Starting phenix.real_space_refine on Thu Sep 18 14:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ots_70857/09_2025/9ots_70857.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.109 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 10941 2.51 5 N 2937 2.21 5 O 3297 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17238 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3602 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 27, 'TRANS': 418} Chain: "B" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3602 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 27, 'TRANS': 418} Chain: "C" Number of atoms: 3602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3602 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 27, 'TRANS': 418} Chain: "D" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2144 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "E" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2144 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Chain: "F" Number of atoms: 2144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2144 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 13, 'TRANS': 243} Time building chain proxies: 3.43, per 1000 atoms: 0.20 Number of scatterers: 17238 At special positions: 0 Unit cell: (194.7, 112.2, 95.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 3297 8.00 N 2937 7.00 C 10941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 602.9 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3996 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 30 sheets defined 29.4% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 69 through 90 removed outlier: 3.940A pdb=" N TYR A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 136 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.653A pdb=" N ALA A 168 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 173 removed outlier: 3.982A pdb=" N GLN A 173 " --> pdb=" O ARG A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.775A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 removed outlier: 3.694A pdb=" N ASP A 222 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.791A pdb=" N ASN A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE A 242 " --> pdb=" O TRP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.893A pdb=" N THR A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE A 255 " --> pdb=" O THR A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.584A pdb=" N ASP A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 286 removed outlier: 4.205A pdb=" N SER A 281 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 312 Processing helix chain 'A' and resid 344 through 349 removed outlier: 4.043A pdb=" N ASP A 348 " --> pdb=" O TYR A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.622A pdb=" N LEU A 408 " --> pdb=" O PRO A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'B' and resid 69 through 90 removed outlier: 3.939A pdb=" N TYR B 73 " --> pdb=" O THR B 69 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA B 90 " --> pdb=" O ARG B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 Processing helix chain 'B' and resid 164 through 168 removed outlier: 3.652A pdb=" N ALA B 168 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.982A pdb=" N GLN B 173 " --> pdb=" O ARG B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.775A pdb=" N ARG B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 removed outlier: 3.694A pdb=" N ASP B 222 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.791A pdb=" N ASN B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 242 " --> pdb=" O TRP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 255 removed outlier: 3.893A pdb=" N THR B 251 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 252 " --> pdb=" O GLU B 248 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N PHE B 255 " --> pdb=" O THR B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 261 removed outlier: 3.583A pdb=" N ASP B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 286 removed outlier: 4.204A pdb=" N SER B 281 " --> pdb=" O CYS B 277 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 Processing helix chain 'B' and resid 344 through 349 removed outlier: 4.043A pdb=" N ASP B 348 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.622A pdb=" N LEU B 408 " --> pdb=" O PRO B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'C' and resid 69 through 90 removed outlier: 3.939A pdb=" N TYR C 73 " --> pdb=" O THR C 69 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 90 " --> pdb=" O ARG C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 136 Processing helix chain 'C' and resid 164 through 168 removed outlier: 3.652A pdb=" N ALA C 168 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.984A pdb=" N GLN C 173 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 3.776A pdb=" N ARG C 179 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 removed outlier: 3.694A pdb=" N ASP C 222 " --> pdb=" O SER C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.791A pdb=" N ASN C 240 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 242 " --> pdb=" O TRP C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 255 removed outlier: 3.893A pdb=" N THR C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE C 255 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 261 removed outlier: 3.583A pdb=" N ASP C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 286 removed outlier: 4.205A pdb=" N SER C 281 " --> pdb=" O CYS C 277 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 283 " --> pdb=" O TRP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 312 Processing helix chain 'C' and resid 344 through 349 removed outlier: 4.044A pdb=" N ASP C 348 " --> pdb=" O TYR C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.622A pdb=" N LEU C 408 " --> pdb=" O PRO C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'D' and resid 28 through 39 removed outlier: 3.648A pdb=" N ARG D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG D 37 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 66 removed outlier: 4.335A pdb=" N VAL D 64 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 65 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.850A pdb=" N SER D 88 " --> pdb=" O GLY D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 119 removed outlier: 3.859A pdb=" N PHE D 118 " --> pdb=" O PHE D 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY D 119 " --> pdb=" O LEU D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 201 removed outlier: 3.700A pdb=" N ILE D 196 " --> pdb=" O PRO D 192 " (cutoff:3.500A) Proline residue: D 198 - end of helix removed outlier: 3.603A pdb=" N ALA D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 224 removed outlier: 3.540A pdb=" N PHE D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 removed outlier: 4.033A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 271 removed outlier: 3.605A pdb=" N LYS D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET D 254 " --> pdb=" O ASP D 250 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU D 255 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER D 256 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS D 257 " --> pdb=" O LYS D 253 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG D 258 " --> pdb=" O MET D 254 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.549A