Starting phenix.real_space_refine on Wed Sep 17 21:57:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.map" model { file = "/net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bph_44777/09_2025/9bph_44777.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.050 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 76 5.16 5 C 7412 2.51 5 N 1988 2.21 5 O 2252 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11740 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2907 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 Conformer: "B" Number of residues, atoms: 371, 2899 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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 bond proxies already assigned to first conformer: 2953 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.89, per 1000 atoms: 0.25 Number of scatterers: 11740 At special positions: 0 Unit cell: (100.683, 77.517, 169.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 76 16.00 P 8 15.00 Mg 4 11.99 O 2252 8.00 N 1988 7.00 C 7412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 956.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 49.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.857A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.716A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.099A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.831A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.577A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.733A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE A 255 " --> pdb=" O ASN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'A' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 305 Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR A 351 " --> pdb=" O SER A 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.979A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 61 removed outlier: 3.857A pdb=" N GLN B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.716A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.099A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.831A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 205 through 217 removed outlier: 3.577A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.733A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE B 255 " --> pdb=" O ASN B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.587A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.591A pdb=" N ALA B 319 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.979A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 removed outlier: 3.857A pdb=" N GLN C 59 " --> pdb=" O GLY C 55 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.807A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.716A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.098A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.831A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 217 removed outlier: 3.577A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.733A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 255 removed outlier: 3.695A pdb=" N PHE C 255 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 Processing helix chain 'C' and resid 273 through 284 removed outlier: 3.586A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.756A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA C 319 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 320 " --> pdb=" O GLU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.205A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.978A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 61 removed outlier: 3.857A pdb=" N GLN D 59 " --> pdb=" O GLY D 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.808A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.716A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.099A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 removed outlier: 3.943A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.831A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.769A pdb=" N THR D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 197 No H-bonds generated for 'chain 'D' and resid 195 through 197' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.577A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.733A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 255 removed outlier: 3.694A pdb=" N PHE D 255 " --> pdb=" O ASN D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 Processing helix chain 'D' and resid 273 through 284 removed outlier: 3.587A pdb=" N TYR D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.757A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.590A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 320 " --> pdb=" O GLU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 355 removed outlier: 6.204A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 