Starting phenix.real_space_refine on Tue Jun 10 12:24:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bph_44777/06_2025/9bph_44777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bph_44777/06_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_44777/06_2025/9bph_44777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bph_44777/06_2025/9bph_44777.map" model { file = "/net/cci-nas-00/data/ceres_data/9bph_44777/06_2025/9bph_44777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bph_44777/06_2025/9bph_44777.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 7.66, per 1000 atoms: 0.65 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: 2.87 Conformation dependent library (CDL) restraints added in 2.9 seconds 2936 Ramachandran restraints generated. 1468 Oldfield, 0 Emsley, 1468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 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: 1.63 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: 3.86 Time building geometry restraints manager: 3.38 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.970 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (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 TRP 0.007 0.001 TRP C 356 HIS 0.003 0.001 HIS B 101 PHE 0.005 0.001 PHE C 31 TYR 0.006 0.001 TYR C 337 ARG 0.003 0.000 ARG D 37 Details of bonding type rmsd hydrogen bonds : bond 0.33932 ( 484) hydrogen bonds : angle 8.09075 ( 1224) covalent geometry : bond 0.00534 (12000) covalent geometry : angle 0.81536 (16296) *********************** 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 : 1.231 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: 0.2464 time to fit residues: 93.2522 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 : 1.305 ------------------------------------------------------------------------------- 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 124 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.4980 chunk 134 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 371 HIS C 12 ASN C 101 HIS C 121 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.103591 restraints weight = 28445.101| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.81 r_work: 0.2984 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12000 Z= 0.139 Angle : 0.631 7.250 16296 Z= 0.316 Chirality : 0.047 0.155 1812 Planarity : 0.006 0.063 2084 Dihedral : 13.526 179.989 1709 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.26 % Allowed : 18.95 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1468 helix: -0.45 (0.22), residues: 556 sheet: 0.74 (0.30), residues: 284 loop : -1.02 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 356 HIS 0.006 0.001 HIS A 88 PHE 0.014 0.001 PHE A 352 TYR 0.010 0.001 TYR D 294 ARG 0.007 0.001 ARG C 210 Details of bonding type rmsd hydrogen bonds : bond 0.04375 ( 484) hydrogen bonds : angle 4.79924 ( 1224) covalent geometry : bond 0.00334 (12000) covalent geometry : angle 0.63098 (16296) *********************** 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 184 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.253 Fit side-chains REVERT: A 293 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 360 GLN cc_start: 0.7497 (tp40) cc_final: 0.7089 (tt0) REVERT: B 92 ASN cc_start: 0.8055 (m110) cc_final: 0.7826 (m-40) REVERT: B 128 ASN cc_start: 0.8271 (m-40) cc_final: 0.7978 (t0) REVERT: C 95 ARG cc_start: 0.8338 (mtm110) cc_final: 0.8113 (mtm-85) REVERT: C 325 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7061 (ptp) REVERT: C 360 GLN cc_start: 0.7339 (tp40) cc_final: 0.7029 (tt0) REVERT: D 125 GLU cc_start: 0.6614 (mt-10) cc_final: 0.6369 (mm-30) REVERT: D 224 GLU cc_start: 0.7546 (mp0) cc_final: 0.7038 (mm-30) REVERT: D 269 MET cc_start: 0.9073 (mtm) cc_final: 0.8708 (mtt) REVERT: D 296 ASN cc_start: 0.8882 (m-40) cc_final: 0.8591 (m-40) REVERT: D 360 GLN cc_start: 0.7595 (tp40) cc_final: 0.7168 (tt0) outliers start: 37 outliers final: 16 residues processed: 174 average time/residue: 0.2570 time to fit residues: 62.8716 Evaluate side-chains 139 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 160 THR 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 247 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain D residue 28 ARG 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 7 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 14 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 275 HIS C 275 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.118460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.100153 restraints weight = 28925.197| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.18 r_work: 0.2975 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12000 Z= 0.130 Angle : 0.598 7.232 16296 Z= 0.293 Chirality : 0.046 0.137 1812 Planarity : 0.005 0.054 2084 Dihedral : 11.494 176.494 1682 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.03 % Allowed : 19.11 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.22), residues: 1468 helix: 0.27 (0.24), residues: 556 sheet: 0.69 (0.30), residues: 284 loop : -0.98 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 356 HIS 0.003 