Starting phenix.real_space_refine on Sun Aug 24 14:44:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xl6_33273/08_2025/7xl6_33273.map" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.075 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 112 5.16 5 C 13587 2.51 5 N 3430 2.21 5 O 3654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20783 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "B" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "D" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "E" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Chain: "G" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2969 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} Chain breaks: 2 Time building chain proxies: 5.18, per 1000 atoms: 0.25 Number of scatterers: 20783 At special positions: 0 Unit cell: (124.5, 122.84, 125.33, 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 112 16.00 O 3654 8.00 N 3430 7.00 C 13587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 14 sheets defined 61.6% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'F' and resid 2 through 11 removed outlier: 3.817A pdb=" N GLU F 9 " --> pdb=" O HIS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 54 removed outlier: 4.137A pdb=" N SER F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 104 through 121 removed outlier: 4.196A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Proline residue: F 111 - end of helix Processing helix chain 'F' and resid 122 through 132 Processing helix chain 'F' and resid 132 through 148 Processing helix chain 'F' and resid 159 through 168 removed outlier: 3.598A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 174 Processing helix chain 'F' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA F 181 " --> pdb=" O GLU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.865A pdb=" N ALA F 197 " --> pdb=" O GLU F 193 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 230 removed outlier: 3.564A pdb=" N LEU F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 296 removed outlier: 4.163A pdb=" N VAL F 277 " --> pdb=" O SER F 273 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR F 280 " --> pdb=" O SER F 276 " (cutoff:3.500A) Proline residue: F 285 - end of helix removed outlier: 3.748A pdb=" N ILE F 288 " --> pdb=" O VAL F 284 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS F 295 " --> pdb=" O LEU F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 308 removed outlier: 3.754A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU F 308 " --> pdb=" O VAL F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 317 removed outlier: 4.197A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.587A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.056A pdb=" N VAL F 365 " --> pdb=" O ASN F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 371 through 375 Processing helix chain 'A' and resid 3 through 11 removed outlier: 3.814A pdb=" N GLU A 9 " --> pdb=" O HIS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 54 removed outlier: 4.124A pdb=" N SER A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 104 through 121 removed outlier: 4.200A pdb=" N LYS A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 132 through 148 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.921A pdb=" N LEU A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 167 " --> pdb=" O LYS A 163 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 177 through 183 removed outlier: 3.939A pdb=" N ALA A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 201 removed outlier: 3.781A pdb=" N ALA A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 230 removed outlier: 3.556A pdb=" N LEU A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 296 removed outlier: 4.159A pdb=" N VAL A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N TYR A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) Proline residue: A 285 - end of helix removed outlier: 3.758A pdb=" N ILE A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 308 removed outlier: 3.757A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 308 " --> pdb=" O VAL A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 removed outlier: 4.171A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.601A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 366 removed outlier: 4.058A pdb=" N VAL A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 371 through 375 Processing helix chain 'B' and resid 3 through 11 removed outlier: 3.809A pdb=" N GLU B 9 " --> pdb=" O HIS B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 54 removed outlier: 4.129A pdb=" N SER B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 104 through 121 removed outlier: 4.197A pdb=" N LYS B 108 " --> pdb=" O LEU B 104 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 122 through 132 Processing helix chain 'B' and resid 132 through 148 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.924A pdb=" N LEU B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 168 " --> pdb=" O ILE B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 201 removed outlier: 3.767A pdb=" N ALA B 197 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 230 removed outlier: 3.567A pdb=" N LEU B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.096A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) Proline