pdb=" N MET D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 275 through 281' Processing helix chain 'E' and resid 28 through 39 removed outlier: 3.648A pdb=" N ARG E 36 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG E 37 " --> pdb=" O GLU E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 66 removed outlier: 4.334A pdb=" N VAL E 64 " --> pdb=" O SER E 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU E 65 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 removed outlier: 3.851A pdb=" N SER E 88 " --> pdb=" O GLY E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.859A pdb=" N PHE E 118 " --> pdb=" O PHE E 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 201 removed outlier: 3.701A pdb=" N ILE E 196 " --> pdb=" O PRO E 192 " (cutoff:3.500A) Proline residue: E 198 - end of helix removed outlier: 3.603A pdb=" N ALA E 201 " --> pdb=" O ARG E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.540A pdb=" N PHE E 222 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG E 223 " --> pdb=" O ASP E 219 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 246 removed outlier: 4.033A pdb=" N TYR E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 271 removed outlier: 3.605A pdb=" N LYS E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET E 254 " --> pdb=" O ASP E 250 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER E 256 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG E 258 " --> pdb=" O MET E 254 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE E 271 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 281 removed outlier: 4.548A pdb=" N MET E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS E 280 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 281' Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.648A pdb=" N ARG F 36 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG F 37 " --> pdb=" O GLU F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 66 removed outlier: 4.335A pdb=" N VAL F 64 " --> pdb=" O SER F 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU F 65 " --> pdb=" O ASN F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.851A pdb=" N SER F 88 " --> pdb=" O GLY F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 119 removed outlier: 3.859A pdb=" N PHE F 118 " --> pdb=" O PHE F 114 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY F 119 " --> pdb=" O LEU F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 removed outlier: 3.700A pdb=" N ILE F 196 " --> pdb=" O PRO F 192 " (cutoff:3.500A) Proline residue: F 198 - end of helix removed outlier: 3.604A pdb=" N ALA F 201 " --> pdb=" O ARG F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 224 removed outlier: 3.540A pdb=" N PHE F 222 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 223 " --> pdb=" O ASP F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 removed outlier: 4.033A pdb=" N TYR F 245 " --> pdb=" O ALA F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 248 through 271 removed outlier: 3.604A pdb=" N LYS F 253 " --> pdb=" O PRO F 249 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET F 254 " --> pdb=" O ASP F 250 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU F 255 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER F 256 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG F 258 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.549A pdb=" N MET F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS F 280 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN F 281 " --> pdb=" O THR F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 275 through 281' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.506A pdb=" N ILE A 29 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 61 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A 448 " --> pdb=" O TRP A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38 removed outlier: 3.940A pdb=" N GLY A 34 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 58 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 156 through 157 removed outlier: 3.622A pdb=" N TYR A 157 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 229 " --> pdb=" O TYR A 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'A' and resid 194 through 202 removed outlier: 3.652A pdb=" N ILE A 195 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 213 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR A 199 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 211 " --> pdb=" O THR A 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 375 removed outlier: 5.983A pdb=" N ALA A 374 " --> pdb=" O GLY A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 410 through 413 Processing sheet with id=AA9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.506A pdb=" N ILE B 29 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 61 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 448 " --> pdb=" O TRP B 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 38 removed outlier: 3.941A pdb=" N GLY B 34 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 58 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AB3, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.623A pdb=" N TYR B 157 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 229 " --> pdb=" O TYR B 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AB5, first strand: chain 'B' and resid 194 through 202 removed outlier: 3.652A pdb=" N ILE B 195 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE B 213 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 199 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 211 " --> pdb=" O THR B 199 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 374 through 375 removed outlier: 5.984A pdb=" N ALA B 374 " --> pdb=" O GLY B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 410 through 413 Processing sheet with id=AB8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.506A pdb=" N ILE C 29 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE C 61 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG C 448 " --> pdb=" O TRP C 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.941A pdb=" N GLY C 34 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 58 " --> pdb=" O GLY C 34 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.622A pdb=" N TYR C 157 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 229 " --> pdb=" O TYR C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AC4, first strand: chain 'C' and resid 194 through 202 removed outlier: 3.652A pdb=" N ILE C 195 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE C 213 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR C 199 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 211 " --> pdb=" O THR C 199 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 374 through 375 removed outlier: 5.983A pdb=" N ALA C 374 " --> pdb=" O GLY C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 410 through 413 Processing sheet with id=AC7, first strand: chain 'D' and resid 184 through 187 removed outlier: 4.067A pdb=" N ARG D 184 " --> pdb=" O GLY D 176 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 176 " --> pdb=" O ARG D 184 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE D 165 " --> pdb=" O TYR D 155 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR D 155 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 167 " --> pdb=" O GLU D 153 