3.979A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (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 169 through 170 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL A 163 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU A 242 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.152A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.554A pdb=" N VAL B 163 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 242 removed outlier: 4.592A pdb=" N LEU B 242 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB6, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL C 163 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU C 242 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 4.151A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'D' and resid 169 through 170 removed outlier: 3.553A pdb=" N VAL D 163 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 238 through 242 removed outlier: 4.593A pdb=" N LEU D 242 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) 492 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.01 Time building geometry restraints manager: 1.19 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: 3654 1.34 - 1.45: 1680 1.45 - 1.57: 6518 1.57 - 1.69: 16 1.69 - 1.81: 132 Bond restraints: 12000 Sorted by residual: bond pdb=" C ARG C 183 " pdb=" O ARG C 183 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.17e-02 7.31e+03 2.40e+01 bond pdb=" C ARG D 183 " pdb=" O ARG D 183 " ideal model delta sigma weight residual 1.237 1.294 -0.057 1.17e-02 7.31e+03 2.39e+01 bond pdb=" C ARG A 183 " pdb=" O ARG A 183 " ideal model delta sigma weight residual 1.237 1.293 -0.057 1.17e-02 7.31e+03 2.36e+01 bond pdb=" C ARG B 183 " pdb=" CA AARG B 183 " ideal model delta sigma weight residual 1.524 1.586 -0.062 1.29e-02 6.01e+03 2.32e+01 bond pdb=" C ARG B 183 " pdb=" O ARG B 183 " ideal model delta sigma weight residual 1.237 1.293 -0.056 1.17e-02 7.31e+03 2.30e+01 ... (remaining 11995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 15340 1.56 - 3.12: 704 3.12 - 4.69: 187 4.69 - 6.25: 53 6.25 - 7.81: 12 Bond angle restraints: 16296 Sorted by residual: angle pdb=" O ARG B 183 " pdb=" C ARG B 183 " pdb=" CA AARG B 183 " ideal model delta sigma weight residual 120.42 127.60 -7.18 1.06e+00 8.90e-01 4.59e+01 angle pdb=" O ARG B 183 " pdb=" C ARG B 183 " pdb=" CA BARG B 183 " ideal model delta sigma weight residual 120.55 127.73 -7.18 1.06e+00 8.90e-01 4.58e+01 angle pdb=" O ARG C 183 " pdb=" C ARG C 183 " pdb=" CA AARG C 183 " ideal model delta sigma weight residual 120.42 127.58 -7.16 1.06e+00 8.90e-01 4.57e+01 angle pdb=" O ARG A 183 " pdb=" C ARG A 183 " pdb=" CA AARG A 183 " ideal model delta sigma weight residual 120.42 127.58 -7.16 1.06e+00 8.90e-01 4.56e+01 angle pdb=" O ARG D 183 " pdb=" C ARG D 183 " pdb=" CA AARG D 183 " ideal model delta sigma weight residual 120.42 127.58 -7.16 1.06e+00 8.90e-01 4.56e+01 ... (remaining 16291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 6900 34.99 - 69.98: 296 69.98 - 104.97: 16 104.97 - 139.96: 4 139.96 - 174.95: 8 Dihedral angle restraints: 7224 sinusoidal: 2920 harmonic: 4304 Sorted by residual: dihedral pdb=" CD ARG A 372 " pdb=" NE ARG A 372 " pdb=" CZ ARG A 372 " pdb=" NH1 ARG A 372 " ideal model delta sinusoidal sigma weight residual 0.00 66.03 -66.03 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CD ARG D 372 " pdb=" NE ARG D 372 " pdb=" CZ ARG D 372 " pdb=" NH1 ARG D 372 " ideal model delta sinusoidal sigma weight residual 0.00 65.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CD ARG C 372 " pdb=" NE ARG C 372 " pdb=" CZ ARG C 372 " pdb=" NH1 ARG C 372 " ideal model delta sinusoidal sigma weight residual 0.00 65.96 -65.96 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 7221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1495 0.067 - 0.133: 273 0.133 - 0.200: 20 0.200 - 0.267: 16 0.267 - 0.333: 8 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA ILE C 327 " pdb=" N ILE C 327 " pdb=" C ILE C 327 " pdb=" CB ILE C 327 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ILE A 327 " pdb=" N ILE A 327 " pdb=" C ILE A 327 " pdb=" CB ILE A 327 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ILE D 327 " pdb=" N ILE D 327 " pdb=" C ILE D 327 " pdb=" CB ILE D 327 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.33 2.00e-01 2.50e+01 2.71e+00 ... (remaining 1809 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 335 " 1.002 9.50e-02 1.11e+02 4.49e-01 1.22e+02 pdb=" NE ARG A 335 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 335 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 335 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 335 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 335 " 1.002 9.50e-02 1.11e+02 4.49e-01 1.22e+02 pdb=" NE ARG D 335 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG D 335 