Starting phenix.real_space_refine on Tue Nov 18 10:15:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.map" model { file = "/net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cae_30328/11_2025/7cae_30328.cif" } resolution = 3.44 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= 0.021 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 41 5.16 5 C 8565 2.51 5 N 2263 2.21 5 O 2496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13365 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2911 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2908 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2155 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 267} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2035 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 253} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 3356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3356 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 31, 'TRANS': 411} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.32, per 1000 atoms: 0.25 Number of scatterers: 13365 At special positions: 0 Unit cell: (79.54, 93.48, 170.56, 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 41 16.00 O 2496 8.00 N 2263 7.00 C 8565 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: 1.21 Conformation dependent library (CDL) restraints added in 629.5 milliseconds 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3266 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 16 sheets defined 47.2% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'C' and resid 48 through 56 Processing helix chain 'C' and resid 96 through 108 Proline residue: C 104 - end of helix Processing helix chain 'C' and resid 111 through 126 Processing helix chain 'C' and resid 130 through 134 removed outlier: 3.997A pdb=" N ASP C 133 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.865A pdb=" N LEU C 139 " --> pdb=" O PRO C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 155 removed outlier: 4.773A pdb=" N ARG C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 removed outlier: 4.427A pdb=" N ASN C 168 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 169 " --> pdb=" O LEU C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 165 through 169' Processing helix chain 'C' and resid 170 through 189 removed outlier: 4.368A pdb=" N VAL C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN C 176 " --> pdb=" O LYS C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.654A pdb=" N ALA C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 229 Processing helix chain 'C' and resid 233 through 238 Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 299 through 303 Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'D' and resid 48 through 56 Processing helix chain 'D' and resid 76 through 80 removed outlier: 3.714A pdb=" N ARG D 80 " --> pdb=" O PRO D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 107 Proline residue: D 104 - end of helix Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.636A pdb=" N LEU D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 155 removed outlier: 4.514A pdb=" N ARG D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 189 removed outlier: 4.062A pdb=" N VAL D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N GLN D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.587A pdb=" N ALA D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 266 through 274 Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 335 through 343 Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.686A pdb=" N LEU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Proline residue: A 30 - end of helix Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.736A pdb=" N VAL A 47 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TRP A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 91 through 110 removed outlier: 3.702A pdb=" N ALA A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALA A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 162 through 190 removed outlier: 3.614A pdb=" N VAL A 169 " --> pdb=" O SER A 165 " (cutoff:3.500A) Proline residue: A 179 - end of helix removed outlier: 4.193A pdb=" N LEU A 183 " --> pdb=" O PRO A 179 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 206 through 211 removed outlier: 3.978A pdb=" N LEU A 211 " --> pdb=" O PRO A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.795A pdb=" N ALA A 234 " --> pdb=" O ARG A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 238 through 244 removed outlier: 3.964A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 244 " --> pdb=" O ASN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.891A