residue: B 285 - end of helix removed outlier: 3.745A pdb=" N ILE B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.752A pdb=" N MET B 307 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 308 " --> pdb=" O VAL B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 317 removed outlier: 4.176A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.594A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 removed outlier: 4.062A pdb=" N VAL B 365 " --> pdb=" O ASN B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 371 through 375 Processing helix chain 'C' and resid 3 through 11 removed outlier: 3.810A pdb=" N GLU C 9 " --> pdb=" O HIS C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 54 removed outlier: 4.126A pdb=" N SER C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 104 through 121 removed outlier: 4.189A pdb=" N LYS C 108 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Proline residue: C 111 - end of helix Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 Processing helix chain 'C' and resid 159 through 168 removed outlier: 3.503A pdb=" N LYS C 163 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 168 " --> pdb=" O ILE C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 174 Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.931A pdb=" N ALA C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 201 removed outlier: 3.726A pdb=" N ALA C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 201 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 230 removed outlier: 3.563A pdb=" N LEU C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 296 removed outlier: 4.159A pdb=" N VAL C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) Proline residue: C 285 - end of helix removed outlier: 3.751A pdb=" N ILE C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS C 295 " --> pdb=" O LEU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 308 removed outlier: 3.756A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 308 " --> pdb=" O VAL C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 317 removed outlier: 4.176A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.584A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 366 removed outlier: 4.063A pdb=" N VAL C 365 " --> pdb=" O ASN C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 371 through 375 Processing helix chain 'D' and resid 3 through 11 removed outlier: 3.812A pdb=" N GLU D 9 " --> pdb=" O HIS D 5 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 54 removed outlier: 4.120A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 121 removed outlier: 4.187A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Proline residue: D 111 - end of helix Processing helix chain 'D' and resid 122 through 132 Processing helix chain 'D' and resid 132 through 148 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.928A pdb=" N LEU D 162 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 174 Processing helix chain 'D' and resid 177 through 183 removed outlier: 3.947A pdb=" N ALA D 181 " --> pdb=" O GLU D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 3.845A pdb=" N ALA D 197 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 230 removed outlier: 3.562A pdb=" N LEU D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 296 removed outlier: 4.101A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TYR D 280 " --> pdb=" O SER D 276 " (cutoff:3.500A) Proline residue: D 285 - end of helix removed outlier: 3.752A pdb=" N ILE D 288 " --> pdb=" O VAL D 284 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 308 removed outlier: 3.774A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU D 308 " --> pdb=" O VAL D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 317 removed outlier: 4.189A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.613A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 removed outlier: 4.060A pdb=" N VAL D 365 " --> pdb=" O ASN D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 371 through 375 Processing helix chain 'E' and resid 3 through 11 removed outlier: 3.815A pdb=" N GLU E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 54 removed outlier: 4.123A pdb=" N SER E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 104 through 121 removed outlier: 4.212A pdb=" N LYS E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Proline residue: E 111 - end of helix Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'E' and resid 132 through 148 Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.915A pdb=" N LEU E 162 " --> pdb=" O VAL E 158 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER E 168 " --> pdb=" O ILE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.937A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 201 removed outlier: 3.846A pdb=" N ALA E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 230 removed outlier: 3.553A pdb=" N LEU E 216 " --> pdb=" O ARG E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 296 removed outlier: 4.120A pdb=" N VAL E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N TYR E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) Proline residue: E 285 - end of helix removed outlier: 3.747A pdb=" N ILE E 288 " --> pdb=" O VAL E 284 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 308 removed outlier: 