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 335 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 335 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 335 " 1.001 9.50e-02 1.11e+02 4.49e-01 1.22e+02 pdb=" NE ARG C 335 " -0.060 2.00e-02 2.50e+03 pdb=" CZ ARG C 335 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 335 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 335 " 0.023 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3130 2.80 - 3.33: 9610 3.33 - 3.85: 17274 3.85 - 4.38: 20633 4.38 - 4.90: 37179 Nonbonded interactions: 87826 Sorted by model distance: nonbonded pdb=" O THR B 304 " pdb=" NH2 ARG B 335 " model vdw 2.280 3.120 nonbonded pdb=" O THR D 304 " pdb=" NH2 ARG D 335 " model vdw 2.280 3.120 nonbonded pdb=" O THR C 304 " pdb=" NH2 ARG C 335 " model vdw 2.281 3.120 nonbonded pdb=" O THR A 304 " pdb=" NH2 ARG A 335 " model vdw 2.281 3.120 nonbonded pdb=" OD2 ASP B 157 " pdb=" O3' ADP B 402 " model vdw 2.316 3.040 ... (remaining 87821 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.520 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 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 : 0.005 0.062 12000 Z= 0.373 Angle : 0.815 7.808 16296 Z= 0.526 Chirality : 0.058 0.333 1812 Planarity : 0.030 0.449 2084 Dihedral : 19.164 174.946 4472 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.34 % Allowed : 19.90 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.20), residues: 1468 helix: -1.87 (0.19), residues: 532 sheet: 0.76 (0.31), residues: 268 loop : -1.10 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 37 TYR 0.006 0.001 TYR C 337 PHE 0.005 0.001 PHE C 31 TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS B 101 Details of bonding type rmsd covalent geometry : bond 0.00534 (12000) covalent geometry : angle 0.81536 (16296) hydrogen bonds : bond 0.33932 ( 484) hydrogen bonds : angle 8.09075 ( 1224) *********************** 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 288 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.448 Fit side-chains REVERT: A 313 MET cc_start: 0.8668 (mmm) cc_final: 0.8419 (mmm) REVERT: A 328 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8226 (mttp) REVERT: A 330 ILE cc_start: 0.8633 (mt) cc_final: 0.8368 (mt) REVERT: B 92 ASN cc_start: 0.8494 (m110) cc_final: 0.8235 (m110) REVERT: B 95 ARG cc_start: 0.8121 (mtm110) cc_final: 0.7903 (mtm-85) REVERT: B 288 ASP cc_start: 0.6937 (p0) cc_final: 0.6696 (p0) REVERT: B 328 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7966 (mttp) REVERT: C 67 LEU cc_start: 0.8298 (mt) cc_final: 0.7974 (mp) REVERT: C 82 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6984 (tpt) REVERT: C 92 ASN cc_start: 0.8197 (m110) cc_final: 0.7933 (m-40) REVERT: C 95 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7780 (mmt180) REVERT: D 96 VAL cc_start: 0.8145 (p) cc_final: 0.7877 (m) REVERT: D 269 MET cc_start: 0.8865 (mtm) cc_final: 0.8605 (mtt) REVERT: D 296 ASN cc_start: 0.8840 (m-40) cc_final: 0.8447 (m-40) REVERT: D 328 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8124 (mttp) REVERT: D 330 ILE cc_start: 0.8516 (mt) cc_final: 0.8230 (mt) outliers start: 38 outliers final: 8 residues processed: 272 average time/residue: 0.1131 time to fit residues: 43.1734 Evaluate side-chains 168 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 92 ASN A 101 HIS A 121 GLN A 275 HIS A 371 HIS B 12 ASN B 101 HIS B 121 GLN B 275 HIS B 371 HIS C 12 ASN C 101 HIS C 121 GLN C 275 HIS C 371 HIS D 12 ASN D 101 HIS D 121 GLN D 275 HIS D 371 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103603 restraints weight = 39601.344| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.45 r_work: 0.2966 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12000 Z= 0.137 Angle : 0.625 8.081 16296 Z= 0.314 Chirality : 0.047 0.150 1812 Planarity : 0.006 0.062 2084 Dihedral : 13.836 179.024 1709 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.87 % Allowed : 19.19 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.21), residues: 1468 helix: -0.29 (0.22), residues: 556 sheet: 0.80 (0.30), residues: 284 loop : -1.00 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 210 TYR 0.010 0.001 TYR D 294 PHE 0.015 0.001 PHE A 352 TRP 0.012 0.001 TRP D 356 HIS 0.004 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00326 (12000) covalent geometry : angle 0.62521 (16296) hydrogen bonds : bond 0.04520 ( 484) hydrogen bonds : angle 4.80331 ( 1224) *********************** 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 176 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 144 time to evaluate : 0.362 Fit side-chains REVERT: A 293 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8024 (mp) REVERT: A 360 GLN cc_start: 0.7500 (tp40) cc_final: 0.7065 (tt0) REVERT: B 128 ASN cc_start: 0.8277 (m-40) cc_final: 0.8009 (t0) REVERT: C 95 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8113 (mtm-85) REVERT: C 360 GLN cc_start: 0.7499 (tp40) cc_final: 0.7190 (tt0) REVERT: D 224 GLU cc_start: 0.7586 (mp0) cc_final: 0.7035 (mm-30) REVERT: D 269 MET cc_start: 0.9019 (mtm) cc_final: 0.8662 (mtt) REVERT: D 296 ASN cc_start: 0.8898 (m-40) cc_final: 0.8468 (m-40) REVERT: D 360 GLN cc_start: 0.7614 (tp40) cc_final: 0.7161 (tt0) outliers start: 32 outliers final: 15 residues processed: 166 average time/residue: 0.1252 time to fit residues: 28.6940 Evaluate side-chains 135 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 chunk 110 optimal weight: 0.0870 chunk 140 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 95 optimal weight: 0.0870 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 101 optimal weight: 8.9990 chunk 116 optimal weight: 0.0370 overall best weight: 0.2572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN C 121 GLN D 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102118 restraints weight = 38603.849| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 3.13 r_work: 0.2955 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 12000 Z= 0.098 Angle : 0.539 7.781 16296 Z= 0.258 Chirality : 0.043 0.135 1812 Planarity : 0.005 0.051 2084 Dihedral : 11.215 163.281 1682 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.71 % Allowed : 19.67 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.22), residues: 1468 helix: 0.44 (0.24), residues: 556 sheet: 0.77 (0.30), residues: 284 loop : -0.87 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 210 TYR 0.007 0.001 TYR B 133 PHE 0.011 0.001 PHE A 352 TRP 0.007 0.001 TRP D 356 HIS 0.003 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00235 (12000) covalent geometry : angle 0.53947 (16296) hydrogen bonds : bond 0.03258 ( 484) hydrogen bonds : angle 4.34579 ( 1224) *********************** 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 163 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 133 time to evaluate : 0.460 Fit side-chains REVERT: A 176 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8486 (mmt) REVERT: A 360 GLN cc_start: 0.7762 (tp40) cc_final: 0.7361 (tt0) REVERT: B 34 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8349 (pt) REVERT: C 44 MET cc_start: 0.7404 (mtm) cc_final: 0.7172 (mtm) REVERT: C 95 ARG cc_start: 0.8321 (mtm110) cc_final: 0.8121 (mtm-85) REVERT: C 325 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6937 (mtm) REVERT: C 360 GLN cc_start: 0.7688 (tp40) cc_final: 0.7352 (tt0) REVERT: D 96 VAL cc_start: 0.8381 (p) cc_final: 0.8050 (m) REVERT: D 224 GLU cc_start: 0.7883 (mp0) cc_final: 0.7361 (mm-30) REVERT: D 334 GLU cc_start: 0.6105 (pm20) cc_final: 0.5787 (pm20) REVERT: D 360 GLN cc_start: 0.7726 (tp40) cc_final: 0.7247 (tt0) outliers start: 30 outliers final: 11 residues processed: 150 average time/residue: 0.1001 time to fit residues: 22.2254 Evaluate side-chains 133 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 92 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 121 GLN C 121 GLN D 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.115038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097551 restraints weight = 29420.347| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.87 r_work: 0.2955 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12000 Z= 0.154 Angle : 0.622 6.975 16296 Z= 0.310 Chirality : 0.048 0.140 1812 Planarity : 0.005 0.052 2084 Dihedral : 10.405 164.373 1682 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.15 % Allowed : 19.82 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.21), residues: 1468 helix: 0.43 (0.24), residues: 552 sheet: 0.51 (0.29), residues: 292 loop : -0.92 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 210 TYR 0.008 0.001 TYR B 188 PHE 0.011 0.001 PHE A 352 TRP 0.019 0.002 TRP A 356 HIS 0.006 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00385 (12000) covalent geometry : angle 0.62245 (16296) hydrogen bonds : bond 0.05093 ( 484) hydrogen bonds : angle 4.50029 ( 1224) *********************** 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 155 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.448 Fit side-chains REVERT: A 80 ASP cc_start: 0.7217 (t0) cc_final: 0.6578 (m-30) REVERT: A 125 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6910 (mm-30) REVERT: A 128 ASN cc_start: 0.8455 (m-40) cc_final: 0.8232 (m110) REVERT: A 360 GLN cc_start: 0.7680 (tp40) cc_final: 0.7307 (tt0) REVERT: B 195 GLU cc_start: 0.8629 (pt0) cc_final: 0.8289 (pt0) REVERT: C 95 ARG cc_start: 0.8411 (mtm110) cc_final: 0.8169 (mtm-85) REVERT: C 326 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8050 (mmmt) REVERT: C 360 GLN cc_start: 0.7443 (tp40) cc_final: 0.7159 (tt0) REVERT: D 80 ASP cc_start: 0.7207 (t0) cc_final: 0.6698 (m-30) REVERT: D 224 GLU cc_start: 0.7911 (mp0) cc_final: 0.7449 (mm-30) REVERT: D 360 GLN cc_start: 0.7729 (tp40) cc_final: 