Starting phenix.real_space_refine on Wed Jan 14 17:51:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.map" model { file = "/net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y23_33584/01_2026/7y23_33584.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 49 5.16 5 C 11118 2.51 5 N 3191 2.21 5 O 3475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17833 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2443 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 10, 'TRANS': 316} Chain breaks: 1 Chain: "A" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain: "C" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain: "D" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain: "E" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Chain: "F" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2565 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 12, 'TRANS': 331} Time building chain proxies: 4.18, per 1000 atoms: 0.23 Number of scatterers: 17833 At special positions: 0 Unit cell: (221.285, 187.985, 129.978, 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 49 16.00 O 3475 8.00 N 3191 7.00 C 11118 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 752.6 milliseconds 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4334 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 30 sheets defined 23.8% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'G' and resid 43 through 48 removed outlier: 3.813A pdb=" N THR G 46 " --> pdb=" O SER G 43 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN G 47 " --> pdb=" O VAL G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 117 through 146 removed outlier: 3.585A pdb=" N SER G 123 " --> pdb=" O SER G 119 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 132 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL G 145 " --> pdb=" O LEU G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 196 removed outlier: 3.708A pdb=" N GLN G 180 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE G 188 " --> pdb=" O ALA G 184 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN G 196 " --> pdb=" O ALA G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 220 Processing helix chain 'G' and resid 331 through 335 removed outlier: 3.578A pdb=" N SER G 334 " --> pdb=" O ARG G 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 4.342A pdb=" N ASN A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 117 through 146 removed outlier: 3.851A pdb=" N VAL A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.551A pdb=" N GLN A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.566A pdb=" N SER A 334 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 48 removed outlier: 4.280A pdb=" N ASN B 47 " --> pdb=" O VAL B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 117 through 146 removed outlier: 3.815A pdb=" N SER B 123 " --> pdb=" O SER B 119 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 195 removed outlier: 3.556A pdb=" N THR B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'C' and resid 107 through 112 Processing helix chain 'C' and resid 117 through 146 removed outlier: 3.726A pdb=" N SER C 123 " --> pdb=" O SER C 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 145 " --> pdb=" O LEU C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 195 removed outlier: 3.645A pdb=" N ILE C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 191 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 117 through 146 removed outlier: 3.548A pdb=" N ALA D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 152 removed outlier: 4.233A pdb=" N ASN D 152 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 196 removed outlier: 3.666A pdb=" N ILE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 117 through 146 removed outlier: 3.768A pdb=" N VAL E 145 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 196 removed outlier: 3.524A pdb=" N THR E 187 " --> pdb=" O ILE E 183 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ILE E 188 " --> pdb=" O ALA E 184 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN E 196 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'F' and resid 44 through 48 removed outlier: 4.296A pdb=" N ASN F 47 " --> pdb=" O VAL F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 4.122A pdb=" N LYS F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 117 through 146 removed outlier: 3.588A pdb=" N VAL F 145 " --> pdb=" O LEU F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 196 removed outlier: 3.651A pdb=" N ILE F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN F 196 " --> pdb=" O ALA F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.645A pdb=" N LEU F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing sheet with id=AA1, first strand: chain 'G' and resid 52 through 53 removed outlier: 6.913A pdb=" N ARG G 52 " --> pdb=" O LYS G 300 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS G 302 " --> pdb=" O ARG G 52 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA G 324 " --> pdb=" O LEU G 301 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP G 303 " --> pdb=" O LYS G 322 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LYS G 322 " --> pdb=" O ASP G 303 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA G 305 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N VAL G 320 " --> pdb=" O ALA G 305 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU G 307 " --> pdb=" O GLN G 318 