3.760A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 317 removed outlier: 4.175A pdb=" N LEU E 313 " --> pdb=" O PRO E 309 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU E 314 " --> pdb=" O ALA E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.603A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 4.065A pdb=" N VAL E 365 " --> pdb=" O ASN E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 371 through 375 Processing helix chain 'G' and resid 3 through 11 removed outlier: 3.821A pdb=" N GLU G 9 " --> pdb=" O HIS G 5 " (cutoff:3.500A) Processing helix chain 'G' and resid 32 through 54 removed outlier: 4.136A pdb=" N SER G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 104 through 121 removed outlier: 4.205A pdb=" N LYS G 108 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Proline residue: G 111 - end of helix Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 132 through 148 Processing helix chain 'G' and resid 159 through 168 removed outlier: 3.602A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 174 Processing helix chain 'G' and resid 177 through 183 removed outlier: 3.945A pdb=" N ALA G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 201 removed outlier: 3.853A pdb=" N ALA G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG G 201 " --> pdb=" O ALA G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 230 removed outlier: 3.558A pdb=" N LEU G 216 " --> pdb=" O ARG G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 282 removed outlier: 4.103A pdb=" N VAL G 277 " --> pdb=" O SER G 273 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TYR G 280 " --> pdb=" O SER G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 296 removed outlier: 3.749A pdb=" N ILE G 288 " --> pdb=" O VAL G 284 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU G 294 " --> pdb=" O ASN G 290 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS G 295 " --> pdb=" O LEU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 308 removed outlier: 3.751A pdb=" N MET G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU G 308 " --> pdb=" O VAL G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 317 removed outlier: 4.164A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.603A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 366 removed outlier: 4.058A pdb=" N VAL G 365 " --> pdb=" O ASN G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 371 through 375 Processing sheet with id=AA1, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AA2, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.592A pdb=" N LYS F 102 " --> pdb=" O HIS F 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 64 through 66 Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 3.593A pdb=" N LYS A 102 " --> pdb=" O HIS A 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 66 Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 91 removed outlier: 3.588A pdb=" N LYS B 102 " --> pdb=" O HIS B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 66 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 91 removed outlier: 3.591A pdb=" N LYS C 102 " --> pdb=" O HIS C 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'D' and resid 89 through 91 removed outlier: 3.586A pdb=" N LYS D 102 " --> pdb=" O HIS D 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'E' and resid 89 through 91 removed outlier: 3.592A pdb=" N LYS E 102 " --> pdb=" O HIS E 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 89 through 91 removed outlier: 3.585A pdb=" N LYS G 102 " --> pdb=" O HIS G 90 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2685 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 2.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6419 1.35 - 1.46: 5052 1.46 - 1.58: 9634 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 21273 Sorted by residual: bond pdb=" CA VAL C 284 " pdb=" CB VAL C 284 " ideal model delta sigma weight residual 1.537 1.543 -0.006 5.00e-03 4.00e+04 1.58e+00 bond pdb=" C VAL B 284 " pdb=" N PRO B 285 " ideal model delta sigma weight residual 1.337 1.352 -0.015 1.24e-02 6.50e+03 1.46e+00 bond pdb=" C VAL A 284 " pdb=" N PRO A 285 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.24e-02 6.50e+03 1.24e+00 bond pdb=" C VAL D 284 " pdb=" N PRO D 285 " ideal model delta sigma weight residual 1.337 1.351 -0.014 1.24e-02 6.50e+03 1.22e+00 bond pdb=" C VAL B 158 " pdb=" O VAL B 158 " ideal model delta sigma weight residual 1.241 1.229 0.012 1.06e-02 8.90e+03 1.20e+00 ... (remaining 21268 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 28411 2.02 - 4.05: 358 4.05 - 6.07: 96 6.07 - 8.09: 8 8.09 - 10.11: 2 Bond angle restraints: 28875 Sorted by residual: angle pdb=" N VAL G 277 " pdb=" CA VAL G 277 " pdb=" C VAL G 277 " ideal model delta sigma weight residual 111.81 108.40 3.41 8.60e-01 1.35e+00 1.57e+01 angle pdb=" N VAL E 277 " pdb=" CA VAL E 277 " pdb=" C VAL E 277 " ideal model delta sigma weight residual 111.81 108.52 3.29 8.60e-01 1.35e+00 1.46e+01 angle pdb=" N VAL F 277 " pdb=" CA VAL F 277 " pdb=" C VAL F 277 " ideal model delta sigma weight residual 111.81 108.68 3.13 8.60e-01 1.35e+00 1.32e+01 angle pdb=" N VAL A 277 " pdb=" CA VAL A 277 " pdb=" C VAL A 277 " ideal model delta sigma weight residual 111.67 108.66 3.01 9.50e-01 1.11e+00 1.00e+01 angle pdb=" N VAL B 277 " pdb=" CA VAL B 277 " pdb=" C VAL B 277 " ideal model delta sigma weight residual 111.67 108.69 2.98 9.50e-01 1.11e+00 9.86e+00 ... (remaining 28870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.92: 9987 13.92 - 27.84: 1858 27.84 - 41.77: 679 41.77 - 55.69: 259 55.69 - 69.61: 55 Dihedral angle restraints: 12838 sinusoidal: 5138 harmonic: 7700 Sorted by residual: dihedral pdb=" CA ASN A 176 " pdb=" C ASN A 176 " pdb=" N GLU A 177 " pdb=" CA GLU A 177 " ideal model delta harmonic sigma weight residual 180.00 154.48 25.52 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA ASN F 176 " pdb=" C ASN F 176 " pdb=" N GLU F 177 " pdb=" CA GLU F 177 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASN E 176 " pdb=" C ASN E 176 " pdb=" N GLU E 177 " pdb=" CA GLU E 177 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 12835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2112 0.030 - 0.059: 926 0.059 - 0.089: 226 0.089 - 0.118: 116 0.118 - 0.148: 8 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA ASP B 81 " pdb=" N ASP B 81 " pdb=" C ASP B 81 " pdb=" CB ASP B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA ASP C 81 " pdb=" N ASP C 81 " pdb=" C ASP C 81 " pdb=" CB ASP C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 3385 not shown) Planarity restraints: 3535 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP C 105 " -0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 106 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 105 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO A 106 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP F 105 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO F 106 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO F 106 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 106 " 0.021 5.00e-02 4.00e+02 ... (remaining 3532 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 293 2.67 - 3.23: 19065 3.23 - 3.78: 30318 3.78 - 4.34: 39752 4.34 - 4.90: 68051 Nonbonded interactions: 157479 Sorted by model distance: nonbonded pdb=" OD1 ASP F 139 " pdb=" OH TYR F 195 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP A 139 " pdb=" OH TYR A 195 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASP G 139 " pdb=" OH TYR G 195 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP D 139 " pdb=" OH TYR D 195 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP C 139 " pdb=" OH TYR C 195 " model vdw 2.264 3.040 ... (remaining 157474 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: 0.07 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 3.020 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: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.990 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 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:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.002 0.041 21273 Z= 0.115 Angle : 0.581 10.113 28875 Z= 0.297 Chirality : 0.037 0.148 3388 Planarity : 0.003 0.038 3535 Dihedral : 17.806 69.609 7798 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.13 % Allowed : 31.37 % Favored : 68.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.13 (0.18), residues: 2534 helix: 0.67 (0.15), residues: 1428 sheet: None (None), residues: 0 loop : -2.80 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.007 0.001 TYR E 280 PHE 0.012 0.001 PHE C 269 TRP 0.007 0.001 TRP E 175 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00244 (21273) covalent geometry : angle 0.58125 (28875) hydrogen bonds : bond 0.16601 ( 916) hydrogen bonds : angle 5.60317 ( 2685) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 0.839 Fit side-chains REVERT: F 307 MET cc_start: 0.5767 (ttp) cc_final: 0.5512 (mtp) REVERT: A 193 GLU cc_start: 0.6793 (pm20) cc_final: 0.6518 (pm20) REVERT: C 316 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.7027 (mtp-110) REVERT: E 318 MET cc_start: 0.6607 (tpp) cc_final: 0.6231 (tpp) REVERT: G 307 MET cc_start: 0.5724 (ttp) cc_final: 0.5477 (mtp) outliers start: 3 outliers final: 1 residues processed: 197 average time/residue: 0.1322 time to fit residues: 43.5747 Evaluate side-chains 168 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 305 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 247 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 129 GLN A 336 ASN B 336 ASN C 336 ASN D 213 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.208930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.157786 restraints weight = 24942.718| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 3.49 r_work: 0.3459 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21273 Z= 0.221 Angle : 0.694 9.480 28875 Z= 0.342 Chirality : 0.043 0.192 3388 Planarity : 0.005 0.049 3535 Dihedral : 4.736 44.394 2802 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 4.79 % Allowed : 29.89 % Favored : 65.