_final: 0.6655 (ptp) REVERT: B 283 MET cc_start: 0.9406 (tpp) cc_final: 0.9126 (tpp) REVERT: C 78 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8428 (t0) REVERT: C 82 MET cc_start: 0.9339 (mmm) cc_final: 0.8587 (tmm) REVERT: C 132 MET cc_start: 0.8990 (ttp) cc_final: 0.8763 (ptm) REVERT: C 176 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: C 205 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8776 (mt-10) REVERT: C 283 MET cc_start: 0.9101 (mmm) cc_final: 0.8698 (mmm) REVERT: D 82 MET cc_start: 0.9468 (tpt) cc_final: 0.8822 (mmm) REVERT: D 227 MET cc_start: 0.9361 (tpp) cc_final: 0.8803 (tpp) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.2118 time to fit residues: 26.5738 Evaluate side-chains 81 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 202 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 100 optimal weight: 0.0870 chunk 105 optimal weight: 9.9990 chunk 117 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.0000 chunk 30 optimal weight: 5.9990 overall best weight: 1.7766 ------------------------------------------------------------------------------- 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 = 0.2916 r_free = 0.2916 target = 0.034298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.028221 restraints weight = 75760.432| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 4.03 r_work: 0.2523 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.3704 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= 0.094 Angle : 0.517 7.820 16292 Z= 0.240 Chirality : 0.043 0.127 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.577 58.114 1673 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.96 % Allowed : 17.36 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1468 helix: 0.49 (0.24), residues: 564 sheet: -0.58 (0.32), residues: 268 loop : 0.08 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.004 0.001 HIS B 87 PHE 0.008 0.001 PHE D 255 TYR 0.009 0.001 TYR C 306 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02315 ( 404) hydrogen bonds : angle 4.29716 ( 1008) covalent geometry : bond 0.00219 (12004) covalent geometry : angle 0.51702 (16292) *********************** 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 78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.253 Fit side-chains REVERT: A 44 MET cc_start: 0.8361 (mmt) cc_final: 0.7251 (pmm) REVERT: A 227 MET cc_start: 0.9159 (tpp) cc_final: 0.8935 (mpp) REVERT: A 325 MET cc_start: 0.7987 (ptm) cc_final: 0.7210 (ppp) REVERT: B 44 MET cc_start: 0.7938 (mmm) cc_final: 0.6619 (ptp) REVERT: B 132 MET cc_start: 0.9304 (ptm) cc_final: 0.8880 (ptm) REVERT: B 283 MET cc_start: 0.9395 (tpp) cc_final: 0.9125 (tpp) REVERT: C 78 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8444 (t0) REVERT: C 82 MET cc_start: 0.9343 (mmm) cc_final: 0.8568 (tmm) REVERT: C 176 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8386 (mtt) REVERT: C 283 MET cc_start: 0.9097 (mmm) cc_final: 0.8679 (mmm) REVERT: D 82 MET cc_start: 0.9431 (tpt) cc_final: 0.8773 (mmm) REVERT: D 227 MET cc_start: 0.9394 (tpp) cc_final: 0.8907 (tpp) outliers start: 12 outliers final: 8 residues processed: 77 average time/residue: 0.2051 time to fit residues: 24.9317 Evaluate side-chains 76 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 C residue 78 ASN Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.0970 chunk 147 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 chunk 121 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 15 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 = 0.2910 r_free = 0.2910 target = 0.034171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.028118 restraints weight = 75110.685| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.98 r_work: 0.2519 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3728 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= 0.109 Angle : 0.527 7.605 16292 Z= 0.245 Chirality : 0.043 0.126 1808 Planarity : 0.003 0.027 2084 Dihedral : 5.495 57.535 1672 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.96 % Allowed : 17.20 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.23), residues: 1468 helix: 0.62 (0.24), residues: 564 sheet: -0.56 (0.32), residues: 268 loop : 0.14 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 79 HIS 0.004 0.001 HIS B 87 PHE 0.008 0.001 PHE C 255 TYR 0.007 0.001 TYR C 306 ARG 0.002 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.02375 ( 404) hydrogen bonds : angle 4.25851 ( 1008) covalent geometry : bond 0.00253 (12004) covalent geometry : angle 0.52657 (16292) ********************** 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 78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.526 Fit side-chains REVERT: A 44 MET cc_start: 0.8346 (mmt) cc_final: 0.7218 (pmm) REVERT: A 82 MET cc_start: 0.9099 (tpt) cc_final: 0.8862 (tpt) REVERT: A 227 MET cc_start: 0.9180 (tpp) cc_final: 0.8937 (mpp) REVERT: B 44 MET cc_start: 0.7995 (mmm) cc_final: 0.6707 (ptp) REVERT: B 132 MET cc_start: 0.9300 (ptm) cc_final: 0.8894 (ptm) REVERT: B 176 MET cc_start: 0.9171 (mmm) cc_final: 0.8968 (mmm) REVERT: B 283 MET cc_start: 0.9398 (tpp) cc_final: 0.9124 (tpp) REVERT: C 47 MET cc_start: 0.6553 (mpp) cc_final: 0.4860 (mtp) REVERT: C 78 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8433 (t0) REVERT: C 82 MET cc_start: 0.9339 (mmm) cc_final: 0.8563 (tmm) REVERT: C 176 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8380 (mtt) REVERT: D 82 MET cc_start: 0.9447 (tpt) cc_final: 0.8796 (mmm) REVERT: D 227 MET cc_start: 0.9400 (tpp) cc_final: 0.8907 (tpp) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.2128 time to fit residues: 25.9042 Evaluate side-chains 78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 C residue 78 ASN Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 235 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 143 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.032836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.026811 restraints weight = 77795.665| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 3.98 r_work: 0.2449 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12004 Z= 0.281 Angle : 0.647 8.496 16292 Z= 0.310 Chirality : 0.047 0.144 1808 Planarity : 0.004 0.027 2084 Dihedral : 6.065 59.542 1672 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.19 % Allowed : 16.96 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.23), residues: 1468 helix: 0.52 (0.23), residues: 568 sheet: -0.81 (0.34), residues: 244 loop : 0.13 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 79 HIS 0.003 0.001 HIS D 101 PHE 0.010 0.001 PHE C 255 TYR 0.011 0.001 TYR A 166 ARG 0.003 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 404) hydrogen bonds : angle 4.60104 ( 1008) covalent geometry : bond 0.00625 (12004) covalent geometry : angle 0.64684 (16292) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4061.33 seconds wall clock time: 70 minutes 59.49 seconds (4259.49 seconds total)