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN G 318 " --> pdb=" O GLU G 307 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ALA G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA G 316 " --> pdb=" O ALA G 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 59 through 65 removed outlier: 3.567A pdb=" N THR G 89 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 237 through 240 removed outlier: 5.527A pdb=" N ARG G 238 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL G 245 " --> pdb=" O ARG G 238 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ARG G 203 " --> pdb=" O GLU G 244 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL G 246 " --> pdb=" O ARG G 203 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE G 205 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA5, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.615A pdb=" N THR F 89 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 53 removed outlier: 7.197A pdb=" N ARG A 52 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LYS A 302 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A 297 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP A 303 " --> pdb=" O LYS A 322 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYS A 322 " --> pdb=" O ASP A 303 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA A 305 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL A 320 " --> pdb=" O ALA A 305 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU A 307 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN A 318 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ALA A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA A 316 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 98 " --> pdb=" O LEU F 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 94 removed outlier: 3.844A pdb=" N THR A 89 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N SER A 59 " --> pdb=" O VAL B 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 71 through 73 removed outlier: 3.850A pdb=" N LEU B 98 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA B 316 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ALA B 309 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLN B 318 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU B 307 " --> pdb=" O GLN B 318 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 320 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ALA B 305 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS B 322 " --> pdb=" O ASP B 303 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 303 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 245 through 247 removed outlier: 7.940A pdb=" N VAL A 246 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N PHE A 205 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 88 through 94 removed outlier: 3.751A pdb=" N THR B 89 " --> pdb=" O VAL B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 88 through 94 removed outlier: 3.751A pdb=" N THR B 89 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N LEU C 36 " --> pdb=" O GLN B 61 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.110A pdb=" N LEU C 98 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA C 324 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASP C 303 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N GLY C 326 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU C 301 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N GLY C 328 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL C 299 " --> pdb=" O GLY C 328 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AB5, first strand: chain 'B' and resid 243 through 247 removed outlier: 7.188A pdb=" N ARG B 203 " --> pdb=" O GLU B 244 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL B 246 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N PHE B 205 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 257 through 258 removed outlier: 4.194A pdb=" N ASN B 269 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 88 through 94 removed outlier: 3.669A pdb=" N THR C 89 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N SER C 59 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 88 through 94 removed outlier: 3.669A pdb=" N THR C 89 " --> pdb=" O VAL C 64 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 36 " --> pdb=" O GLN C 61 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.084A pdb=" N LEU D 98 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA D 324 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASP D 303 " --> pdb=" O ALA D 324 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N GLY D 326 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU D 301 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N GLY D 328 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL D 299 " --> pdb=" O GLY D 328 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 243 through 247 Processing sheet with id=AC2, first strand: chain 'D' and resid 88 through 94 removed outlier: 3.836A pdb=" N THR D 89 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N SER D 59 " --> pdb=" O VAL E 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 88 through 94 removed outlier: 3.836A pdb=" N THR D 89 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU E 36 " --> pdb=" O GLN D 61 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 71 through 73 removed outlier: 3.938A pdb=" N LEU E 98 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 