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.78 (0.17), residues: 2534 helix: 0.01 (0.14), residues: 1540 sheet: None (None), residues: 0 loop : -3.18 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.023 0.002 TYR A 280 PHE 0.026 0.002 PHE D 269 TRP 0.015 0.002 TRP B 297 HIS 0.007 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00537 (21273) covalent geometry : angle 0.69423 (28875) hydrogen bonds : bond 0.04876 ( 916) hydrogen bonds : angle 4.45207 ( 2685) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 188 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: B 120 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8209 (mp) REVERT: B 307 MET cc_start: 0.6261 (ttp) cc_final: 0.6052 (mtp) REVERT: B 339 GLU cc_start: 0.7465 (pm20) cc_final: 0.7202 (pm20) REVERT: C 120 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 139 ASP cc_start: 0.7684 (m-30) cc_final: 0.7447 (m-30) REVERT: C 213 ASN cc_start: 0.8527 (m-40) cc_final: 0.8220 (m-40) REVERT: D 120 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8332 (mp) REVERT: E 120 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8262 (mp) REVERT: G 188 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6618 (pp20) outliers start: 113 outliers final: 74 residues processed: 285 average time/residue: 0.1111 time to fit residues: 54.1161 Evaluate side-chains 252 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 174 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 244 ILE Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 351 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 25 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 245 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 132 optimal weight: 0.3980 chunk 211 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.212464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.163232 restraints weight = 25002.453| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.26 r_work: 0.3512 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21273 Z= 0.119 Angle : 0.576 9.646 28875 Z= 0.282 Chirality : 0.039 0.154 3388 Planarity : 0.004 0.044 3535 Dihedral : 4.350 45.173 2802 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.50 % Allowed : 31.79 % Favored : 65.71 % 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: -1.32 (0.17), residues: 2534 helix: 0.49 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -3.06 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 316 TYR 0.015 0.001 TYR C 280 PHE 0.014 0.001 PHE E 269 TRP 0.009 0.001 TRP C 297 HIS 0.003 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00272 (21273) covalent geometry : angle 0.57563 (28875) hydrogen bonds : bond 0.03785 ( 916) hydrogen bonds : angle 4.09559 ( 2685) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 170 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 193 GLU cc_start: 0.7187 (pm20) cc_final: 0.6910 (pm20) REVERT: B 307 MET cc_start: 0.6312 (ttp) cc_final: 0.6101 (mtp) REVERT: C 139 ASP cc_start: 0.7644 (m-30) cc_final: 0.7372 (m-30) outliers start: 59 outliers final: 39 residues processed: 217 average time/residue: 0.1061 time to fit residues: 39.8727 Evaluate side-chains 205 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 41 optimal weight: 7.9990 chunk 119 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 97 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.209023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.163479 restraints weight = 24986.516| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.16 r_work: 0.3435 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21273 Z= 0.191 Angle : 0.622 8.988 28875 Z= 0.307 Chirality : 0.041 0.170 3388 Planarity : 0.004 0.047 3535 Dihedral : 4.494 45.209 2802 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 4.87 % Allowed : 31.11 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -1.52 (0.17), residues: 2534 helix: 0.23 (0.14), residues: 1533 sheet: None (None), residues: 0 loop : -3.09 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 316 TYR 0.019 0.002 TYR B 280 PHE 0.021 0.002 PHE A 269 TRP 0.010 0.001 TRP G 297 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00467 (21273) covalent geometry : angle 0.62193 (28875) hydrogen bonds : bond 0.04234 ( 916) hydrogen bonds : angle 4.10339 ( 2685) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 175 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 120 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 193 GLU cc_start: 0.7378 (pm20) cc_final: 0.7068 (pm20) REVERT: B 307 MET cc_start: 0.6427 (ttp) cc_final: 0.6179 (mtp) REVERT: C 139 ASP cc_start: 0.7824 (m-30) cc_final: 0.7554 (m-30) REVERT: D 120 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8348 (mp) REVERT: E 120 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8372 (mp) REVERT: G 120 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8260 (mp) REVERT: G 188 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6880 (pp20) outliers start: 115 outliers final: 86 residues processed: 271 average time/residue: 0.1060 time to fit residues: 50.0355 Evaluate side-chains 257 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 167 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 281 THR Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 15 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 109 optimal weight: 0.0060 chunk 155 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 205 optimal weight: 0.9990 chunk 203 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.215208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168094 restraints weight = 24341.293| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.78 r_work: 0.3561 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 21273 Z= 0.106 Angle : 0.556 8.503 28875 Z= 0.270 Chirality : 0.038 0.145 3388 Planarity : 0.004 0.045 3535 Dihedral : 4.197 46.581 2802 