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU D 153 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 169 " --> pdb=" O LYS D 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA D 147 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR D 175 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL D 145 " --> pdb=" O THR D 175 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 233 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG D 54 " --> pdb=" O ILE D 231 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE D 231 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ASP D 56 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY D 229 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 204 through 205 removed outlier: 3.840A pdb=" N SER D 216 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 184 through 187 removed outlier: 4.066A pdb=" N ARG E 184 " --> pdb=" O GLY E 176 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY E 176 " --> pdb=" O ARG E 184 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE E 165 " --> pdb=" O TYR E 155 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR E 155 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE E 167 " --> pdb=" O GLU E 153 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU E 153 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 169 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA E 147 " --> pdb=" O ILE E 173 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR E 175 " --> pdb=" O VAL E 145 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 145 " --> pdb=" O THR E 175 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS E 233 " --> pdb=" O TYR E 52 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG E 54 " --> pdb=" O ILE E 231 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 231 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP E 56 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY E 229 " --> pdb=" O ASP E 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 204 through 205 removed outlier: 3.840A pdb=" N SER E 216 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 184 through 187 removed outlier: 4.066A pdb=" N ARG F 184 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY F 176 " --> pdb=" O ARG F 184 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE F 165 " --> pdb=" O TYR F 155 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR F 155 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE F 167 " --> pdb=" O GLU F 153 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU F 153 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA F 169 " --> pdb=" O LYS F 151 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA F 147 " --> pdb=" O ILE F 173 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N THR F 175 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL F 145 " --> pdb=" O THR F 175 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS F 233 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG F 54 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 231 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N ASP F 56 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLY F 229 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 204 through 205 removed outlier: 3.840A pdb=" N SER F 216 " --> pdb=" O VAL F 205 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 936 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5261 1.33 - 1.45: 2924 1.45 - 1.57: 9401 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 17694 Sorted by residual: bond pdb=" C ARG B 246 " pdb=" N THR B 247 " ideal model delta sigma weight residual 1.331 1.386 -0.056 1.48e-02 4.57e+03 1.41e+01 bond pdb=" CA ASN B 393 " pdb=" C ASN B 393 " ideal model delta sigma weight residual 1.531 1.559 -0.028 7.40e-03 1.83e+04 1.39e+01 bond pdb=" CA ASN A 393 " pdb=" C ASN A 393 " ideal model delta sigma weight residual 1.531 1.558 -0.027 7.40e-03 1.83e+04 1.35e+01 bond pdb=" C ARG C 246 " pdb=" N THR C 247 " ideal model delta sigma weight residual 1.331 1.385 -0.054 1.48e-02 4.57e+03 1.34e+01 bond pdb=" C ARG A 246 " pdb=" N THR A 247 " ideal model delta sigma weight residual 1.331 1.384 -0.054 1.48e-02 4.57e+03 1.32e+01 ... (remaining 17689 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 21240 1.71 - 3.42: 1912 3.42 - 5.13: 583 5.13 - 6.83: 214 6.83 - 8.54: 66 Bond angle restraints: 24015 Sorted by residual: angle pdb=" C VAL E 232 " pdb=" CA VAL E 232 " pdb=" CB VAL E 232 " ideal model delta sigma weight residual 111.80 106.14 5.66 1.18e+00 7.18e-01 2.30e+01 angle pdb=" C PRO F 68 " pdb=" N PRO F 69 " pdb=" CA PRO F 69 " ideal model delta sigma weight residual 119.87 114.89 4.98 1.04e+00 9.25e-01 2.29e+01 angle pdb=" C VAL F 232 " pdb=" CA VAL F 232 " pdb=" CB VAL F 232 " ideal model delta sigma weight residual 111.80 106.17 5.63 1.18e+00 7.18e-01 2.28e+01 angle pdb=" C PRO E 68 " pdb=" N PRO E 69 " pdb=" CA PRO E 69 " ideal model delta sigma weight residual 119.87 114.91 4.96 1.04e+00 9.25e-01 2.28e+01 angle pdb=" C VAL D 232 " pdb=" CA VAL D 232 " pdb=" CB VAL D 232 " ideal model delta sigma weight residual 111.80 106.18 5.62 1.18e+00 7.18e-01 2.27e+01 ... (remaining 24010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9817 17.95 - 35.90: 659 35.90 - 53.85: 96 53.85 - 71.80: 9 71.80 - 89.76: 6 Dihedral angle restraints: 10587 sinusoidal: 4365 harmonic: 6222 Sorted by residual: dihedral pdb=" N THR E 213 " pdb=" C THR E 213 " pdb=" CA THR E 213 " pdb=" CB THR E 213 " ideal model delta harmonic sigma weight residual 123.40 110.24 13.16 0 2.50e+00 1.60e-01 2.77e+01 dihedral pdb=" N THR D 213 " pdb=" C THR D 213 " pdb=" CA THR D 213 " pdb=" CB THR D 213 " ideal model delta harmonic sigma weight residual 123.40 110.26 13.14 0 2.50e+00 1.60e-01 2.76e+01 dihedral pdb=" N THR F 213 " pdb=" C THR F 213 " pdb=" CA THR F 213 " pdb=" CB THR F 213 " ideal model delta harmonic sigma weight residual 123.40 110.26 13.14 0 2.50e+00 1.60e-01 2.76e+01 ... (remaining 10584 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1734 0.098 - 0.195: 534 0.195 - 0.293: 162 0.293 - 0.391: 45 0.391 - 0.488: 18 Chirality restraints: 2493 Sorted by residual: chirality pdb=" CA ARG D 184 " pdb=" N ARG D 184 " pdb=" C ARG D 184 " pdb=" CB ARG D 184 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ARG F 184 " pdb=" N ARG F 184 " pdb=" C ARG F 184 " pdb=" CB ARG F 184 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ARG E 184 " pdb=" N ARG E 184 " pdb=" C ARG E 184 " pdb=" CB ARG E 184 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 ... (remaining 2490 not shown) Planarity restraints: 3159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 106 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C LYS A 106 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS A 106 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE A 107 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 106 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C LYS B 106 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B 106 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE B 107 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 106 " 0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C LYS C 106 " -0.060 2.00e-02 2.50e+03 pdb=" O LYS C 106 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE C 107 " 0.020 2.00e-02 2.50e+03 ... (remaining 3156 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5239 2.82 - 3.34: 14269 3.34 - 3.86: 24752 3.86 - 4.38: 27879 4.38 - 4.90: 47494 Nonbonded interactions: 119633 Sorted by model distance: nonbonded pdb=" OE2 GLU B 308 " pdb=" NH1 ARG B 414 " model vdw 2.298 3.120 nonbonded pdb=" OE2 GLU A 308 " pdb=" NH1 ARG A 414 " model vdw 2.298 3.120 nonbonded pdb=" OE2 GLU C 308 " pdb=" NH1 ARG C 414 " model vdw 2.299 3.120 nonbonded pdb=" O ASP A 315 " pdb=" OD1 ASP A 315 " model vdw 2.308 3.040 nonbonded pdb=" O ASP B 315 " pdb=" OD1 ASP B 315 " model vdw 2.308 3.040 ... (remaining 119628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.610 Find NCS groups from input model: 0.130 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 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 0.056 17694 Z= 0.306 Angle : 1.285 8.542 24015 Z= 0.795 Chirality : 0.113 0.488 2493 Planarity : 0.007 0.065 3159 Dihedral : 11.807 89.755 6591 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Cbeta Deviations : 2.