324 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASP E 303 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N GLY E 326 " --> pdb=" O LEU E 301 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N LEU E 301 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY E 328 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL E 299 " --> pdb=" O GLY E 328 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AC6, first strand: chain 'E' and resid 88 through 94 removed outlier: 3.619A pdb=" N THR E 89 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER E 59 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 88 through 94 removed outlier: 3.619A pdb=" N THR E 89 " --> pdb=" O VAL E 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU F 36 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.110A pdb=" N LEU F 98 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA F 316 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ALA F 309 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLN F 318 " --> pdb=" O GLU F 307 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLU F 307 " --> pdb=" O GLN F 318 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL F 320 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ALA F 305 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS F 322 " --> pdb=" O ASP F 303 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ASP F 303 " --> pdb=" O LYS F 322 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 324 " --> pdb=" O LEU F 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 243 through 247 removed outlier: 7.283A pdb=" N ARG E 203 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL E 246 " --> pdb=" O ARG E 203 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE E 205 " --> pdb=" O VAL E 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 230 through 231 removed outlier: 3.913A pdb=" N SER E 236 " --> pdb=" O ASP E 231 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 257 through 258 removed outlier: 4.035A pdb=" N ASN E 269 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 243 through 247 removed outlier: 7.272A pdb=" N ARG F 203 " --> pdb=" O GLU F 244 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL F 246 " --> pdb=" O ARG F 203 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE F 205 " --> pdb=" O VAL F 246 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1704 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.81 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6039 1.34 - 1.45: 1755 1.45 - 1.57: 10196 1.57 - 1.69: 0 1.69 - 1.81: 98 Bond restraints: 18088 Sorted by residual: bond pdb=" CA SER E 236 " pdb=" C SER E 236 " ideal model delta sigma weight residual 1.522 1.507 0.015 1.22e-02 6.72e+03 1.47e+00 bond pdb=" CA ASN A 201 " pdb=" CB ASN A 201 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.69e-02 3.50e+03 1.40e+00 bond pdb=" N PHE F 62 " pdb=" CA PHE F 62 " ideal model delta sigma weight residual 1.463 1.448 0.014 1.22e-02 6.72e+03 1.38e+00 bond pdb=" CB ASN G 201 " pdb=" CG ASN G 201 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CB ASP D 259 " pdb=" CG ASP D 259 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.36e+00 ... (remaining 18083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 23957 2.13 - 4.25: 462 4.25 - 6.38: 44 6.38 - 8.50: 5 8.50 - 10.63: 17 Bond angle restraints: 24485 Sorted by residual: angle pdb=" N ARG B 238 " pdb=" CA ARG B 238 " pdb=" C ARG B 238 " ideal model delta sigma weight residual 109.07 119.48 -10.41 1.61e+00 3.86e-01 4.18e+01 angle pdb=" N GLU F 233 " pdb=" CA GLU F 233 " pdb=" C GLU F 233 " ideal model delta sigma weight residual 111.07 117.95 -6.88 1.07e+00 8.73e-01 4.14e+01 angle pdb=" C ASP C 258 " pdb=" N ASP C 259 " pdb=" CA ASP C 259 " ideal model delta sigma weight residual 121.54 132.17 -10.63 1.91e+00 2.74e-01 3.10e+01 angle pdb=" C ALA B 200 " pdb=" N ASN B 201 " pdb=" CA ASN B 201 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.93e+01 angle pdb=" C ALA D 200 " pdb=" N ASN D 201 " pdb=" CA ASN D 201 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.68e+01 ... (remaining 24480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9910 17.96 - 35.91: 829 35.91 - 53.87: 177 53.87 - 71.83: 33 71.83 - 89.78: 17 Dihedral angle restraints: 10966 sinusoidal: 4180 harmonic: 6786 Sorted by residual: dihedral pdb=" CA HIS G 49 " pdb=" C HIS G 49 " pdb=" N MET G 50 " pdb=" CA MET G 50 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA HIS C 250 " pdb=" C HIS C 250 " pdb=" N LEU C 251 " pdb=" CA LEU C 251 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA HIS E 250 " pdb=" C HIS E 250 " pdb=" N LEU E 251 " pdb=" CA LEU E 251 " ideal model delta harmonic sigma weight residual 180.00 156.05 23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 10963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2503 0.068 - 0.136: 305 0.136 - 0.204: 8 0.204 - 0.273: 5 0.273 - 0.341: 2 Chirality restraints: 2823 Sorted by residual: chirality pdb=" CA ARG C 234 " pdb=" N ARG C 234 " pdb=" C ARG C 234 " pdb=" CB ARG C 234 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA ARG B 238 " pdb=" N ARG B 238 " pdb=" C ARG B 238 " pdb=" CB ARG B 238 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CA THR G 45 " pdb=" N THR G 45 " pdb=" C THR G 45 " pdb=" CB THR G 45 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2820 not shown) Planarity restraints: 3250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 