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.01 % Allowed : 33.40 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.17), residues: 2534 helix: 0.62 (0.14), residues: 1505 sheet: None (None), residues: 0 loop : -2.99 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 316 TYR 0.013 0.001 TYR C 280 PHE 0.014 0.001 PHE F 343 TRP 0.007 0.001 TRP G 297 HIS 0.002 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00239 (21273) covalent geometry : angle 0.55597 (28875) hydrogen bonds : bond 0.03339 ( 916) hydrogen bonds : angle 3.92333 ( 2685) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8129 (mp) REVERT: B 120 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 193 GLU cc_start: 0.7151 (pm20) cc_final: 0.6836 (pm20) REVERT: B 307 MET cc_start: 0.6364 (ttp) cc_final: 0.6123 (mtp) REVERT: C 139 ASP cc_start: 0.7686 (m-30) cc_final: 0.7416 (m-30) REVERT: G 120 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8160 (mp) outliers start: 71 outliers final: 54 residues processed: 234 average time/residue: 0.1073 time to fit residues: 43.2155 Evaluate side-chains 228 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 171 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 343 PHE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 148 ASP Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 146 optimal weight: 0.0770 chunk 127 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 179 optimal weight: 30.0000 chunk 217 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.210320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164755 restraints weight = 24427.286| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.60 r_work: 0.3511 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21273 Z= 0.151 Angle : 0.586 8.055 28875 Z= 0.285 Chirality : 0.039 0.161 3388 Planarity : 0.004 0.046 3535 Dihedral : 4.271 46.720 2802 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 4.28 % Allowed : 32.43 % Favored : 63.29 % 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: -1.21 (0.17), residues: 2534 helix: 0.52 (0.14), residues: 1512 sheet: None (None), residues: 0 loop : -2.97 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 156 TYR 0.016 0.001 TYR A 280 PHE 0.019 0.001 PHE D 343 TRP 0.010 0.001 TRP G 297 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00365 (21273) covalent geometry : angle 0.58594 (28875) hydrogen bonds : bond 0.03714 ( 916) hydrogen bonds : angle 3.93462 ( 2685) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 165 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 120 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 136 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7401 (tp) REVERT: B 193 GLU cc_start: 0.7258 (pm20) cc_final: 0.6935 (pm20) REVERT: C 139 ASP cc_start: 0.7838 (m-30) cc_final: 0.7538 (m-30) REVERT: D 120 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 120 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8316 (mp) REVERT: G 120 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8223 (mp) outliers start: 101 outliers final: 78 residues processed: 254 average time/residue: 0.1194 time to fit residues: 52.5538 Evaluate side-chains 247 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 163 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 343 PHE Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 87 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 179 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 129 GLN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.204709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.153667 restraints weight = 24179.794| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.55 r_work: 0.3433 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21273 Z= 0.252 Angle : 0.665 7.333 28875 Z= 0.331 Chirality : 0.043 0.187 3388 Planarity : 0.005 0.048 3535 Dihedral : 4.680 48.013 2802 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 5.26 % Allowed : 31.71 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: 2534 helix: 0.18 (0.14), residues: 1498 sheet: None (None), residues: 0 loop : -3.10 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 334 TYR 0.020 0.002 TYR D 280 PHE 0.023 0.002 PHE G 269 TRP 0.017 0.002 TRP F 297 HIS 0.005 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00612 (21273) covalent geometry : angle 0.66542 (28875) hydrogen bonds : bond 0.04647 ( 916) hydrogen bonds : angle 4.14190 ( 2685) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 163 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 81 ASP cc_start: 0.8614 (p0) cc_final: 0.8335 (p0) REVERT: A 81 ASP cc_start: 0.8582 (p0) cc_final: 0.8304 (p0) REVERT: A 120 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 81 ASP cc_start: 0.8631 (p0) cc_final: 0.8215 (p0) REVERT: B 120 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (mp) REVERT: C 81 ASP cc_start: 0.8564 (p0) cc_final: 0.8117 (p0) REVERT: C 139 ASP cc_start: 0.7911 (m-30) cc_final: 0.7644 (m-30) REVERT: D 81 ASP cc_start: 0.8595 (p0) cc_final: 0.8320 (p0) REVERT: D 120 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8294 (mp) REVERT: E 120 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8320 (mp) REVERT: G 81 ASP cc_start: 0.8512 (p0) cc_final: 0.8059 (p0) REVERT: G 120 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8322 (mp) outliers start: 124 outliers final: 