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.16), residues: 2097 helix: -0.90 (0.24), residues: 366 sheet: -0.84 (0.31), residues: 258 loop : -1.97 (0.14), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 215 TYR 0.042 0.002 TYR A 79 PHE 0.031 0.002 PHE A 242 TRP 0.046 0.003 TRP A 117 HIS 0.005 0.001 HIS A 114 Details of bonding type rmsd covalent geometry : bond 0.00451 (17694) covalent geometry : angle 1.28485 (24015) hydrogen bonds : bond 0.29835 ( 354) hydrogen bonds : angle 7.89543 ( 936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8135 (t0) cc_final: 0.7784 (t0) REVERT: A 203 ASP cc_start: 0.7942 (p0) cc_final: 0.7725 (p0) REVERT: A 204 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 308 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7345 (mm-30) REVERT: B 119 LYS cc_start: 0.7384 (tmtt) cc_final: 0.6723 (tptm) REVERT: B 209 ILE cc_start: 0.8168 (tt) cc_final: 0.7921 (pt) REVERT: B 297 ASP cc_start: 0.7529 (t0) cc_final: 0.6983 (m-30) REVERT: C 64 ASP cc_start: 0.7199 (m-30) cc_final: 0.6760 (m-30) REVERT: C 198 ASP cc_start: 0.7315 (m-30) cc_final: 0.6514 (m-30) REVERT: C 297 ASP cc_start: 0.7807 (t0) cc_final: 0.7204 (t0) REVERT: D 115 LEU cc_start: 0.7999 (tp) cc_final: 0.7781 (tp) REVERT: D 142 SER cc_start: 0.8351 (t) cc_final: 0.8112 (p) REVERT: D 170 ILE cc_start: 0.8423 (mt) cc_final: 0.8079 (mm) REVERT: D 209 SER cc_start: 0.8816 (m) cc_final: 0.8442 (t) REVERT: E 76 LYS cc_start: 0.6729 (mmtm) cc_final: 0.6497 (mttm) REVERT: E 80 SER cc_start: 0.8117 (m) cc_final: 0.7676 (p) REVERT: E 95 GLU cc_start: 0.7467 (tt0) cc_final: 0.7224 (pt0) REVERT: E 134 LYS cc_start: 0.7674 (mttt) cc_final: 0.7472 (mtpp) REVERT: E 174 MET cc_start: 0.6576 (ptm) cc_final: 0.6210 (ptm) REVERT: E 251 SER cc_start: 0.7534 (t) cc_final: 0.7099 (m) REVERT: E 254 MET cc_start: 0.7981 (tpt) cc_final: 0.7744 (tpp) REVERT: F 127 ASN cc_start: 0.7390 (t0) cc_final: 0.7070 (t0) REVERT: F 185 ASN cc_start: 0.7944 (m-40) cc_final: 0.7640 (m-40) REVERT: F 195 ASN cc_start: 0.6947 (m-40) cc_final: 0.6708 (m110) REVERT: F 248 THR cc_start: 0.7268 (p) cc_final: 0.7023 (t) REVERT: F 255 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6166 (mt-10) outliers start: 0 outliers final: 0 residues processed: 542 average time/residue: 0.1441 time to fit residues: 112.2729 Evaluate side-chains 346 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 HIS A 318 ASN B 244 ASN B 436 ASN C 40 ASN C 97 ASN ** C 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 160 ASN E 225 ASN F 35 ASN F 40 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 212 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142178 restraints weight = 22806.112| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.89 r_work: 0.3652 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17694 Z= 0.271 Angle : 0.717 7.751 24015 Z= 0.387 Chirality : 0.051 0.194 2493 Planarity : 0.007 0.064 3159 Dihedral : 5.256 19.974 2376 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 3.00 % Allowed : 11.36 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.16), residues: 2097 helix: -0.54 (0.23), residues: 393 sheet: -1.03 (0.33), residues: 243 loop : -1.82 (0.15), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 240 TYR 0.026 0.003 TYR F 149 PHE 0.029 0.003 PHE E 156 TRP 0.026 0.002 TRP B 62 HIS 0.006 0.002 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00622 (17694) covalent geometry : angle 0.71733 (24015) hydrogen bonds : bond 0.06996 ( 354) hydrogen bonds : angle 5.34717 ( 936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 393 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7267 (m-30) cc_final: 0.6824 (m-30) REVERT: A 136 ASN cc_start: 0.6822 (t0) cc_final: 0.6411 (m110) REVERT: A 147 ASP cc_start: 0.6624 (p0) cc_final: 0.6265 (p0) REVERT: A 163 ASP cc_start: 0.8248 (t0) cc_final: 0.7809 (t0) REVERT: A 235 GLU cc_start: 0.7448 (mt-10) cc_final: 0.6981 (tp30) REVERT: A 308 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7058 (tp30) REVERT: B 99 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5227 (mp0) REVERT: B 119 LYS cc_start: 0.7525 (tmtt) cc_final: 0.7003 (tppp) REVERT: B 180 ASN cc_start: 0.8193 (t0) cc_final: 0.7925 (t0) REVERT: B 236 THR cc_start: 0.9014 (p) cc_final: 0.8805 (t) REVERT: B 344 ASP cc_start: 0.7658 (m-30) cc_final: 0.7385 (m-30) REVERT: B 437 VAL cc_start: 0.9178 (p) cc_final: 0.8974 (m) REVERT: C 42 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 99 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6682 (pm20) REVERT: C 100 TYR cc_start: 0.6848 (m-80) cc_final: 0.6304 (m-80) REVERT: C 182 ASN cc_start: 0.7605 (t0) cc_final: 0.7299 (t0) REVERT: C 297 ASP cc_start: 0.7553 (t0) cc_final: 0.7220 (t0) REVERT: C 363 ASP cc_start: 0.6202 (t0) cc_final: 0.5896 (t0) REVERT: D 116 ASP cc_start: 0.5847 (t0) cc_final: 0.4589 (m-30) REVERT: D 170 ILE cc_start: 0.8591 (mt) cc_final: 0.8237 (mm) REVERT: D 174 MET cc_start: 0.7666 (ptm) cc_final: 0.7161 (tmm) REVERT: D 209 SER cc_start: 0.9021 (m) cc_final: 0.8674 (t) REVERT: D 252 MET cc_start: 0.7320 (ttm) cc_final: 0.6771 (tpt) REVERT: E 76 LYS cc_start: 0.6856 (mmtm) cc_final: 0.6527 (mtpp) REVERT: E 207 LEU cc_start: 0.8650 (mt) cc_final: 0.8369 (mt) REVERT: E 254 MET cc_start: 0.7982 (tpt) cc_final: 0.7678 (tpp) REVERT: F 127 ASN cc_start: 0.7485 (t0) cc_final: 0.7118 (t0) REVERT: F 168 GLN cc_start: 0.7909 (mt0) cc_final: 0.7573 (mt0) REVERT: F 230 ASP cc_start: 0.7121 (t0) cc_final: 0.6585 (p0) outliers start: 56 outliers final: 36 residues processed: 427 average time/residue: 0.1299 time to fit residues: 83.2878 Evaluate side-chains 378 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 274 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 419 LYS Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 218 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 231 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 11 optimal weight: 0.0070 chunk 107 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 193 optimal weight: 0.0570 chunk 24 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN C 40 ASN C 240 ASN C 337 ASN E 168 GLN E 225 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.167860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.142255 restraints weight = 22636.028| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.94 r_work: 0.3641 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17694 Z= 0.102 Angle : 0.518 