pdb=" N ASN A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 272 Processing helix chain 'A' and resid 274 through 291 removed outlier: 3.807A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 15 through 26 removed outlier: 4.344A pdb=" N ILE B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 24 " --> pdb=" O VAL B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'B' and resid 67 through 93 removed outlier: 4.157A pdb=" N SER B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N MET B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 105 through 113 removed outlier: 4.231A pdb=" N LEU B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 3.712A pdb=" N LEU B 121 " --> pdb=" O PRO B 117 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR B 123 " --> pdb=" O ILE B 119 " (cutoff:3.500A) Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 137 through 140 Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.604A pdb=" N TYR B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Proline residue: B 151 - end of helix Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.749A pdb=" N LYS B 170 " --> pdb=" O TRP B 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET B 174 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.550A pdb=" N ARG B 184 " --> pdb=" O ALA B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 196 removed outlier: 3.655A pdb=" N ALA B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Proline residue: B 193 - end of helix Processing helix chain 'B' and resid 197 through 207 removed outlier: 3.714A pdb=" N LEU B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N PHE B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 242 through 273 Proline residue: B 255 - end of helix removed outlier: 3.848A pdb=" N ILE B 262 " --> pdb=" O ILE B 258 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ARG B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 56 removed outlier: 4.255A pdb=" N ALA E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL E 47 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA E 48 " --> pdb=" O PHE E 44 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 56 " --> pdb=" O ASN E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 83 Processing helix chain 'E' and resid 97 through 105 removed outlier: 3.989A pdb=" N GLY E 105 " --> pdb=" O PHE E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 165 through 177 Processing helix chain 'E' and resid 192 through 207 removed outlier: 3.675A pdb=" N VAL E 196 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 243 removed outlier: 3.674A pdb=" N ILE E 236 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA E 241 " --> pdb=" O ILE E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.980A pdb=" N GLN E 252 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR E 253 " --> pdb=" O ILE E 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 249 through 253' Processing helix chain 'E' and resid 254 through 264 Processing helix chain 'E' and resid 275 through 284 removed outlier: 3.644A pdb=" N SER E 279 " --> pdb=" O TYR E 275 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 281 " --> pdb=" O LEU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 304 removed outlier: 4.422A pdb=" N GLN E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 325 Processing helix chain 'E' and resid 359 through 371 Processing helix chain 'E' and resid 372 through 382 Processing helix chain 'E' and resid 389 through 394 removed outlier: 4.473A pdb=" N TYR E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ASP E 394 " --> pdb=" O THR E 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 389 through 394' Processing helix chain 'E' and resid 397 through 402 removed outlier: 4.421A pdb=" N LYS E 401 " --> pdb=" O ALA E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 424 through 433 Processing helix chain 'E' and resid 442 through 459 removed outlier: 3.911A pdb=" N ALA E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASP E 448 " --> pdb=" O GLU E 444 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU E 449 " --> pdb=" O ARG E 445 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU E 452 " --> pdb=" O ASP E 448 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 9 removed outlier: 5.079A pdb=" N PHE C 27 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.589A pdb=" N ILE C 38 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY C 221 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN C 219 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU C 213 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.550A pdb=" N ALA C 83 " --> pdb=" O LEU C 161 