0.7424 (tt0) outliers start: 23 outliers final: 16 residues processed: 143 average time/residue: 0.1111 time to fit residues: 22.7794 Evaluate side-chains 124 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 108 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ARG Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 375 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 7.9990 chunk 112 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.109976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.092239 restraints weight = 35057.121| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.09 r_work: 0.2858 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 12000 Z= 0.223 Angle : 0.683 7.430 16296 Z= 0.341 Chirality : 0.051 0.165 1812 Planarity : 0.006 0.051 2084 Dihedral : 8.689 120.230 1682 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.11 % Allowed : 18.71 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.21), residues: 1468 helix: 0.13 (0.24), residues: 556 sheet: 0.24 (0.29), residues: 292 loop : -1.11 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 210 TYR 0.009 0.001 TYR C 294 PHE 0.012 0.002 PHE A 352 TRP 0.017 0.002 TRP C 356 HIS 0.005 0.002 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00573 (12000) covalent geometry : angle 0.68312 (16296) hydrogen bonds : bond 0.05821 ( 484) hydrogen bonds : angle 4.60425 ( 1224) *********************** 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 148 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.409 Fit side-chains REVERT: A 80 ASP cc_start: 0.7463 (t0) cc_final: 0.6871 (m-30) REVERT: A 293 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8469 (mp) REVERT: A 360 GLN cc_start: 0.7534 (tp40) cc_final: 0.7109 (tt0) REVERT: B 195 GLU cc_start: 0.8984 (pt0) cc_final: 0.8639 (pt0) REVERT: C 293 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8653 (mp) REVERT: C 326 LYS cc_start: 0.8443 (mmtm) cc_final: 0.8086 (mmmt) REVERT: D 80 ASP cc_start: 0.7314 (t0) cc_final: 0.6863 (m-30) REVERT: D 360 GLN cc_start: 0.7642 (tp40) cc_final: 0.7284 (tt0) outliers start: 35 outliers final: 20 residues processed: 140 average time/residue: 0.1184 time to fit residues: 23.5567 Evaluate side-chains 123 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 2 optimal weight: 0.4980 chunk 132 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.3313 r_free = 0.3313 target = 0.113307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.095067 restraints weight = 37035.370| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.23 r_work: 0.2898 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12000 Z= 0.135 Angle : 0.588 6.231 16296 Z= 0.287 Chirality : 0.047 0.142 1812 Planarity : 0.005 0.052 2084 Dihedral : 7.785 94.737 1680 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.15 % Allowed : 19.35 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.22), residues: 1468 helix: 0.41 (0.24), residues: 552 sheet: 0.22 (0.29), residues: 292 loop : -0.93 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 95 TYR 0.008 0.001 TYR C 294 PHE 0.012 0.001 PHE C 31 TRP 0.011 0.002 TRP A 356 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00340 (12000) covalent geometry : angle 0.58763 (16296) hydrogen bonds : bond 0.04276 ( 484) hydrogen bonds : angle 4.43219 ( 1224) *********************** 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 128 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.380 Fit side-chains REVERT: A 65 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8362 (pp) REVERT: A 80 ASP cc_start: 0.7193 (t0) cc_final: 0.6645 (m-30) REVERT: A 227 MET cc_start: 0.8365 (mmm) cc_final: 0.8139 (mmm) REVERT: A 293 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 360 GLN cc_start: 0.7491 (tp40) cc_final: 0.7058 (tt0) REVERT: B 195 GLU cc_start: 0.8925 (pt0) cc_final: 0.8542 (pt0) REVERT: C 293 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8612 (mp) REVERT: C 325 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7006 (mtm) REVERT: C 326 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8074 (mmmt) REVERT: D 65 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8421 (pp) REVERT: D 80 ASP cc_start: 0.7165 (t0) cc_final: 0.6773 (m-30) REVERT: D 95 ARG cc_start: 0.8481 (mtt-85) cc_final: 0.8108 (mtm-85) outliers start: 23 outliers final: 17 residues processed: 117 average time/residue: 0.0967 time to fit residues: 16.8754 Evaluate side-chains 118 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 7 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 97 optimal weight: 0.2980 chunk 104 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.111938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.093914 restraints weight = 38137.112| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.22 r_work: 0.2877 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12000 