233 " 0.021 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C GLU C 233 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU C 233 " 0.028 2.00e-02 2.50e+03 pdb=" N ARG C 234 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 233 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C GLU B 233 " 0.043 2.00e-02 2.50e+03 pdb=" O GLU B 233 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG B 234 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 220 " -0.040 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO D 221 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " -0.034 5.00e-02 4.00e+02 ... (remaining 3247 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1271 2.73 - 3.28: 17960 3.28 - 3.82: 27224 3.82 - 4.36: 34669 4.36 - 4.90: 59337 Nonbonded interactions: 140461 Sorted by model distance: nonbonded pdb=" O ASN G 285 " pdb=" ND2 ASN G 285 " model vdw 2.192 3.120 nonbonded pdb=" O PRO D 161 " pdb=" OG SER D 162 " model vdw 2.208 3.040 nonbonded pdb=" ND2 ASN D 146 " pdb=" O LYS D 280 " model vdw 2.231 3.120 nonbonded pdb=" O ALA A 142 " pdb=" ND2 ASN A 146 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG C 331 " pdb=" O THR D 37 " model vdw 2.243 3.120 ... (remaining 140456 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 220 or resid 235 through 342)) selection = (chain 'B' and (resid 2 through 220 or resid 235 through 342)) selection = (chain 'C' and (resid 2 through 220 or resid 235 through 342)) selection = (chain 'D' and (resid 2 through 220 or resid 235 through 342)) selection = (chain 'E' and (resid 2 through 220 or resid 235 through 342)) selection = (chain 'F' and (resid 2 through 220 or resid 235 through 342)) 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: 90.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.790 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.003 0.029 18088 Z= 0.166 Angle : 0.745 10.628 24485 Z= 0.440 Chirality : 0.044 0.341 2823 Planarity : 0.004 0.061 3250 Dihedral : 14.377 89.782 6632 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.73 % Favored : 93.64 % Rotamer: Outliers : 0.17 % Allowed : 0.39 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.15), residues: 2375 helix: -0.37 (0.20), residues: 512 sheet: 1.04 (0.22), residues: 482 loop : -1.62 (0.15), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 48 TYR 0.020 0.001 TYR G 212 PHE 0.017 0.001 PHE G 274 HIS 0.007 0.001 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00301 (18088) covalent geometry : angle 0.74491 (24485) hydrogen bonds : bond 0.24860 ( 585) hydrogen bonds : angle 7.94827 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 174 time to evaluate : 0.675 Fit side-chains REVERT: G 238 ARG cc_start: 0.7512 (mtm180) cc_final: 0.6977 (mtt90) REVERT: A 306 LEU cc_start: 0.9329 (pt) cc_final: 0.9109 (pt) REVERT: D 112 MET cc_start: 0.8996 (mtt) cc_final: 0.8770 (mtt) REVERT: E 210 ASP cc_start: 0.7955 (m-30) cc_final: 0.7726 (m-30) outliers start: 3 outliers final: 1 residues processed: 175 average time/residue: 0.1428 time to fit residues: 38.1210 Evaluate side-chains 130 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 237 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.0370 chunk 103 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN B 318 GLN ** E 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.089782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.079174 restraints weight = 27569.882| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.26 r_work: 0.2703 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18088 Z= 0.177 Angle : 0.653 8.297 24485 Z= 0.351 Chirality : 0.044 0.154 2823 Planarity : 0.004 0.062 3250 Dihedral : 4.908 39.505 2572 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.63 % Allowed : 6.19 % Favored : 93.18 % Rotamer: Outliers : 0.94 % Allowed : 8.76 % Favored : 90.31 % 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 are not related in a simple way. whole: -0.61 (0.16), residues: 2375 helix: 1.07 (0.22), residues: 530 sheet: 0.84 (0.22), residues: 488 loop : -1.57 (0.15), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 67 TYR 0.029 0.002 TYR B 323 PHE 0.013 0.001 PHE B 290 HIS 0.007 0.002 HIS E 272 Details of bonding type rmsd covalent geometry : bond 0.00406 (18088) covalent geometry : angle 0.65338 (24485) hydrogen bonds : bond 0.06541 ( 585) hydrogen bonds : angle 5.42407 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: G 134 ASP cc_start: 0.8511 (t0) cc_final: 0.8202 (t0) REVERT: G 238 ARG cc_start: 0.8117 (mtm180) cc_final: 0.7138 (mtt90) REVERT: A 241 MET cc_start: 0.8409 (mmt) cc_final: 0.8169 (mmp) REVERT: D 131 MET cc_start: 0.9139 (mmp) cc_final: 0.8690 (mmm) REVERT: E 220 MET cc_start: 0.9076 (mmt) cc_final: 0.8733 (mmp) outliers start: 17 outliers final: 13 residues processed: 137 average time/residue: 0.1447 time to fit residues: 30.2991 Evaluate side-chains 125 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain D residue 42 THR Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 156 optimal weight: 0.1980 chunk 170 optimal weight: 4.9990 chunk 211 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 159 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 285 ASN D 61 GLN E 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.091656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.080978 restraints weight = 27470.968| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.27 