0.001 HIS A 87 PHE 0.012 0.001 PHE A 352 TYR 0.007 0.001 TYR B 133 ARG 0.013 0.001 ARG D 254 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 484) hydrogen bonds : angle 4.48758 ( 1224) covalent geometry : bond 0.00319 (12000) covalent geometry : angle 0.59804 (16296) *********************** 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 161 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 1.353 Fit side-chains REVERT: A 125 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6919 (mm-30) REVERT: A 176 MET cc_start: 0.8942 (OUTLIER) cc_final: 0.8537 (mmt) REVERT: A 269 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8834 (mtp) REVERT: A 293 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8392 (mp) REVERT: A 360 GLN cc_start: 0.7657 (tp40) cc_final: 0.7266 (tt0) REVERT: B 92 ASN cc_start: 0.8315 (m110) cc_final: 0.8084 (m-40) REVERT: B 296 ASN cc_start: 0.8998 (m-40) cc_final: 0.8727 (m-40) REVERT: C 34 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8205 (pt) REVERT: C 95 ARG cc_start: 0.8389 (mtm110) cc_final: 0.7988 (mtp85) REVERT: C 325 MET cc_start: 0.7567 (OUTLIER) cc_final: 0.7047 (ptp) REVERT: C 360 GLN cc_start: 0.7401 (tp40) cc_final: 0.7128 (tt0) REVERT: D 96 VAL cc_start: 0.8263 (p) cc_final: 0.7938 (m) REVERT: D 125 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6756 (mm-30) REVERT: D 224 GLU cc_start: 0.7848 (mp0) cc_final: 0.7326 (mm-30) REVERT: D 296 ASN cc_start: 0.9029 (m-40) cc_final: 0.8652 (m-40) REVERT: D 360 GLN cc_start: 0.7794 (tp40) cc_final: 0.7385 (tt0) REVERT: D 370 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7429 (p) outliers start: 34 outliers final: 14 residues processed: 145 average time/residue: 0.2327 time to fit residues: 49.5814 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 : 1.298 ------------------------------------------------------------------------------- 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 269 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 MET 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 159 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 370 VAL 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 89 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.092664 restraints weight = 37337.663| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.53 r_work: 0.2858 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12000 Z= 0.182 Angle : 0.645 6.504 16296 Z= 0.322 Chirality : 0.049 0.168 1812 Planarity : 0.005 0.053 2084 Dihedral : 9.761 147.060 1682 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 2.79 % Allowed : 19.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1468 helix: 0.22 (0.24), residues: 556 sheet: 0.34 (0.29), residues: 292 loop : -1.10 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 356 HIS 0.005 0.001 HIS C 161 PHE 0.015 0.002 PHE C 200 TYR 0.007 0.001 TYR A 294 ARG 0.005 0.001 ARG A 210 Details of bonding type rmsd hydrogen bonds : bond 0.05435 ( 484) hydrogen bonds : angle 4.54860 ( 1224) covalent geometry : bond 0.00466 (12000) covalent geometry : angle 0.64491 (16296) *********************** 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 145 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.363 Fit side-chains REVERT: A 80 ASP cc_start: 0.7391 (t0) cc_final: 0.6759 (m-30) REVERT: A 99 GLU cc_start: 0.7767 (mp0) cc_final: 0.7563 (mt-10) REVERT: A 125 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7176 (mm-30) REVERT: A 269 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8998 (mtp) REVERT: A 293 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 360 GLN cc_start: 0.7444 (tp40) cc_final: 0.7018 (tt0) REVERT: C 325 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.6919 (ptp) REVERT: D 80 ASP cc_start: 0.7224 (t0) cc_final: 0.6719 (m-30) REVERT: D 360 GLN cc_start: 0.7648 (tp40) cc_final: 0.7252 (tt0) outliers start: 31 outliers final: 21 residues processed: 133 average time/residue: 0.2328 time to fit residues: 45.5356 Evaluate side-chains 126 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 1.433 ------------------------------------------------------------------------------- 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 A residue 269 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 325 MET 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 159 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 325 MET 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 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.115779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097509 restraints weight = 35640.061| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.19 r_work: 0.2935 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12000 Z= 0.112 Angle : 0.558 6.130 16296 Z= 0.273 Chirality : 0.045 0.149 1812 Planarity : 0.005 0.052 2084 Dihedral : 8.026 110.378 1680 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.47 % Allowed : 19.43 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1468 helix: 0.49 (0.24), residues: 556 sheet: 0.37 (0.30), residues: 284 loop : -0.93 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 356 HIS 