Z= 0.152 Angle : 0.612 6.420 16296 Z= 0.299 Chirality : 0.047 0.153 1812 Planarity : 0.005 0.052 2084 Dihedral : 7.724 95.182 1680 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.39 % Allowed : 18.95 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.22), residues: 1468 helix: 0.40 (0.24), residues: 552 sheet: 0.22 (0.29), residues: 292 loop : -0.90 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.007 0.001 TYR C 294 PHE 0.010 0.001 PHE C 31 TRP 0.012 0.002 TRP A 356 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00389 (12000) covalent geometry : angle 0.61167 (16296) hydrogen bonds : bond 0.04639 ( 484) hydrogen bonds : angle 4.43484 ( 1224) *********************** 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 131 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.468 Fit side-chains REVERT: A 65 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8341 (pp) REVERT: A 80 ASP cc_start: 0.7317 (t0) cc_final: 0.6800 (m-30) REVERT: A 293 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 360 GLN cc_start: 0.7524 (tp40) cc_final: 0.7090 (tt0) REVERT: B 195 GLU cc_start: 0.8947 (pt0) cc_final: 0.8568 (pt0) REVERT: B 326 LYS cc_start: 0.8363 (mmtm) cc_final: 0.8028 (mmmt) REVERT: C 65 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8344 (pp) REVERT: C 325 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7044 (mtm) REVERT: C 326 LYS cc_start: 0.8450 (mmtm) cc_final: 0.8094 (mmmt) REVERT: D 80 ASP cc_start: 0.7257 (t0) cc_final: 0.6830 (m-30) REVERT: D 95 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.8100 (mtm-85) outliers start: 26 outliers final: 19 residues processed: 123 average time/residue: 0.0981 time to fit residues: 17.9691 Evaluate side-chains 122 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 107 optimal weight: 0.1980 chunk 71 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- 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 = 0.3325 r_free = 0.3325 target = 0.113779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096687 restraints weight = 31093.051| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.84 r_work: 0.2935 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12000 Z= 0.151 Angle : 0.611 6.464 16296 Z= 0.298 Chirality : 0.047 0.151 1812 Planarity : 0.005 0.052 2084 Dihedral : 7.638 97.094 1680 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.39 % Allowed : 18.63 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.22), residues: 1468 helix: 0.43 (0.24), residues: 552 sheet: 0.24 (0.30), residues: 292 loop : -0.82 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 95 TYR 0.008 0.001 TYR C 294 PHE 0.009 0.001 PHE C 31 TRP 0.012 0.002 TRP A 356 HIS 0.004 0.001 HIS C 161 Details of bonding type rmsd covalent geometry : bond 0.00386 (12000) covalent geometry : angle 0.61081 (16296) hydrogen bonds : bond 0.04535 ( 484) hydrogen bonds : angle 4.42803 ( 1224) *********************** 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 130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.428 Fit side-chains REVERT: A 65 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8442 (pp) REVERT: A 80 ASP cc_start: 0.7324 (t0) cc_final: 0.6849 (m-30) REVERT: A 293 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8488 (mp) REVERT: A 360 GLN cc_start: 0.7591 (tp40) cc_final: 0.7156 (tt0) REVERT: B 93 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: B 195 GLU cc_start: 0.8920 (pt0) cc_final: 0.8549 (pt0) REVERT: B 326 LYS cc_start: 0.8354 (mmtm) cc_final: 0.8051 (mmmt) REVERT: C 65 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8363 (pp) REVERT: C 325 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.7159 (mtt) REVERT: C 326 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8135 (mmmt) REVERT: D 80 ASP cc_start: 0.7298 (t0) cc_final: 0.6911 (m-30) REVERT: D 95 ARG cc_start: 0.8482 (mtt-85) cc_final: 0.8165 (mtm-85) outliers start: 26 outliers final: 21 residues processed: 123 average time/residue: 0.0981 time to fit residues: 18.1656 Evaluate side-chains 125 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.117443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.099539 restraints weight = 37040.501| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.15 r_work: 0.2965 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12000 Z= 0.105 Angle : 0.553 6.408 16296 Z= 0.266 Chirality : 0.045 0.148 1812 Planarity : 0.005 0.051 2084 Dihedral : 7.256 94.991 1680 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.91 % Allowed : 19.11 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.22), residues: 1468 helix: 0.58 (0.24), residues: 556 sheet: 0.37 (0.30), residues: 284 loop : -0.65 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.006 0.001 TYR C 294 PHE 0.008 0.001 PHE A 352 TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS B 371 Details of bonding type