r_work: 0.2732 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18088 Z= 0.137 Angle : 0.585 8.329 24485 Z= 0.315 Chirality : 0.043 0.143 2823 Planarity : 0.003 0.060 3250 Dihedral : 4.724 46.990 2572 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.59 % Allowed : 5.94 % Favored : 93.47 % Rotamer: Outliers : 2.04 % Allowed : 10.68 % Favored : 87.28 % 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 are not related in a simple way. whole: -0.43 (0.16), residues: 2375 helix: 1.58 (0.22), residues: 529 sheet: 0.82 (0.23), residues: 487 loop : -1.57 (0.15), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 67 TYR 0.024 0.002 TYR D 323 PHE 0.011 0.001 PHE F 290 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00300 (18088) covalent geometry : angle 0.58488 (24485) hydrogen bonds : bond 0.04904 ( 585) hydrogen bonds : angle 4.74125 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 128 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: G 151 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9001 (p) REVERT: G 238 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7171 (mtt90) REVERT: G 259 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8481 (p0) REVERT: A 259 ASP cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (p0) REVERT: D 131 MET cc_start: 0.9135 (mmp) cc_final: 0.8755 (mmm) REVERT: E 220 MET cc_start: 0.9011 (mmt) cc_final: 0.8703 (mmp) REVERT: E 234 ARG cc_start: 0.8683 (mtp85) cc_final: 0.8261 (mtt90) REVERT: E 259 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8530 (p0) outliers start: 37 outliers final: 24 residues processed: 160 average time/residue: 0.1389 time to fit residues: 34.5148 Evaluate side-chains 146 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 97 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 chunk 54 optimal weight: 0.0000 chunk 11 optimal weight: 0.0770 chunk 231 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 285 ASN A 51 GLN D 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.093895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.083299 restraints weight = 27301.159| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.24 r_work: 0.2774 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18088 Z= 0.119 Angle : 0.550 8.118 24485 Z= 0.297 Chirality : 0.041 0.139 2823 Planarity : 0.003 0.057 3250 Dihedral : 4.502 47.621 2572 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.15 % Favored : 93.39 % Rotamer: Outliers : 2.59 % Allowed : 12.17 % Favored : 85.24 % 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 are not related in a simple way. whole: -0.29 (0.16), residues: 2375 helix: 1.88 (0.22), residues: 529 sheet: 0.73 (0.23), residues: 493 loop : -1.50 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 293 TYR 0.018 0.001 TYR E 323 PHE 0.012 0.001 PHE G 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00248 (18088) covalent geometry : angle 0.54959 (24485) hydrogen bonds : bond 0.04192 ( 585) hydrogen bonds : angle 4.44083 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 135 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: G 151 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8936 (p) REVERT: G 238 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7112 (mtt90) REVERT: G 259 ASP cc_start: 0.8814 (OUTLIER) cc_final: 0.8523 (p0) REVERT: G 285 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8265 (p0) REVERT: A 259 ASP cc_start: 0.8811 (OUTLIER) cc_final: 0.8594 (p0) REVERT: C 85 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8319 (p0) REVERT: C 116 ASP cc_start: 0.8066 (p0) cc_final: 0.7687 (p0) REVERT: D 131 MET cc_start: 0.9103 (mmp) cc_final: 0.8738 (mmm) REVERT: D 291 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8171 (pp30) REVERT: E 193 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8900 (mp) REVERT: E 210 ASP cc_start: 0.8585 (m-30) cc_final: 0.8252 (m-30) REVERT: E 220 MET cc_start: 0.8951 (mmt) cc_final: 0.8711 (mmp) REVERT: E 234 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8261 (mtt90) REVERT: E 259 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8448 (p0) REVERT: F 110 ASP cc_start: 0.8647 (t0) cc_final: 0.8416 (t0) REVERT: F 291 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8600 (pp30) outliers start: 47 outliers final: 25 residues processed: 176 average time/residue: 0.1363 time to fit residues: 37.2280 Evaluate side-chains 154 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 285 ASN Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 25 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 232 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN C 291 GLN F 51 GLN F 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.092946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.082299 restraints weight = 27227.366| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.25 r_work: 0.2757 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18088 Z= 0.127 Angle : 0.553 7.948 24485 Z= 0.297 Chirality : 0.042 0.137 2823 Planarity : 0.003 0.057 3250 Dihedral : 4.498 48.476 2572 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.06 % Favored : 93.47 % Rotamer: Outliers : 3.52 % Allowed : 12.44 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.16), residues: 2375 helix: 1.95 (0.22), residues: 529 sheet: 0.71 (0.23), residues: 493 loop : -1.47 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 293 TYR 0.019 0.001 TYR A 323 PHE 0.011 0.001 PHE G 