0.003 0.001 HIS B 371 PHE 0.010 0.001 PHE C 31 TYR 0.006 0.001 TYR C 294 ARG 0.008 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 484) hydrogen bonds : angle 4.34635 ( 1224) covalent geometry : bond 0.00276 (12000) covalent geometry : angle 0.55764 (16296) *********************** 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 146 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.592 Fit side-chains REVERT: A 65 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (pp) REVERT: A 80 ASP cc_start: 0.7178 (t0) cc_final: 0.6632 (m-30) REVERT: A 125 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7063 (mm-30) REVERT: A 360 GLN cc_start: 0.7488 (tp40) cc_final: 0.7073 (tt0) REVERT: C 34 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8436 (pt) REVERT: C 325 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6697 (ptp) REVERT: C 326 LYS cc_start: 0.8442 (mmtm) cc_final: 0.8078 (mmmt) REVERT: D 65 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8341 (pp) REVERT: D 80 ASP cc_start: 0.7100 (t0) cc_final: 0.6689 (m-30) REVERT: D 95 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8155 (mtm-85) REVERT: D 360 GLN cc_start: 0.7585 (tp40) cc_final: 0.7224 (tt0) outliers start: 27 outliers final: 17 residues processed: 133 average time/residue: 0.2323 time to fit residues: 45.8780 Evaluate side-chains 130 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 364 GLU 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 159 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 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 Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 12 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.113976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095008 restraints weight = 34872.667| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.47 r_work: 0.2869 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4888 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= 0.131 Angle : 0.582 6.198 16296 Z= 0.284 Chirality : 0.046 0.144 1812 Planarity : 0.005 0.052 2084 Dihedral : 7.638 93.186 1680 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.79 % Allowed : 19.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1468 helix: 0.57 (0.24), residues: 552 sheet: 0.28 (0.29), residues: 292 loop : -0.86 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 356 HIS 0.004 0.001 HIS C 161 PHE 0.010 0.001 PHE A 352 TYR 0.007 0.001 TYR C 166 ARG 0.009 0.001 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 484) hydrogen bonds : angle 4.33184 ( 1224) covalent geometry : bond 0.00330 (12000) covalent geometry : angle 0.58235 (16296) *********************** 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 147 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 116 time to evaluate : 1.430 Fit side-chains REVERT: A 65 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8226 (pp) REVERT: A 80 ASP cc_start: 0.7102 (t0) cc_final: 0.6523 (m-30) REVERT: A 125 GLU cc_start: 0.7258 (mt-10) cc_final: 0.7040 (mm-30) REVERT: A 293 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 360 GLN cc_start: 0.7390 (tp40) cc_final: 0.6961 (tt0) REVERT: B 326 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7971 (mmmt) REVERT: C 34 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8354 (pt) REVERT: C 65 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8247 (pp) REVERT: C 325 MET cc_start: 0.7470 (OUTLIER) cc_final: 0.6538 (ptp) REVERT: C 326 LYS cc_start: 0.8336 (mmtm) cc_final: 0.7975 (mmmt) REVERT: D 80 ASP cc_start: 0.7107 (t0) cc_final: 0.6688 (m-30) REVERT: D 95 ARG cc_start: 0.8402 (mtt-85) cc_final: 0.7985 (mtm-85) REVERT: D 360 GLN cc_start: 0.7518 (tp40) cc_final: 0.7118 (tt0) outliers start: 31 outliers final: 22 residues processed: 134 average time/residue: 0.2401 time to fit residues: 47.1607 Evaluate side-chains 135 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 A residue 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL 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 28 ARG 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 Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 40 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 36 optimal weight: 0.0170 chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.117806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.100762 restraints weight = 29068.723| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.77 r_work: 0.2996 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12000 Z= 0.106 Angle : 0.553 6.179 16296 Z= 0.266 Chirality : 0.045 0.147 1812 Planarity : 0.005 0.051 2084 Dihedral : 7.431 94.101 1680 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.55 % Allowed : 18.87 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1468 helix: 0.64 (0.24), residues: 556 sheet: 0.37 (0.30), residues: 284 loop : -0.72 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE A 352 TYR 0.006 0.001 TYR C 166 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 484) hydrogen bonds : angle 4.23811 ( 1224) covalent geometry : bond 0.00264 (12000) covalent geometry : angle 0.55321 (16296) *********************** 