6.279 24015 Z= 0.272 Chirality : 0.042 0.160 2493 Planarity : 0.005 0.048 3159 Dihedral : 4.598 18.349 2376 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.04 % Allowed : 14.09 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.17), residues: 2097 helix: 0.28 (0.25), residues: 408 sheet: -0.99 (0.33), residues: 252 loop : -1.43 (0.15), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 75 TYR 0.019 0.001 TYR A 398 PHE 0.027 0.001 PHE F 100 TRP 0.018 0.001 TRP A 418 HIS 0.003 0.001 HIS B 432 Details of bonding type rmsd covalent geometry : bond 0.00226 (17694) covalent geometry : angle 0.51818 (24015) hydrogen bonds : bond 0.04547 ( 354) hydrogen bonds : angle 4.65078 ( 936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 346 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7152 (m-30) cc_final: 0.6762 (m-30) REVERT: A 106 LYS cc_start: 0.5459 (pttt) cc_final: 0.4519 (mmtt) REVERT: A 163 ASP cc_start: 0.8030 (t0) cc_final: 0.7640 (t0) REVERT: A 235 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 308 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7068 (tp30) REVERT: A 439 ARG cc_start: 0.8077 (ttm-80) cc_final: 0.7769 (ttm110) REVERT: B 53 SER cc_start: 0.7862 (p) cc_final: 0.7572 (m) REVERT: B 119 LYS cc_start: 0.7454 (tmtt) cc_final: 0.6920 (tptm) REVERT: B 328 ARG cc_start: 0.9014 (mtp85) cc_final: 0.8517 (ttm-80) REVERT: C 42 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 154 GLN cc_start: 0.8353 (tp40) cc_final: 0.8106 (tp-100) REVERT: C 297 ASP cc_start: 0.7281 (t0) cc_final: 0.6985 (t0) REVERT: C 298 ASP cc_start: 0.8151 (m-30) cc_final: 0.7834 (m-30) REVERT: C 363 ASP cc_start: 0.5999 (t0) cc_final: 0.5746 (t0) REVERT: D 98 ASP cc_start: 0.6577 (t0) cc_final: 0.6073 (m-30) REVERT: D 155 TYR cc_start: 0.8405 (p90) cc_final: 0.7943 (p90) REVERT: D 164 ASP cc_start: 0.7032 (t0) cc_final: 0.6752 (t0) REVERT: D 174 MET cc_start: 0.7484 (ptm) cc_final: 0.7048 (tmm) REVERT: D 209 SER cc_start: 0.8965 (m) cc_final: 0.8633 (t) REVERT: D 252 MET cc_start: 0.7136 (ttm) cc_final: 0.6612 (tpt) REVERT: D 275 ASP cc_start: 0.7365 (m-30) cc_final: 0.5364 (t70) REVERT: D 279 MET cc_start: 0.6418 (mmm) cc_final: 0.6195 (mmm) REVERT: E 116 ASP cc_start: 0.8141 (t0) cc_final: 0.6178 (m-30) REVERT: E 207 LEU cc_start: 0.8663 (mt) cc_final: 0.8416 (mt) REVERT: E 275 ASP cc_start: 0.8387 (m-30) cc_final: 0.6544 (t0) REVERT: F 115 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6642 (mp) REVERT: F 133 PHE cc_start: 0.7800 (m-80) cc_final: 0.7554 (m-10) REVERT: F 254 MET cc_start: 0.6285 (tpt) cc_final: 0.5257 (tmm) outliers start: 38 outliers final: 21 residues processed: 369 average time/residue: 0.1263 time to fit residues: 70.6730 Evaluate side-chains 340 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 318 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 260 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 36 optimal weight: 10.0000 chunk 147 optimal weight: 5.9990 chunk 177 optimal weight: 0.0670 chunk 108 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 435 GLN C 40 ASN E 62 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 168 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134569 restraints weight = 23484.119| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.92 r_work: 0.3563 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 17694 Z= 0.228 Angle : 0.645 6.062 24015 Z= 0.347 Chirality : 0.048 0.168 2493 Planarity : 0.006 0.052 3159 Dihedral : 5.100 17.309 2376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.27 % Allowed : 14.95 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.17), residues: 2097 helix: 0.17 (0.25), residues: 393 sheet: -1.41 (0.34), residues: 240 loop : -1.58 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 214 TYR 0.028 0.002 TYR F 149 PHE 0.027 0.003 PHE E 156 TRP 0.019 0.002 TRP B 62 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00535 (17694) covalent geometry : angle 0.64489 (24015) hydrogen bonds : bond 0.06222 ( 354) hydrogen bonds : angle 4.89834 ( 936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 0.489 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7218 (m-30) cc_final: 0.6468 (t70) REVERT: A 136 ASN cc_start: 0.7160 (t0) cc_final: 0.6727 (m-40) REVERT: A 163 ASP cc_start: 0.8214 (t0) cc_final: 0.7756 (t0) REVERT: A 308 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7193 (mm-30) REVERT: B 53 SER cc_start: 0.7918 (p) cc_final: 0.7578 (m) REVERT: B 99 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5766 (mp0) REVERT: B 119 LYS cc_start: 0.7528 (tmtt) cc_final: 0.7010 (tppp) REVERT: B 344 ASP cc_start: 0.7597 (m-30) cc_final: 0.7376 (m-30) REVERT: B 388 GLN cc_start: 0.8309 (mt0) cc_final: 0.8043 (tt0) REVERT: B 437 VAL cc_start: 0.9025 (p) cc_final: 0.8771 (m) REVERT: C 99 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: C 297 ASP cc_start: 0.7725 (t0) cc_final: 0.7503 (t0) REVERT: C 407 ILE cc_start: 0.8849 (tp) cc_final: 0.8557 (tt) REVERT: C 429 THR cc_start: 0.8572 (m) cc_final: 0.8333 (p) REVERT: D 33 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8123 (tm-30) REVERT: D 165 ILE cc_start: 0.8898 (mt) cc_final: 0.8616 (mt) REVERT: D 174 MET cc_start: 0.7610 (ptm) cc_final: 0.7284 (tmm) REVERT: D 206 MET cc_start: 0.7932 (ptp) cc_final: 0.7408 (ptp) REVERT: D 209 SER cc_start: 0.9052 (m) cc_final: 0.8748 (t) REVERT: D 275 ASP cc_start: 0.7484 (m-30) cc_final: 0.7068 (m-30) REVERT: E 116 ASP cc_start: 0.8228 (t0) cc_final: 0.6224 (m-30) REVERT: E 255 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: E 275 ASP cc_start: 0.8247 (m-30) cc_final: 0.6266 (t0) REVERT: F 115 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7029 (mp) REVERT: F 230 ASP cc_start: 0.7219 (t0) cc_final: 0.6651 (p0) REVERT: F 252 MET cc_start: 0.6035 (tmm) cc_final: 0.5674 (tmm) REVERT: F 279 MET cc_start: 0.4876 (OUTLIER) cc_final: 0.4562 (ptp) outliers start: 61 outliers final: 44 residues processed: 375 average time/residue: 0.1252 time to fit residues: 71.9514 Evaluate side-chains 365 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 316 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 432 HIS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 215 ASN Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 279 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 138 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 175 optimal weight: 0.1980 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.158621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134608 restraints weight = 23251.561| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.85 r_work: 0.3567 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17694 Z= 0.213 Angle : 0.605 6.474 24015 Z= 0.323 Chirality : 0.046 0.165 2493 Planarity : 0.005 0.053 3159 Dihedral : 5.101 18.861 2376 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.75 % Allowed : 16.18 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.17), residues: 2097 helix: 0.22 (0.26), residues: 393 sheet: -1.15 (0.36), residues: 210 loop : -1.74 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 439 TYR 0.020 0.002 TYR B 221 PHE 0.036 0.002 PHE C 381 TRP 0.017 0.002 TRP B 62 HIS 0.006 0.001 HIS C 432 Details of bonding type rmsd covalent geometry : bond 0.00494 (17694) covalent geometry : angle 0.60547 (24015) hydrogen bonds : bond 0.05487 ( 354) hydrogen bonds : angle 4.80331 ( 