rmsd covalent geometry : bond 0.00262 (12000) covalent geometry : angle 0.55271 (16296) hydrogen bonds : bond 0.03382 ( 484) hydrogen bonds : angle 4.25893 ( 1224) *********************** 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 134 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.361 Fit side-chains REVERT: A 34 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8355 (pt) REVERT: A 65 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8422 (pp) REVERT: A 80 ASP cc_start: 0.7080 (t0) cc_final: 0.6615 (m-30) REVERT: A 227 MET cc_start: 0.8442 (mmm) cc_final: 0.8220 (mmm) REVERT: A 293 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8480 (mp) REVERT: A 360 GLN cc_start: 0.7592 (tp40) cc_final: 0.7147 (tt0) REVERT: B 326 LYS cc_start: 0.8414 (mmtm) cc_final: 0.8096 (mmmt) REVERT: C 34 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8510 (pt) REVERT: C 65 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8319 (pp) REVERT: C 326 LYS cc_start: 0.8470 (mmtm) cc_final: 0.8174 (mmmt) REVERT: D 80 ASP cc_start: 0.7196 (t0) cc_final: 0.6794 (m-30) REVERT: D 95 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.8155 (mtm-85) outliers start: 20 outliers final: 12 residues processed: 127 average time/residue: 0.1035 time to fit residues: 19.5860 Evaluate side-chains 126 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 100 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 0.0020 chunk 58 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 90 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3418 r_free = 0.3418 target = 0.120886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.103492 restraints weight = 24331.779| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.85 r_work: 0.3032 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 12000 Z= 0.093 Angle : 0.530 6.468 16296 Z= 0.252 Chirality : 0.043 0.159 1812 Planarity : 0.004 0.050 2084 Dihedral : 6.898 91.689 1680 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.27 % Allowed : 19.59 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.22), residues: 1468 helix: 0.77 (0.24), residues: 556 sheet: 0.42 (0.30), residues: 284 loop : -0.47 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.007 0.001 TYR C 133 PHE 0.008 0.001 PHE A 352 TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A 101 Details of bonding type rmsd covalent geometry : bond 0.00227 (12000) covalent geometry : angle 0.52978 (16296) hydrogen bonds : bond 0.02799 ( 484) hydrogen bonds : angle 4.08642 ( 1224) ********************** 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 137 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.467 Fit side-chains REVERT: A 34 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8350 (pt) REVERT: A 65 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8255 (pp) REVERT: A 80 ASP cc_start: 0.6832 (t0) cc_final: 0.6368 (m-30) REVERT: A 227 MET cc_start: 0.8181 (mmm) cc_final: 0.7960 (mmm) REVERT: A 360 GLN cc_start: 0.7453 (tp40) cc_final: 0.7030 (tt0) REVERT: B 34 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8455 (pt) REVERT: B 326 LYS cc_start: 0.8325 (mmtm) cc_final: 0.7994 (mmmt) REVERT: C 34 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8476 (pt) REVERT: C 65 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8094 (pp) REVERT: C 95 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.7921 (mtp85) REVERT: C 326 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8095 (mmmt) REVERT: D 80 ASP cc_start: 0.6957 (t0) cc_final: 0.6528 (m-30) outliers start: 12 outliers final: 6 residues processed: 132 average time/residue: 0.1063 time to fit residues: 20.8267 Evaluate side-chains 127 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 63 optimal weight: 0.0010 chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.117338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.100808 restraints weight = 23928.061| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 2.53 r_work: 0.3000 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12000 Z= 0.103 Angle : 0.547 6.551 16296 Z= 0.261 Chirality : 0.044 0.160 1812 Planarity : 0.005 0.063 2084 Dihedral : 6.801 89.872 1680 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.19 % Allowed : 19.90 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.22), residues: 1468 helix: 0.78 (0.24), residues: 556 sheet: 0.46 (0.30), residues: 284 loop : -0.41 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 95 TYR 0.006 0.001 TYR C 294 PHE 0.007 0.001 PHE A 352 TRP 0.009 0.001 TRP A 356 HIS 0.002 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00256 (12000) covalent geometry : angle 0.54724 (16296) hydrogen bonds : bond 0.03288 ( 484) hydrogen bonds : angle 4.07973 ( 1224) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2501.93 seconds wall clock time: 43 minutes 42.85 seconds (2622.85 seconds total)