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 142 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 2.333 Fit side-chains REVERT: A 34 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8340 (pt) REVERT: A 65 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8401 (pp) REVERT: A 80 ASP cc_start: 0.7059 (t0) cc_final: 0.6564 (m-30) REVERT: A 293 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8482 (mp) REVERT: A 360 GLN cc_start: 0.7515 (tp40) cc_final: 0.7100 (tt0) REVERT: B 326 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8074 (mmmt) REVERT: C 34 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8486 (pt) REVERT: C 65 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8370 (pp) REVERT: C 325 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6407 (ptp) REVERT: C 326 LYS cc_start: 0.8400 (mmtm) cc_final: 0.8081 (mmmt) REVERT: D 80 ASP cc_start: 0.7130 (t0) cc_final: 0.6762 (m-30) REVERT: D 95 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.8189 (mtm-85) outliers start: 28 outliers final: 19 residues processed: 131 average time/residue: 0.2768 time to fit residues: 53.8362 Evaluate side-chains 132 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 A residue 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL 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 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 247 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 132 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 137 optimal weight: 0.0870 chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- 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 = 0.3374 r_free = 0.3374 target = 0.117641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.100286 restraints weight = 31037.785| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.87 r_work: 0.2990 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.4997 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= 0.106 Angle : 0.551 6.241 16296 Z= 0.264 Chirality : 0.045 0.148 1812 Planarity : 0.005 0.057 2084 Dihedral : 7.303 94.040 1680 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.31 % Allowed : 18.87 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1468 helix: 0.68 (0.24), residues: 556 sheet: 0.40 (0.30), residues: 284 loop : -0.64 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.003 0.001 HIS D 161 PHE 0.008 0.001 PHE A 352 TYR 0.006 0.001 TYR C 294 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 484) hydrogen bonds : angle 4.17964 ( 1224) covalent geometry : bond 0.00264 (12000) covalent geometry : angle 0.55062 (16296) *********************** 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 137 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.580 Fit side-chains REVERT: A 34 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8368 (pt) REVERT: A 65 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8419 (pp) REVERT: A 80 ASP cc_start: 0.7062 (t0) cc_final: 0.6572 (m-30) REVERT: A 293 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 360 GLN cc_start: 0.7545 (tp40) cc_final: 0.7125 (tt0) REVERT: B 326 LYS cc_start: 0.8384 (mmtm) cc_final: 0.8086 (mmmt) REVERT: C 34 ILE cc_start: 0.8904 (OUTLIER) cc_final: 0.8500 (pt) REVERT: C 65 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8384 (pp) REVERT: C 325 MET cc_start: 0.7452 (OUTLIER) cc_final: 0.6421 (ptp) REVERT: C 326 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8126 (mmmt) REVERT: D 80 ASP cc_start: 0.7185 (t0) cc_final: 0.6796 (m-30) REVERT: D 95 ARG cc_start: 0.8461 (mtt-85) cc_final: 0.8197 (mtm-85) outliers start: 25 outliers final: 17 residues processed: 127 average time/residue: 0.2966 time to fit residues: 55.9893 Evaluate side-chains 129 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 A residue 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL 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 325 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 54 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 Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 45 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 124 optimal weight: 0.0070 chunk 118 optimal weight: 3.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 = 0.3410 r_free = 0.3410 target = 0.120355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102526 restraints weight = 27586.193| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.01 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 12000 Z= 0.094 Angle : 0.530 6.262 16296 Z= 0.252 Chirality : 0.044 0.148 1812 Planarity : 0.005 0.061 2084 Dihedral : 7.153 94.050 1680 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.15 % Allowed : 18.