936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 340 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7181 (m-30) cc_final: 0.6405 (t70) REVERT: A 163 ASP cc_start: 0.8064 (t0) cc_final: 0.7615 (t0) REVERT: A 235 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7314 (mm-30) REVERT: A 248 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 270 TRP cc_start: 0.8401 (OUTLIER) cc_final: 0.7555 (t60) REVERT: A 308 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 439 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.7852 (ttm-80) REVERT: B 53 SER cc_start: 0.7952 (p) cc_final: 0.7621 (m) REVERT: B 99 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: B 119 LYS cc_start: 0.7533 (tmtt) cc_final: 0.7020 (tppp) REVERT: B 180 ASN cc_start: 0.8327 (t0) cc_final: 0.7985 (t0) REVERT: B 331 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7001 (ptm160) REVERT: B 344 ASP cc_start: 0.7780 (m-30) cc_final: 0.7508 (m-30) REVERT: B 388 GLN cc_start: 0.8344 (mt0) cc_final: 0.8104 (tt0) REVERT: C 65 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8212 (mtp85) REVERT: C 99 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: C 308 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 407 ILE cc_start: 0.8863 (tp) cc_final: 0.8534 (tt) REVERT: C 429 THR cc_start: 0.8594 (m) cc_final: 0.8378 (p) REVERT: D 33 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8228 (tm-30) REVERT: D 58 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.7000 (tpt) REVERT: D 174 MET cc_start: 0.7691 (ptm) cc_final: 0.7395 (tmm) REVERT: D 179 GLU cc_start: 0.4397 (OUTLIER) cc_final: 0.3976 (mp0) REVERT: D 209 SER cc_start: 0.9026 (m) cc_final: 0.8743 (t) REVERT: D 275 ASP cc_start: 0.7534 (m-30) cc_final: 0.6996 (m-30) REVERT: E 101 GLU cc_start: 0.7910 (pm20) cc_final: 0.7385 (pm20) REVERT: E 116 ASP cc_start: 0.8263 (t0) cc_final: 0.6328 (m-30) REVERT: E 255 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: E 275 ASP cc_start: 0.8284 (m-30) cc_final: 0.6255 (t0) REVERT: F 115 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7013 (mp) outliers start: 70 outliers final: 46 residues processed: 386 average time/residue: 0.1315 time to fit residues: 77.8359 Evaluate side-chains 374 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 225 ASN Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 256 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 81 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 154 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 154 GLN C 388 GLN D 177 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN F 281 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135722 restraints weight = 23144.092| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.87 r_work: 0.3586 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17694 Z= 0.152 Angle : 0.559 6.833 24015 Z= 0.295 Chirality : 0.044 0.160 2493 Planarity : 0.005 0.053 3159 Dihedral : 4.907 17.037 2376 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.27 % Allowed : 17.79 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.17), residues: 2097 helix: 0.54 (0.26), residues: 390 sheet: -1.14 (0.35), residues: 210 loop : -1.72 (0.15), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 184 TYR 0.017 0.001 TYR D 245 PHE 0.023 0.002 PHE F 100 TRP 0.020 0.001 TRP A 418 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00353 (17694) covalent geometry : angle 0.55874 (24015) hydrogen bonds : bond 0.04951 ( 354) hydrogen bonds : angle 4.63238 ( 936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 319 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7189 (m-30) cc_final: 0.6374 (t70) REVERT: A 163 ASP cc_start: 0.8000 (t0) cc_final: 0.7551 (t0) REVERT: A 235 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7310 (mm-30) REVERT: A 248 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7852 (tm-30) REVERT: A 270 TRP cc_start: 0.8375 (OUTLIER) cc_final: 0.7535 (t60) REVERT: A 297 ASP cc_start: 0.7397 (t0) cc_final: 0.6933 (m-30) REVERT: A 308 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7321 (mm-30) REVERT: A 395 GLU cc_start: 0.7354 (tp30) cc_final: 0.7145 (tp30) REVERT: A 439 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7799 (ttm-80) REVERT: B 53 SER cc_start: 0.7901 (p) cc_final: 0.7584 (m) REVERT: B 99 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.5766 (mp0) REVERT: B 119 LYS cc_start: 0.7494 (tmtt) cc_final: 0.6958 (tppp) REVERT: B 331 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7121 (ptm160) REVERT: B 344 ASP cc_start: 0.7577 (m-30) cc_final: 0.7275 (m-30) REVERT: B 388 GLN cc_start: 0.8296 (mt0) cc_final: 0.8085 (tt0) REVERT: C 64 ASP cc_start: 0.7514 (t0) cc_final: 0.6953 (p0) REVERT: C 65 ARG cc_start: 0.8400 (mtp85) cc_final: 0.8172 (mtp85) REVERT: C 99 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.6982 (pm20) REVERT: C 298 ASP cc_start: 0.8100 (m-30) cc_final: 0.7830 (m-30) REVERT: C 429 THR cc_start: 0.8558 (m) cc_final: 0.8341 (p) REVERT: D 58 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.7042 (tpt) REVERT: D 174 MET cc_start: 0.7672 (ptm) cc_final: 0.7375 (tmm) REVERT: D 209 SER cc_start: 0.9028 (m) cc_final: 0.8737 (t) REVERT: E 101 GLU cc_start: 0.7878 (pm20) cc_final: 0.7442 (pm20) REVERT: E 116 ASP cc_start: 0.8236 (t0) cc_final: 0.6337 (m-30) REVERT: E 255 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: E 275 ASP cc_start: 0.8281 (m-30) cc_final: 0.6224 (t0) REVERT: F 92 ASP cc_start: 0.7888 (m-30) cc_final: 0.7673 (t0) REVERT: F 115 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6992 (mp) REVERT: F 254 MET cc_start: 0.6182 (tpt) cc_final: 0.5080 (tmm) outliers start: 61 outliers final: 44 residues processed: 358 average time/residue: 0.1268 time to fit residues: 69.5388 Evaluate side-chains 359 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 308 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 140 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 47 optimal weight: 0.0670 chunk 198 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 154 GLN C 388 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.159985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135800 restraints weight = 23252.553| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.88 r_work: 0.3586 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17694 Z= 0.157 Angle : 0.559 12.752 24015 Z= 0.293 Chirality : 0.044 0.157 2493 Planarity : 0.005 0.053 3159 Dihedral : 4.812 17.434 2376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.13 % Allowed : 16.88 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.17), residues: 2097 helix: 0.62 (0.27), residues: 387 sheet: -1.15 (0.35), residues: 210 loop : -1.73 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.015 0.001 TYR D 245 PHE 0.020 0.002 PHE F 100 TRP 0.019 0.001 TRP A 418 HIS 0.002 0.001 HIS B 114 Details of bonding type rmsd covalent geometry : bond 0.00366 (17694) covalent geometry : angle 0.55875 (24015) hydrogen bonds : bond 0.04820 ( 354) hydrogen bonds : angle 4.54530 ( 936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 319 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7148 (m-30) cc_final: 0.6350 (t70) REVERT: A 103 THR cc_start: 0.7114 (p) cc_final: 0.6327 (t) REVERT: A 163 ASP cc_start: 0.8069 (t0) cc_final: 0.7577 (t0) REVERT: A 235 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7346 (mm-30) REVERT: A 248 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7802 (tm-30) REVERT: A 270 TRP cc_start: 0.8370 (OUTLIER) cc_final: 0.7507 (t60) REVERT: A 292 GLU cc_start: 0.6422 (mp0) cc_final: 0.5713 (tp30) REVERT: A 296 MET cc_start: 0.6708 (mmt) cc_final: 0.5770 (mtt) REVERT: A 297 ASP cc_start: 0.7370 (t0) cc_final: 0.6865 (m-30) REVERT: A 308 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7323 (mm-30) REVERT: A 331 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.6033 (ptm-80) REVERT: A 395 GLU cc_start: 0.7384 (tp30) cc_final: 0.7111 (tp30) REVERT: B 53 SER cc_start: 0.7885 (p) cc_final: 0.7559 (m) REVERT: B 99 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.5558 (mp0) REVERT: B 119 LYS cc_start: 0.7490 (tmtt) cc_final: 0.6947 (tppp) REVERT: B 296 MET cc_start: 0.5523 (tpp) cc_final: 0.4571 (mmm) REVERT: B 331 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7007 (ptm160) REVERT: B 344 ASP cc_start: 0.7583 (m-30) cc_final: 0.7269 (m-30) REVERT: B 388 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: C 99 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: C 429 THR cc_start: 0.8595 (m) cc_final: 0.8374 (p) REVERT: D 58 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6895 (tpt) REVERT: D 70 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7727 (mpp80) REVERT: D 209 SER cc_start: 0.8980 (m) cc_final: 0.8695 (t) REVERT: D 228 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8422 (mtmm) REVERT: E 101 GLU cc_start: 0.7857 (pm20) cc_final: 0.7465 (pm20) REVERT: E 116 ASP cc_start: 0.8229 (t0) cc_final: 0.6338 (m-30) REVERT: E 255 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7143 (mm-30) REVERT: E 275 ASP cc_start: 0.8259 (m-30) cc_final: 0.6221 (t0) REVERT: F 87 ASN cc_start: 0.8277 (t0) cc_final: 0.8073 (t0) REVERT: F 115 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6986 (mp) REVERT: F 254 MET cc_start: 0.5955 (tpt) cc_final: 0.4804 (tmm) outliers start: 77 outliers final: 54 residues processed: 366 average time/residue: 0.1214 time to fit residues: 68.5782 Evaluate side-chains 371 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 6 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 54 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 154 GLN D 168 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137185 restraints weight = 23034.124| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.90 r_work: 0.3597 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17694 Z= 0.124 Angle : 0.526 9.781 24015 Z= 0.275 Chirality : 0.043 0.153 2493 Planarity : 0.004 0.052 3159 Dihedral : 4.589 16.830 2376 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.22 % Allowed : 18.22 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.17), residues: 2097 helix: 0.61 (0.26), residues: 405 sheet: -1.08 (0.35), residues: 210 loop : -1.67 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 184 TYR 0.020 0.001 TYR D 199 PHE 0.024 0.001 PHE F 266 TRP 0.026 0.001 TRP A 418 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00290 (17694) covalent geometry : angle 0.52612 (24015) hydrogen bonds : bond 0.04224 ( 354) hydrogen bonds : angle 4.39037 ( 936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7126 (m-30) cc_final: 0.6341 (t70) REVERT: A 103 THR cc_start: 0.7136 (p) cc_final: 0.6368 (t) REVERT: A 163 ASP cc_start: 0.8098 (t0) cc_final: 0.7593 (t0) REVERT: A 235 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7351 (mm-30) REVERT: A 248 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7727 (tm-30) REVERT: A 270 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.7444 (t60) REVERT: A 292 GLU cc_start: 0.6370 (mp0) cc_final: 0.5625 (tp30) REVERT: A 296 MET cc_start: 0.6713 (mmt) cc_final: 0.6064 (mtt) REVERT: A 297 ASP cc_start: 0.7581 (t0) cc_final: 0.6994 (m-30) REVERT: A 331 ARG cc_start: 0.6395 (OUTLIER) cc_final: 0.6127 (ptm-80) REVERT: A 395 GLU cc_start: 0.7398 (tp30) cc_final: 0.7178 (tp30) REVERT: A 397 GLU cc_start: 0.8086 (tp30) cc_final: 0.7857 (tp30) REVERT: B 53 SER cc_start: 0.7936 (p) cc_final: 0.7616 (m) REVERT: B 99 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.5538 (mp0) REVERT: B 119 LYS cc_start: 0.7482 (tmtt) cc_final: 0.6938 (tppp) REVERT: B 296 MET cc_start: 0.5585 (tpp) cc_final: 0.4668 (mmm) REVERT: B 331 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7073 (ptm160) REVERT: B 344 ASP cc_start: 0.7525 (m-30) cc_final: 0.7220 (m-30) REVERT: B 388 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: D 58 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6885 (tpt) REVERT: D 70 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7743 (mpp80) REVERT: D 209 SER cc_start: 0.8994 (m) cc_final: 0.8689 (t) REVERT: D 252 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (tpp) REVERT: D 275 ASP cc_start: 0.7256 (m-30) cc_final: 0.6772 (m-30) REVERT: E 116 ASP cc_start: 0.8208 (t0) cc_final: 0.6359 (m-30) REVERT: E 275 ASP cc_start: 0.8234 (m-30) cc_final: 0.6184 (t0) REVERT: F 115 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6958 (mp) REVERT: F 230 ASP cc_start: 0.7424 (t0) cc_final: 0.6533 (p0) REVERT: F 254 MET cc_start: 0.5783 (tpt) cc_final: 0.4740 (tmm) outliers start: 60 outliers final: 42 residues processed: 344 average time/residue: 0.1186 time to fit residues: 62.5803 Evaluate side-chains 351 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 300 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 146 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 206 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 188 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 68 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 overall best weight: 2.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 154 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.160836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136558 restraints weight = 23161.449| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.87 r_work: 0.3591 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17694 Z= 0.140 Angle : 0.540 10.430 24015 Z= 0.283 Chirality : 0.043 0.152 2493 Planarity : 0.005 0.052 3159 Dihedral : 4.597 17.259 2376 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.38 % Allowed : 18.27 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.17), residues: 2097 helix: 0.44 (0.26), residues: 423 sheet: -1.11 (0.33), residues: 246 loop : -1.65 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 184 TYR 0.019 0.001 TYR D 155 PHE 0.023 0.002 PHE F 266 TRP 0.026 0.001 TRP A 418 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00328 (17694) covalent geometry : angle 0.54028 (24015) hydrogen bonds : bond 0.04459 ( 354) hydrogen bonds : angle 4.40010 ( 936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 303 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7033 (m-30) cc_final: 0.6285 (t70) REVERT: A 65 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8342 (ttm-80) REVERT: A 103 THR cc_start: 0.7132 (p) cc_final: 0.6360 (t) REVERT: A 163 ASP cc_start: 0.8058 (t0) cc_final: 0.7572 (t0) REVERT: A 235 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7423 (mm-30) REVERT: A 248 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 270 TRP cc_start: 0.8283 (OUTLIER) cc_final: 0.7411 (t60) REVERT: A 292 GLU cc_start: 0.6351 (mp0) cc_final: 0.5660 (tp30) REVERT: A 296 MET cc_start: 0.6861 (mmt) cc_final: 0.6333 (mtt) REVERT: A 297 ASP cc_start: 0.7546 (t0) cc_final: 0.6945 (m-30) REVERT: A 331 ARG