92 residues processed: 270 average time/residue: 0.1192 time to fit residues: 55.7939 Evaluate side-chains 258 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 161 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ILE Chi-restraints excluded: chain F residue 281 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 336 ASN Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 281 THR Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 281 THR Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 101 MET Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 288 ILE Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 244 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 6.9990 chunk 163 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 129 GLN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.210346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.159364 restraints weight = 24611.423| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.95 r_work: 0.3511 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21273 Z= 0.121 Angle : 0.570 7.647 28875 Z= 0.278 Chirality : 0.038 0.153 3388 Planarity : 0.004 0.046 3535 Dihedral : 4.363 50.137 2802 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.69 % Allowed : 33.36 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.17), residues: 2534 helix: 0.64 (0.14), residues: 1456 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 334 TYR 0.013 0.001 TYR D 280 PHE 0.019 0.001 PHE G 343 TRP 0.012 0.001 TRP A 297 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00284 (21273) covalent geometry : angle 0.57007 (28875) hydrogen bonds : bond 0.03542 ( 916) hydrogen bonds : angle 3.94856 ( 2685) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: F 120 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 120 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 120 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (mp) REVERT: C 139 ASP cc_start: 0.7886 (m-30) cc_final: 0.7626 (m-30) REVERT: D 120 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8284 (mp) REVERT: D 140 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7319 (mp) REVERT: D 148 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 120 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8299 (mp) REVERT: E 157 LEU cc_start: 0.5608 (OUTLIER) cc_final: 0.5095 (tt) REVERT: G 120 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8285 (mp) outliers start: 87 outliers final: 61 residues processed: 243 average time/residue: 0.1222 time to fit residues: 51.1846 Evaluate side-chains 231 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 161 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 134 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 230 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 336 ASN A 336 ASN B 129 GLN B 336 ASN C 129 GLN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.209244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159751 restraints weight = 24440.146| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.78 r_work: 0.3485 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21273 Z= 0.140 Angle : 0.585 8.970 28875 Z= 0.284 Chirality : 0.039 0.163 3388 Planarity : 0.004 0.047 3535 Dihedral : 4.320 51.022 2802 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.82 % Allowed : 33.36 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2534 helix: 0.62 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -3.03 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 262 TYR 0.015 0.001 TYR A 280 PHE 0.023 0.001 PHE G 343 TRP 0.013 0.001 TRP F 297 HIS 0.004 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00340 (21273) covalent geometry : angle 0.58523 (28875) hydrogen bonds : bond 0.03662 ( 916) hydrogen bonds : angle 3.91708 ( 2685) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 163 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: F 120 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (mp) REVERT: A 120 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8318 (mp) REVERT: C 139 ASP cc_start: 0.7954 (m-30) cc_final: 0.7693 (m-30) REVERT: D 120 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 316 ARG cc_start: 0.7005 (mtm-85) cc_final: 0.6789 (mtm-85) REVERT: E 120 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8297 (mp) REVERT: E 157 LEU cc_start: 0.5595 (OUTLIER) cc_final: 0.5091 (tt) REVERT: G 120 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8278 (mp) REVERT: G 292 THR cc_start: 0.6869 (OUTLIER) cc_final: 0.6585 (p) outliers start: 90 outliers final: 70 residues processed: 242 average time/residue: 0.1230 time to fit residues: 51.4501 Evaluate side-chains 239 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 162 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 336 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 336 ASN Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 271 ILE Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 185 optimal weight: 7.9990 chunk 169 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 89 optimal weight: 0.0070 chunk 171 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN B 129 GLN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 GLN C 336 ASN ** D 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 336 ASN G 336 