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.22), residues: 1468 helix: 0.78 (0.24), residues: 556 sheet: 0.40 (0.30), residues: 284 loop : -0.50 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE A 352 TYR 0.005 0.001 TYR C 133 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 484) hydrogen bonds : angle 4.08969 ( 1224) covalent geometry : bond 0.00231 (12000) covalent geometry : angle 0.53021 (16296) *********************** 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: 23 poor density : 111 time to evaluate : 1.293 Fit side-chains REVERT: A 34 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8377 (pt) REVERT: A 65 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8329 (pp) REVERT: A 80 ASP cc_start: 0.6905 (t0) cc_final: 0.6435 (m-30) REVERT: A 360 GLN cc_start: 0.7429 (tp40) cc_final: 0.6997 (tt0) REVERT: B 326 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8056 (mmmt) REVERT: C 34 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8470 (pt) REVERT: C 65 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8226 (pp) REVERT: C 95 ARG cc_start: 0.8597 (mtm-85) cc_final: 0.7969 (mtp85) REVERT: C 325 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6995 (mtm) REVERT: C 326 LYS cc_start: 0.8364 (mmtm) cc_final: 0.8059 (mmmt) REVERT: D 80 ASP cc_start: 0.7023 (t0) cc_final: 0.6596 (m-30) REVERT: D 95 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8068 (mtm-85) outliers start: 23 outliers final: 16 residues processed: 124 average time/residue: 0.2346 time to fit residues: 42.8086 Evaluate side-chains 124 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL 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 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 325 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 54 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 Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 100 optimal weight: 0.2980 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 25 optimal weight: 0.0970 chunk 98 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3416 r_free = 0.3416 target = 0.120791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.102267 restraints weight = 31972.945| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.29 r_work: 0.2993 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12000 Z= 0.093 Angle : 0.526 6.296 16296 Z= 0.249 Chirality : 0.043 0.147 1812 Planarity : 0.005 0.056 2084 Dihedral : 7.063 94.344 1680 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.91 % Allowed : 19.27 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.22), residues: 1468 helix: 0.85 (0.24), residues: 556 sheet: 0.47 (0.30), residues: 284 loop : -0.40 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 79 HIS 0.002 0.001 HIS D 161 PHE 0.008 0.001 PHE A 352 TYR 0.006 0.001 TYR C 133 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.02945 ( 484) hydrogen bonds : angle 4.03474 ( 1224) covalent geometry : bond 0.00228 (12000) covalent geometry : angle 0.52593 (16296) ********************** 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 134 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.296 Fit side-chains REVERT: A 34 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8377 (pt) REVERT: A 80 ASP cc_start: 0.6897 (t0) cc_final: 0.6428 (m-30) REVERT: A 360 GLN cc_start: 0.7431 (tp40) cc_final: 0.6995 (tt0) REVERT: B 326 LYS cc_start: 0.8362 (mmtm) cc_final: 0.8052 (mmmt) REVERT: C 34 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8474 (pt) REVERT: C 65 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8219 (pp) REVERT: C 95 ARG cc_start: 0.8571 (mtm-85) cc_final: 0.7933 (mtp85) REVERT: C 325 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7050 (mtt) REVERT: C 326 LYS cc_start: 0.8381 (mmtm) cc_final: 0.8096 (mmmt) REVERT: D 80 ASP cc_start: 0.7072 (t0) cc_final: 0.6645 (m-30) REVERT: D 360 GLN cc_start: 0.7544 (tp40) cc_final: 0.7136 (tt0) outliers start: 20 outliers final: 14 residues processed: 124 average time/residue: 0.2236 time to fit residues: 41.1928 Evaluate side-chains 127 residues out of total 1248 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 325 MET Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 163 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 325 MET Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 370 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 130 optimal weight: 0.0470 chunk 63 optimal weight: 0.2980 overall best weight: 0.9880 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.119060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.100193 restraints weight = 34828.235| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.44 r_work: 0.2970 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12000 Z= 0.103 Angle : 0.541 6.389 16296 Z= 0.258 Chirality : 0.044 0.147 1812 Planarity : 0.005 0.050 2084 Dihedral : 7.106 94.855 1680 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.91 % Allowed : 19.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1468 helix: 0.81 (0.24), residues: 556 sheet: 0.48 (0.30), residues: 284 loop : -0.39 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 356 HIS 0.003 0.001 HIS B 101 PHE 0.007 0.001 PHE A 352 TYR 0.005 0.001 TYR C 294 ARG 0.009 0.000 ARG A 95 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 484) hydrogen bonds : angle 4.05642 ( 1224) covalent geometry : bond 0.00255 (12000) covalent geometry : angle 0.54135 (16296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5737.63 seconds wall clock time: 100 minutes 46.36 seconds (6046.36 seconds total)