cc_start: 0.6319 (OUTLIER) cc_final: 0.6007 (ptm-80) REVERT: A 337 ASN cc_start: 0.6947 (t0) cc_final: 0.6725 (t0) REVERT: B 53 SER cc_start: 0.7927 (p) cc_final: 0.7609 (m) REVERT: B 99 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: B 119 LYS cc_start: 0.7482 (tmtt) cc_final: 0.6917 (tptm) REVERT: B 296 MET cc_start: 0.5534 (tpp) cc_final: 0.4618 (mmm) REVERT: B 328 ARG cc_start: 0.9006 (mtp85) cc_final: 0.8734 (mtt90) REVERT: B 331 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7005 (ptm160) REVERT: B 344 ASP cc_start: 0.7512 (m-30) cc_final: 0.7223 (m-30) REVERT: B 388 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: D 58 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6764 (tpt) REVERT: D 70 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7734 (mpp80) REVERT: D 209 SER cc_start: 0.8970 (m) cc_final: 0.8682 (t) REVERT: D 252 MET cc_start: 0.7746 (OUTLIER) cc_final: 0.7461 (tpp) REVERT: E 116 ASP cc_start: 0.8217 (t0) cc_final: 0.6368 (m-30) REVERT: E 255 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7115 (mm-30) REVERT: E 275 ASP cc_start: 0.8253 (m-30) cc_final: 0.6195 (t0) REVERT: F 115 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6944 (mp) REVERT: F 230 ASP cc_start: 0.7528 (t0) cc_final: 0.6684 (p0) REVERT: F 254 MET cc_start: 0.5766 (tpt) cc_final: 0.4869 (tmm) outliers start: 63 outliers final: 49 residues processed: 341 average time/residue: 0.1244 time to fit residues: 65.0582 Evaluate side-chains 358 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 299 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 270 TRP Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 156 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 180 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN C 40 ASN C 154 GLN E 168 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.160887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.136745 restraints weight = 22946.932| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.86 r_work: 0.3590 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17694 Z= 0.140 Angle : 0.542 10.556 24015 Z= 0.283 Chirality : 0.043 0.155 2493 Planarity : 0.004 0.052 3159 Dihedral : 4.578 18.616 2376 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.27 % Allowed : 18.54 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.17), residues: 2097 helix: 0.45 (0.26), residues: 426 sheet: -1.10 (0.33), residues: 246 loop : -1.65 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 184 TYR 0.016 0.001 TYR D 199 PHE 0.024 0.002 PHE F 266 TRP 0.027 0.001 TRP A 418 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00329 (17694) covalent geometry : angle 0.54175 (24015) hydrogen bonds : bond 0.04362 ( 354) hydrogen bonds : angle 4.38052 ( 936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4194 Ramachandran restraints generated. 2097 Oldfield, 0 Emsley, 2097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 299 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 64 ASP cc_start: 0.7065 (m-30) cc_final: 0.6276 (t70) REVERT: A 65 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8320 (ttm-80) REVERT: A 103 THR cc_start: 0.7106 (p) cc_final: 0.6391 (t) REVERT: A 163 ASP cc_start: 0.8090 (t0) cc_final: 0.7572 (t0) REVERT: A 235 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7386 (mm-30) REVERT: A 248 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 292 GLU cc_start: 0.6345 (mp0) cc_final: 0.5623 (tp30) REVERT: A 296 MET cc_start: 0.6810 (mmt) cc_final: 0.6284 (mtt) REVERT: A 297 ASP cc_start: 0.7591 (t0) cc_final: 0.6907 (m-30) REVERT: A 308 GLU cc_start: 0.7757 (mm-30) cc_final: 0.6981 (tp30) REVERT: A 331 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.6101 (ptm-80) REVERT: A 337 ASN cc_start: 0.6977 (t0) cc_final: 0.6773 (t0) REVERT: A 389 MET cc_start: 0.7799 (ptp) cc_final: 0.7500 (ptp) REVERT: B 53 SER cc_start: 0.7930 (p) cc_final: 0.7598 (m) REVERT: B 99 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5572 (mp0) REVERT: B 119 LYS cc_start: 0.7479 (tmtt) cc_final: 0.6897 (tptm) REVERT: B 297 ASP cc_start: 0.7580 (t0) cc_final: 0.7276 (m-30) REVERT: B 328 ARG cc_start: 0.9003 (mtp85) cc_final: 0.8714 (mtt90) REVERT: B 331 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7108 (ptm160) REVERT: B 344 ASP cc_start: 0.7518 (m-30) cc_final: 0.7234 (m-30) REVERT: B 388 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: D 70 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7717 (mpp80) REVERT: D 206 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7215 (ptp) REVERT: D 209 SER cc_start: 0.8952 (m) cc_final: 0.8650 (t) REVERT: D 252 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7474 (tpp) REVERT: E 116 ASP cc_start: 0.8189 (t0) cc_final: 0.6351 (m-30) REVERT: E 255 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7117 (mm-30) REVERT: E 275 ASP cc_start: 0.8226 (m-30) cc_final: 0.6173 (t0) REVERT: F 115 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6961 (mp) REVERT: F 230 ASP cc_start: 0.7562 (t0) cc_final: 0.6728 (p0) REVERT: F 254 MET cc_start: 0.5804 (tpt) cc_final: 0.4884 (tmm) outliers start: 61 outliers final: 48 residues processed: 331 average time/residue: 0.1244 time to fit residues: 63.5703 Evaluate side-chains 356 residues out of total 1866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 299 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 331 ARG Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 253 MET Chi-restraints excluded: chain B residue 313 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 388 GLN Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 206 MET Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 145 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 216 SER Chi-restraints excluded: chain E residue 255 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 58 MET Chi-restraints excluded: chain F residue 115 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 216 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain F residue 256 SER Chi-restraints excluded: chain F residue 260 ASP Chi-restraints excluded: chain F residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 107 optimal weight: 0.4980 chunk 113 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 ASN C 154 GLN E 168 GLN E 185 ASN ** E 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.161485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137207 restraints weight = 23028.108| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.88 r_work: 0.3600 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17694 Z= 0.123 Angle : 0.533 10.953 24015 Z= 0.276 Chirality : 0.043 0.153 2493 Planarity : 0.004 0.052 3159 Dihedral : 4.486 18.770 2376 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.32 % Allowed : 18.60 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.17), residues: 2097 helix: 0.53 (0.26), residues: 426 sheet: -1.09 (0.33), residues: 246 loop : -1.62 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 184 TYR 0.014 0.001 TYR D 199 PHE 0.032 0.001 PHE F 100 TRP 0.026 0.001 TRP A 418 HIS 0.002 0.001 HIS B 257 Details of bonding type rmsd covalent geometry : bond 0.00292 (17694) covalent geometry : angle 0.53266 (24015) hydrogen bonds : bond 0.04109 ( 354) hydrogen bonds : angle 4.30141 ( 936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3603.83 seconds wall clock time: 62 minutes 23.77 seconds (3743.77 seconds total)