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00279 (18088) covalent geometry : angle 0.55267 (24485) hydrogen bonds : bond 0.04221 ( 585) hydrogen bonds : angle 4.39805 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: G 151 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8955 (p) REVERT: G 238 ARG cc_start: 0.8061 (mtm180) cc_final: 0.7086 (mtt90) REVERT: G 241 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.7019 (mtt) REVERT: G 259 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8513 (p0) REVERT: A 131 MET cc_start: 0.9000 (mmp) cc_final: 0.8795 (mmm) REVERT: A 259 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8659 (p0) REVERT: C 85 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8344 (p0) REVERT: C 116 ASP cc_start: 0.8116 (p0) cc_final: 0.7725 (p0) REVERT: D 131 MET cc_start: 0.9091 (mmp) cc_final: 0.8723 (mmm) REVERT: E 193 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8886 (mp) REVERT: E 210 ASP cc_start: 0.8611 (m-30) cc_final: 0.8277 (m-30) REVERT: E 234 ARG cc_start: 0.8659 (mtp85) cc_final: 0.8216 (mtt90) REVERT: E 259 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8431 (p0) REVERT: F 259 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8610 (p0) REVERT: F 291 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8608 (pp30) outliers start: 64 outliers final: 37 residues processed: 180 average time/residue: 0.1285 time to fit residues: 36.1901 Evaluate side-chains 163 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 117 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 241 MET Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 146 ASN Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 103 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 171 optimal weight: 0.0970 chunk 172 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 137 optimal weight: 0.0010 chunk 159 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN C 146 ASN ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.093997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.083436 restraints weight = 27033.445| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.23 r_work: 0.2775 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18088 Z= 0.116 Angle : 0.541 7.873 24485 Z= 0.291 Chirality : 0.041 0.135 2823 Planarity : 0.003 0.056 3250 Dihedral : 4.403 47.812 2572 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 6.15 % Favored : 93.39 % Rotamer: Outliers : 3.47 % Allowed : 12.89 % Favored : 83.65 % 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 are not related in a simple way. whole: -0.19 (0.17), residues: 2375 helix: 2.08 (0.22), residues: 529 sheet: 0.69 (0.23), residues: 493 loop : -1.44 (0.15), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 293 TYR 0.017 0.001 TYR E 323 PHE 0.011 0.001 PHE G 290 HIS 0.006 0.001 HIS C 292 Details of bonding type rmsd covalent geometry : bond 0.00243 (18088) covalent geometry : angle 0.54098 (24485) hydrogen bonds : bond 0.03970 ( 585) hydrogen bonds : angle 4.29983 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 129 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: G 151 VAL cc_start: 0.9212 (OUTLIER) cc_final: 0.8907 (p) REVERT: G 238 ARG cc_start: 0.8040 (mtm180) cc_final: 0.7077 (mtt90) REVERT: G 241 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.7139 (mtt) REVERT: G 259 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8528 (p0) REVERT: A 259 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8654 (p0) REVERT: C 85 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (p0) REVERT: C 116 ASP cc_start: 0.8102 (p0) cc_final: 0.7679 (p0) REVERT: D 131 MET cc_start: 0.9101 (mmp) cc_final: 0.8738 (mmm) REVERT: E 193 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8899 (mp) REVERT: E 210 ASP cc_start: 0.8606 (m-30) cc_final: 0.8261 (m-30) REVERT: E 234 ARG cc_start: 0.8647 (mtp85) cc_final: 0.8213 (mtt90) REVERT: E 259 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8420 (p0) REVERT: F 259 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8595 (p0) REVERT: F 291 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8605 (pp30) outliers start: 63 outliers final: 42 residues processed: 184 average time/residue: 0.1310 time to fit residues: 37.8189 Evaluate side-chains 171 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain G residue 241 MET Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 101 optimal weight: 0.0060 chunk 200 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN B 291 GLN C 51 GLN C 292 HIS D 94 ASN D 291 GLN F 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.088852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.077812 restraints weight = 27583.973| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 1.33 r_work: 0.2665 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18088 Z= 0.171 Angle : 0.599 8.359 24485 Z= 0.319 Chirality : 0.044 0.141 2823 Planarity : 0.004 0.058 3250 Dihedral : 4.741 50.619 2572 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.78 % Favored : 92.80 % Rotamer: Outliers : 3.74 % Allowed : 13.77 % Favored : 82.49 % 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 are not related in a simple way. whole: -0.33 (0.16), residues: 2375 helix: 1.85 (0.22), residues: 529 sheet: 0.61 (0.23), residues: 504 loop : -1.50 (0.15), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 52 TYR 0.025 0.002 TYR C 323 PHE 0.016 0.001 PHE F 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00403 (18088) covalent geometry : angle 0.59913 (24485) hydrogen bonds : bond 0.04854 ( 585) hydrogen bonds : angle 4.55851 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 117 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: G 238 ARG cc_start: 0.8159 (mtm180) cc_final: 0.7157 (mtt90) REVERT: G 241 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.7189 (mtt) REVERT: G 259 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8540 (p0) REVERT: A 259 ASP cc_start: 0.8910 (OUTLIER) cc_final: 0.8667 (p0) REVERT: A 291 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8985 (pt0) REVERT: C 85 ASP cc_start: 0.8572 (OUTLIER) cc_final: 0.8350 (p0) REVERT: C 116 ASP cc_start: 0.8278 (p0) cc_final: 0.7860 (p0) REVERT: D 131 MET cc_start: 0.9116 (mmp) cc_final: 0.8757 (mmm) REVERT: D 220 MET cc_start: 0.9260 (mmm) cc_final: 0.8846 (mmp) REVERT: E 193 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8935 (mp) REVERT: E 210 ASP cc_start: 0.8659 (m-30) cc_final: 0.8317 (m-30) REVERT: E 234 ARG cc_start: 0.8656 (mtp85) cc_final: 0.8185 (mtt90) REVERT: E 259 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8489 (p0) REVERT: F 259 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8704 (p0) REVERT: F 291 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8708 (pp30) outliers start: 68 outliers final: 45 residues processed: 176 average time/residue: 0.1366 time to fit residues: 37.5051 Evaluate side-chains 167 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 113 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 241 MET Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 259 ASP Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 89 optimal weight: 0.0980 chunk 47 optimal weight: 0.3980 chunk 161 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 218 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN D 94 ASN ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.091696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.081086 restraints weight = 27248.977| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 1.24 r_work: 0.2722 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18088 Z= 0.120 Angle : 0.552 7.937 24485 Z= 0.297 Chirality : 0.041 0.136 2823 Planarity : 0.003 0.057 3250 Dihedral : 4.545 48.642 2572 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.27 % Favored : 93.31 % Rotamer: Outliers : 3.47 % Allowed : 14.15 % Favored : 82.38 % 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 are not related in a simple way. whole: -0.25 (0.17), residues: 2375 helix: 2.05 (0.22), residues: 529 sheet: 0.57 (0.23), residues: 507 loop : -1.47 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 293 TYR 0.018 0.001 TYR D 323 PHE 0.011 0.001 PHE G 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00254 (18088) covalent geometry : angle 0.55240 (24485) hydrogen bonds : bond 0.04228 ( 585) hydrogen bonds : angle 4.36708 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 123 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: G 238 ARG cc_start: 0.8098 (mtm180) cc_final: 0.7079 (mtt90) REVERT: G 259 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.8521 (p0) REVERT: A 291 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8931 (pt0) REVERT: C 116 ASP cc_start: 0.8203 (p0) cc_final: 0.7753 (p0) REVERT: D 131 MET cc_start: 0.9077 (mmp) cc_final: 0.8711 (mmm) REVERT: E 193 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8911 (mp) REVERT: E 210 ASP cc_start: 0.8619 (m-30) cc_final: 0.8267 (m-30) REVERT: E 234 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8123 (mtt90) REVERT: E 259 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8393 (p0) REVERT: F 116 ASP cc_start: 0.8371 (p0) cc_final: 0.8056 (t0) REVERT: F 259 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8595 (p0) REVERT: F 291 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8602 (pp30) outliers start: 63 outliers final: 42 residues processed: 178 average time/residue: 0.1298 time to fit residues: 36.5305 Evaluate side-chains 167 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 94 ASN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 37 optimal weight: 3.9990 chunk 171 optimal weight: 0.3980 chunk 199 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 138 optimal weight: 0.0170 chunk 176 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN D 291 GLN F 51 GLN F 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.079273 restraints weight = 27206.258| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 1.29 r_work: 0.2703 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18088 Z= 0.146 Angle : 0.574 9.977 24485 Z= 0.307 Chirality : 0.043 0.176 2823 Planarity : 0.003 0.057 3250 Dihedral : 4.613 49.775 2572 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.53 % Favored : 93.05 % Rotamer: Outliers : 3.36 % Allowed : 14.26 % Favored : 82.38 % 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 are not related in a simple way. whole: -0.29 (0.17), residues: 2375 helix: 1.99 (0.22), residues: 529 sheet: 0.56 (0.23), residues: 503 loop : -1.48 (0.15), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.021 0.002 TYR D 323 PHE 0.013 0.001 PHE F 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00336 (18088) covalent geometry : angle 0.57356 (24485) hydrogen bonds : bond 0.04460 ( 585) hydrogen bonds : angle 4.40183 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 118 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: G 238 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7110 (mtt90) REVERT: G 259 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8525 (p0) REVERT: A 291 GLN cc_start: 0.9179 (OUTLIER) cc_final: 0.8946 (pt0) REVERT: C 116 ASP cc_start: 0.8244 (p0) cc_final: 0.7797 (p0) REVERT: D 131 MET cc_start: 0.9109 (mmp) cc_final: 0.8759 (mmm) REVERT: E 193 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8927 (mp) REVERT: E 210 ASP cc_start: 0.8625 (m-30) cc_final: 0.8275 (m-30) REVERT: E 234 ARG cc_start: 0.8621 (mtp85) cc_final: 0.8167 (mtt90) REVERT: E 259 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8425 (p0) REVERT: F 116 ASP cc_start: 0.8371 (p0) cc_final: 0.8088 (t0) REVERT: F 259 ASP cc_start: 0.8909 (OUTLIER) cc_final: 0.8663 (p0) REVERT: F 291 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8682 (pp30) outliers start: 61 outliers final: 45 residues processed: 173 average time/residue: 0.1326 time to fit residues: 36.0815 Evaluate side-chains 165 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 114 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 291 GLN Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 198 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 149 optimal weight: 0.0070 chunk 215 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN F 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.092747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.082095 restraints weight = 26957.958| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.25 r_work: 0.2751 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18088 Z= 0.116 Angle : 0.551 9.483 24485 Z= 0.296 Chirality : 0.041 0.136 2823 Planarity : 0.003 0.056 3250 Dihedral : 4.438 48.434 2572 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.36 % Favored : 93.26 % Rotamer: Outliers : 2.97 % Allowed : 14.59 % Favored : 82.43 % 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 are not related in a simple way. whole: -0.20 (0.17), residues: 2375 helix: 2.17 (0.22), residues: 531 sheet: 0.57 (0.23), residues: 499 loop : -1.46 (0.15), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.017 0.001 TYR D 323 PHE 0.011 0.001 PHE G 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00238 (18088) covalent geometry : angle 0.55109 (24485) hydrogen bonds : bond 0.03970 ( 585) hydrogen bonds : angle 4.26146 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4750 Ramachandran restraints generated. 2375 Oldfield, 0 Emsley, 2375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 121 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: G 238 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7053 (mtt90) REVERT: G 259 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8545 (p0) REVERT: D 131 MET cc_start: 0.9071 (mmp) cc_final: 0.8737 (mmm) REVERT: E 193 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8887 (mp) REVERT: E 210 ASP cc_start: 0.8591 (m-30) cc_final: 0.8224 (m-30) REVERT: E 234 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8106 (mtt90) REVERT: E 259 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8374 (p0) REVERT: F 116 ASP cc_start: 0.8350 (p0) cc_final: 0.8089 (t0) REVERT: F 259 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8633 (p0) REVERT: F 291 GLN cc_start: 0.8973 (OUTLIER) cc_final: 0.8570 (pp30) outliers start: 54 outliers final: 44 residues processed: 168 average time/residue: 0.1317 time to fit residues: 34.8314 Evaluate side-chains 165 residues out of total 1816 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 116 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 153 GLU Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 149 ASP Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 248 VAL Chi-restraints excluded: chain E residue 259 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 61 GLN Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 134 ASP Chi-restraints excluded: chain F residue 153 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 259 ASP Chi-restraints excluded: chain F residue 291 GLN Chi-restraints excluded: chain F residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 215 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 69 optimal weight: 0.0270 chunk 147 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.092396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.081704 restraints weight = 27295.096| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.26 r_work: 0.2745 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18088 Z= 0.121 Angle : 0.552 8.967 24485 Z= 0.296 Chirality : 0.041 0.137 2823 Planarity : 0.003 0.056 3250 Dihedral : 4.416 48.653 2572 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.36 % Favored : 93.26 % Rotamer: Outliers : 2.86 % Allowed : 14.76 % Favored : 82.38 % 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 are not related in a simple way. whole: -0.19 (0.17), residues: 2375 helix: 2.19 (0.22), residues: 529 sheet: 0.58 (0.23), residues: 498 loop : -1.44 (0.15), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 293 TYR 0.018 0.001 TYR D 323 PHE 0.011 0.001 PHE G 290 HIS 0.005 0.001 HIS G 49 Details of bonding type rmsd covalent geometry : bond 0.00262 (18088) covalent geometry : angle 0.55234 (24485) hydrogen bonds : bond 0.03993 ( 585) hydrogen bonds : angle 4.23495 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6973.19 seconds wall clock time: 120 minutes 0.42 seconds (7200.42 seconds total)