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASP C 163 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N THR C 191 " --> pdb=" O PHE C 160 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N MET C 162 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL C 193 " --> pdb=" O MET C 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 245 through 247 Processing sheet with id=AA5, first strand: chain 'C' and resid 291 through 293 Processing sheet with id=AA6, first strand: chain 'C' and resid 310 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 315 through 317 Processing sheet with id=AA8, first strand: chain 'D' and resid 27 through 31 removed outlier: 5.337A pdb=" N PHE D 27 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 82 through 85 removed outlier: 6.249A pdb=" N ALA D 83 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N PHE D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL D 195 " --> pdb=" O PHE D 160 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N MET D 162 " --> pdb=" O VAL D 195 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 208 " --> pdb=" O PHE D 36 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 38 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 211 " --> pdb=" O GLN D 218 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 245 through 247 Processing sheet with id=AB2, first strand: chain 'D' and resid 250 through 251 removed outlier: 3.549A pdb=" N GLY D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 291 through 292 Processing sheet with id=AB4, first strand: chain 'D' and resid 310 through 311 Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 317 Processing sheet with id=AB6, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.759A pdb=" N THR E 36 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N TYR E 35 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASP E 94 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU E 349 " --> pdb=" O ILE E 145 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 272 removed outlier: 3.798A pdb=" N GLU E 270 " --> pdb=" O TRP E 153 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1440 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: 2.12 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2238 1.32 - 1.44: 3398 1.44 - 1.56: 7916 1.56 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 13629 Sorted by residual: bond pdb=" N PRO D 223 " pdb=" CA PRO D 223 " ideal model delta sigma weight residual 1.473 1.444 0.029 8.50e-03 1.38e+04 1.17e+01 bond pdb=" C PRO B 139 " pdb=" O PRO B 139 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.30e-02 5.92e+03 1.08e+01 bond pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.20e-02 6.94e+03 9.12e+00 bond pdb=" N SER E 25 " pdb=" CA SER E 25 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.86e+00 bond pdb=" N THR E 27 " pdb=" CA THR E 27 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.76e+00 ... (remaining 13624 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 18540 5.75 - 11.50: 28 11.50 - 17.25: 2 17.25 - 23.00: 1 23.00 - 28.74: 2 Bond angle restraints: 18573 Sorted by residual: angle pdb=" N ILE E 441 " pdb=" CA ILE E 441 " pdb=" C ILE E 441 " ideal model delta sigma weight residual 108.90 80.16 28.74 1.66e+00 3.63e-01 3.00e+02 angle pdb=" N VAL B 186 " pdb=" CA VAL B 186 " pdb=" C VAL B 186 " ideal model delta sigma weight residual 110.72 120.70 -9.98 1.01e+00 9.80e-01 9.76e+01 angle pdb=" N GLY D 221 " pdb=" CA GLY D 221 " pdb=" C GLY D 221 " ideal model delta sigma weight residual 113.18 136.52 -23.34 2.37e+00 1.78e-01 9.70e+01 angle pdb=" N ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta sigma weight residual 111.03 96.25 14.78 1.76e+00 3.23e-01 7.05e+01 angle pdb=" N ASP E 442 " pdb=" CA ASP E 442 " pdb=" C ASP E 442 " ideal model delta sigma weight residual 108.74 90.66 18.08 2.22e+00 2.03e-01 6.64e+01 ... (remaining 18568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 7289 17.63 - 35.26: 750 35.26 - 52.90: 106 52.90 - 70.53: 16 70.53 - 88.16: 18 Dihedral angle restraints: 8179 sinusoidal: 3112 harmonic: 5067 Sorted by residual: dihedral pdb=" N ASP E 442 " pdb=" C ASP E 442 " pdb=" CA ASP E 442 " pdb=" CB ASP E 442 " ideal model delta harmonic sigma weight residual 122.80 96.94 25.86 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" N ILE E 441 " pdb=" C ILE E 441 " pdb=" CA ILE E 441 " pdb=" CB ILE E 441 " ideal model delta harmonic sigma weight residual 123.40 107.92 15.48 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" C ILE E 441 " pdb=" N ILE E 441 " pdb=" CA ILE E 441 " pdb=" CB ILE E 441 " ideal model delta harmonic sigma weight residual -122.00 -108.75 -13.25 0 2.50e+00 1.60e-01 2.81e+01 ... (remaining 8176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 2172 0.131 - 0.262: 24 0.262 - 0.393: 3 0.393 - 0.524: 0 0.524 - 0.655: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CA ASP E 442 " pdb=" N ASP E 442 " pdb=" C ASP E 442 " pdb=" CB ASP E 442 " both_signs ideal model delta sigma weight residual False 2.51 3.17 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA ILE E 441 " pdb=" N ILE E 441 " pdb=" C ILE E 441 " pdb=" CB ILE E 441 " both_signs ideal model delta sigma weight residual False 2.43 3.01 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA LYS B 185 " pdb=" N LYS B 185 " pdb=" C LYS B 185 " pdb=" CB LYS B 185 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 2198 not shown) Planarity restraints: 2388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 221 " -0.023 2.00e-02 2.50e+03 4.95e-02 2.45e+01 pdb=" C GLY D 221 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY D 221 " -0.034 2.00e-02 2.50e+03 pdb=" N THR D 222 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 112 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLU E 112 " -0.063 2.00e-02 2.50e+03 pdb=" O GLU E 112 " 0.024 2.00e-02 2.50e+03 pdb=" N ASP E 113 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 53 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" C GLU E 53 " 0.052 2.00e-02 2.50e+03 pdb=" O GLU E 53 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN E 54 " -0.018 2.00e-02 2.50e+03 ... (remaining 2385 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 131 2.57 - 3.15: 11366 3.15 - 3.73: 19795 3.73 - 4.32: 26994 4.32 - 4.90: 46133 Nonbonded interactions: 104419 Sorted by model distance: nonbonded pdb=" N ILE E 441 " pdb=" O ILE E 441 " model vdw 1.985 2.496 nonbonded pdb=" O ALA C 342 " pdb=" O SER C 345 " model vdw 2.228 3.040 nonbonded pdb=" O ALA D 90 " pdb=" NH2 ARG D 151 " model vdw 2.240 3.120 nonbonded pdb=" OG1 THR E 221 " pdb=" OG1 THR E 451 " model vdw 2.247 3.040 nonbonded pdb=" O SER C 229 " pdb=" OG SER C 229 " model vdw 2.249 3.040 ... (remaining 104414 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 'C' and (resid 2 through 131 or (resid 132 through 133 and (name N or nam \ e CA or name C or name O or name CB )) or resid 134 or (resid 135 and (name N or \ name CA or name C or name O or name CB )) or resid 136 through 274 or (resid 27 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 276 through \ 391)) selection = (chain 'D' and (resid 2 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 through 360 or (resid 361 and (name N or na \ me CA or name C or name O or name CB )) or resid 362 through 383 or (resid 384 a \ nd (name N or name CA or name C or name O or name CB )) or resid 385 through 391 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.610 Find NCS groups from input model: 0.140 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13629 Z= 0.237 Angle : 0.876 28.745 18573 Z= 0.501 Chirality : 0.053 0.655 2201 Planarity : 0.005 0.049 2388 Dihedral : 14.471 88.161 4913 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.06 % Favored : 89.71 % Rotamer: Outliers : 0.43 % Allowed : 10.27 % Favored : 89.30 % Cbeta Deviations : 0.12 % 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: -5.42 (0.15), residues: 1749 helix: -2.73 (0.14), residues: 816 sheet: -4.09 (0.27), residues: 180 loop : -4.45 (0.16), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.016 0.001 TYR E 34 PHE 0.021 0.001 PHE B 232 TRP 0.028 0.001 TRP E 136 HIS 0.003 0.001 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00484 (13629) covalent geometry : angle 0.87612 (18573) hydrogen bonds : bond 0.14681 ( 512) hydrogen bonds : angle 6.75273 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 247 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 127 ASP cc_start: 0.6833 (p0) cc_final: 0.6615 (p0) REVERT: D 143 GLN cc_start: 0.6644 (pt0) cc_final: 0.6396 (tt0) REVERT: D 227 TYR cc_start: 0.8250 (t80) cc_final: 0.7887 (t80) REVERT: A 208 TRP cc_start: 0.8055 (t60) cc_final: 0.7825 (t-100) REVERT: B 113 ILE cc_start: 0.8862 (pt) cc_final: 0.8643 (mt) outliers start: 6 outliers final: 5 residues processed: 253 average time/residue: 0.1379 time to fit residues: 48.7325 Evaluate side-chains 178 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 442 ASP Chi-restraints excluded: chain E residue 452 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN D 168 ASN D 350 ASN A 55 ASN A 201 GLN B 17 ASN B 72 ASN B 237 GLN E 52 ASN E 73 GLN E 137 GLN E 216 GLN E 256 ASN E 358 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.162659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136334 restraints weight = 17298.680| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.67 r_work: 0.3419 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13629 Z= 0.133 Angle : 0.684 7.318 18573 Z= 0.342 Chirality : 0.044 0.199 2201 Planarity : 0.005 0.057 2388 Dihedral : 5.706 69.805 1903 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.00 % Favored : 91.94 % Rotamer: Outliers : 2.51 % Allowed : 14.87 % Favored : 82.61 % 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: -4.22 (0.17), residues: 1749 helix: -1.65 (0.17), residues: 823 sheet: -3.71 (0.29), residues: 187 loop : -3.91 (0.18), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 265 TYR 0.015 0.001 TYR E 34 PHE 0.017 0.001 PHE B 54 TRP 0.013 0.001 TRP E 136 HIS 0.003 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00307 (13629) covalent geometry : angle 0.68355 (18573) hydrogen bonds : bond 0.03667 ( 512) hydrogen bonds : angle 5.15592 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 202 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7684 (ttm110) REVERT: C 127 ASP cc_start: 0.6933 (p0) cc_final: 0.6671 (p0) REVERT: C 306 LEU cc_start: 0.7112 (mm) cc_final: 0.6638 (tt) REVERT: D 257 ARG cc_start: 0.6594 (ttm110) cc_final: 0.6369 (ttp80) REVERT: D 269 MET cc_start: 0.6012 (ttt) cc_final: 0.5668 (mmt) REVERT: A 201 GLN cc_start: 0.8209 (tp40) cc_final: 0.7998 (tp-100) REVERT: A 208 TRP cc_start: 0.8090 (t60) cc_final: 0.7649 (t-100) REVERT: B 52 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8017 (pt) REVERT: B 71 PHE cc_start: 0.8193 (t80) cc_final: 0.7460 (m-10) REVERT: B 115 MET cc_start: 0.8237 (mpp) cc_final: 0.7864 (ptp) REVERT: E 50 ARG cc_start: 0.7432 (ttp-110) cc_final: 0.7073 (ttp-110) REVERT: E 75 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8683 (mm) REVERT: E 452 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7228 (mt-10) outliers start: 35 outliers final: 14 residues processed: 228 average time/residue: 0.1345 time to fit residues: 43.6783 Evaluate side-chains 193 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 452 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 89 optimal weight: 0.0980 chunk 86 optimal weight: 3.9990 chunk 6 optimal weight: 0.0770 chunk 126 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 162 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 HIS D 232 ASN E 76 GLN E 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.186672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.155519 restraints weight = 18798.251| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.12 r_work: 0.3776 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13629 Z= 0.115 Angle : 0.629 7.339 18573 Z= 0.313 Chirality : 0.043 0.206 2201 Planarity : 0.004 0.057 2388 Dihedral : 5.025 62.261 1898 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 3.09 % Allowed : 16.38 % Favored : 80.53 % 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: -3.53 (0.18), residues: 1749 helix: -1.03 (0.18), residues: 814 sheet: -3.32 (0.31), residues: 193 loop : -3.60 (0.18), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 184 TYR 0.011 0.001 TYR E 34 PHE 0.012 0.001 PHE B 54 TRP 0.009 0.001 TRP E 136 HIS 0.005 0.001 HIS C 94 Details of bonding type rmsd covalent geometry : bond 0.00265 (13629) covalent geometry : angle 0.62906 (18573) hydrogen bonds : bond 0.03162 ( 512) hydrogen bonds : angle 4.78677 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7538 (ttm110) REVERT: C 127 ASP cc_start: 0.6920 (p0) cc_final: 0.6643 (p0) REVERT: C 306 LEU cc_start: 0.7070 (mm) cc_final: 0.6694 (tt) REVERT: D 257 ARG cc_start: 0.6774 (ttm110) cc_final: 0.6498 (ttp80) REVERT: A 168 ILE cc_start: 0.9296 (mm) cc_final: 0.9056 (mp) REVERT: A 208 TRP cc_start: 0.8106 (t60) cc_final: 0.7536 (t-100) REVERT: B 52 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7924 (pt) REVERT: B 71 PHE cc_start: 0.8255 (t80) cc_final: 0.7265 (m-10) REVERT: B 115 MET cc_start: 0.8226 (mpp) cc_final: 0.7879 (ptp) REVERT: B 220 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8183 (tp40) REVERT: E 50 ARG cc_start: 0.7160 (ttp-110) cc_final: 0.6776 (ttp-110) REVERT: E 75 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8656 (mm) REVERT: E 431 MET cc_start: 0.8565 (ttt) cc_final: 0.8201 (mtm) outliers start: 43 outliers final: 24 residues processed: 232 average time/residue: 0.1235 time to fit residues: 41.5247 Evaluate side-chains 209 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 195 MET Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 448 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 90 optimal weight: 0.0050 chunk 136 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 153 