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.210848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159973 restraints weight = 24652.365| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.91 r_work: 0.3528 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21273 Z= 0.111 Angle : 0.563 8.700 28875 Z= 0.272 Chirality : 0.037 0.151 3388 Planarity : 0.004 0.046 3535 Dihedral : 4.178 51.867 2802 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.39 % Allowed : 33.83 % Favored : 62.78 % 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: -1.08 (0.18), residues: 2534 helix: 0.72 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.98 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 334 TYR 0.013 0.001 TYR A 280 PHE 0.024 0.001 PHE G 343 TRP 0.010 0.001 TRP F 297 HIS 0.003 0.000 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00261 (21273) covalent geometry : angle 0.56340 (28875) hydrogen bonds : bond 0.03288 ( 916) hydrogen bonds : angle 3.83881 ( 2685) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5068 Ramachandran restraints generated. 2534 Oldfield, 0 Emsley, 2534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 168 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: F 120 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8325 (mp) REVERT: F 157 LEU cc_start: 0.5367 (mp) cc_final: 0.5081 (tp) REVERT: A 120 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8278 (mp) REVERT: B 192 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7633 (mt) REVERT: B 193 GLU cc_start: 0.7291 (pm20) cc_final: 0.6966 (pm20) REVERT: C 139 ASP cc_start: 0.7881 (m-30) cc_final: 0.7607 (m-30) REVERT: D 120 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8291 (mp) REVERT: D 316 ARG cc_start: 0.7022 (mtm-85) cc_final: 0.6816 (mtm-85) REVERT: E 120 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8294 (mp) REVERT: E 157 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5086 (tt) REVERT: G 120 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (mp) REVERT: G 292 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6469 (p) outliers start: 80 outliers final: 68 residues processed: 238 average time/residue: 0.1203 time to fit residues: 49.7791 Evaluate side-chains 239 residues out of total 2359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 163 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 174 PHE Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 351 VAL Chi-restraints excluded: chain F residue 365 VAL Chi-restraints excluded: chain A residue 101 MET Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 174 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 305 TYR Chi-restraints excluded: chain A residue 336 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 305 TYR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 174 PHE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 284 VAL Chi-restraints excluded: chain C residue 305 TYR Chi-restraints excluded: chain C residue 336 ASN Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 174 PHE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 305 TYR Chi-restraints excluded: chain D residue 351 VAL Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 120 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 174 PHE Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 284 VAL Chi-restraints excluded: chain E residue 305 TYR Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 ASN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 351 VAL Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 174 PHE Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain G residue 305 TYR Chi-restraints excluded: chain G residue 336 ASN Chi-restraints excluded: chain G residue 351 VAL Chi-restraints excluded: chain G residue 365 VAL Chi-restraints excluded: chain G residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 80 optimal weight: 0.7980 chunk 207 optimal weight: 0.7980 chunk 220 optimal weight: 0.9980 chunk 119 optimal weight: 0.0470 chunk 126 optimal weight: 2.9990 chunk 198 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 196 optimal weight: 0.5980 chunk 94 optimal weight: 0.1980 chunk 206 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 ASN B 129 GLN B 336 ASN C 336 ASN D 336 ASN E 336 ASN G 336 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.211564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.161263 restraints weight = 24864.673| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 3.39 r_work: 0.3533 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21273 Z= 0.104 Angle : 0.556 9.411 28875 Z= 0.267 Chirality : 0.037 0.149 3388 Planarity : 0.004 0.046 3535 Dihedral : 4.076 52.113 2802 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.01 % Allowed : 34.25 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.18), residues: 2534 helix: 0.80 (0.14), residues: 1484 sheet: None (None), residues: 0 loop : -2.93 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 334 TYR 0.012 0.001 TYR A 280 PHE 0.020 0.001 PHE G 343 TRP 0.009 0.001 TRP A 297 HIS 0.003 0.000 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00240 (21273) covalent geometry : angle 0.55584 (28875) hydrogen bonds : bond 0.03152 ( 916) hydrogen bonds : angle 3.79043 ( 2685) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4775.89 seconds wall clock time: 82 minutes 50.88 seconds (4970.88 seconds total)