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 ASN D 219 GLN D 232 ASN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.183379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.150927 restraints weight = 18648.155| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.34 r_work: 0.3746 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13629 Z= 0.146 Angle : 0.644 7.572 18573 Z= 0.319 Chirality : 0.044 0.207 2201 Planarity : 0.005 0.056 2388 Dihedral : 4.982 63.894 1895 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.66 % Allowed : 17.60 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.19), residues: 1749 helix: -0.82 (0.19), residues: 820 sheet: -3.00 (0.34), residues: 180 loop : -3.45 (0.19), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 265 TYR 0.015 0.001 TYR E 34 PHE 0.011 0.001 PHE D 36 TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00356 (13629) covalent geometry : angle 0.64414 (18573) hydrogen bonds : bond 0.03253 ( 512) hydrogen bonds : angle 4.66162 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7562 (ttm110) REVERT: C 127 ASP cc_start: 0.6965 (p0) cc_final: 0.6692 (p0) REVERT: C 306 LEU cc_start: 0.7098 (mm) cc_final: 0.6729 (tt) REVERT: D 139 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5229 (mp) REVERT: A 168 ILE cc_start: 0.9304 (mm) cc_final: 0.9035 (mp) REVERT: A 208 TRP cc_start: 0.8119 (t60) cc_final: 0.7563 (t-100) REVERT: B 52 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7975 (pt) REVERT: B 71 PHE cc_start: 0.8274 (t80) cc_final: 0.7286 (m-10) REVERT: B 115 MET cc_start: 0.8253 (mpp) cc_final: 0.7941 (ptp) REVERT: B 220 GLN cc_start: 0.8543 (tp-100) cc_final: 0.8265 (tp40) REVERT: E 75 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8703 (mm) REVERT: E 310 PHE cc_start: 0.7263 (t80) cc_final: 0.7025 (t80) outliers start: 51 outliers final: 31 residues processed: 225 average time/residue: 0.1197 time to fit residues: 39.3124 Evaluate side-chains 215 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 135 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 173 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN A 201 GLN ** E 375 ASN ** 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 = 0.4175 r_free = 0.4175 target = 0.184662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.153666 restraints weight = 18607.928| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.23 r_work: 0.3769 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13629 Z= 0.125 Angle : 0.628 9.307 18573 Z= 0.309 Chirality : 0.043 0.217 2201 Planarity : 0.005 0.056 2388 Dihedral : 4.842 60.920 1895 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.09 % Allowed : 19.18 % Favored : 77.73 % 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: -2.96 (0.19), residues: 1749 helix: -0.64 (0.19), residues: 821 sheet: -2.78 (0.35), residues: 178 loop : -3.31 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 265 TYR 0.013 0.001 TYR E 34 PHE 0.014 0.001 PHE B 54 TRP 0.009 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00301 (13629) covalent geometry : angle 0.62798 (18573) hydrogen bonds : bond 0.03058 ( 512) hydrogen bonds : angle 4.56824 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7526 (ttm110) REVERT: C 127 ASP cc_start: 0.7053 (p0) cc_final: 0.6725 (p0) REVERT: C 306 LEU cc_start: 0.7003 (mm) cc_final: 0.6699 (tt) REVERT: D 318 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8260 (pp) REVERT: A 168 ILE cc_start: 0.9293 (mm) cc_final: 0.9045 (mp) REVERT: A 208 TRP cc_start: 0.8124 (t60) cc_final: 0.7575 (t-100) REVERT: B 52 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7800 (pt) REVERT: B 71 PHE cc_start: 0.8267 (t80) cc_final: 0.7286 (m-10) REVERT: B 115 MET cc_start: 0.8235 (mpp) cc_final: 0.7964 (ptp) REVERT: B 220 GLN cc_start: 0.8517 (tp-100) cc_final: 0.8282 (tp40) REVERT: E 75 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8738 (mm) outliers start: 43 outliers final: 29 residues processed: 225 average time/residue: 0.1177 time to fit residues: 38.7700 Evaluate side-chains 216 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 132 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 108 optimal weight: 0.0070 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 60 optimal weight: 0.0470 chunk 161 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN D 351 GLN A 201 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.186259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.154808 restraints weight = 18491.675| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.35 r_work: 0.3774 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13629 Z= 0.115 Angle : 0.609 7.639 18573 Z= 0.302 Chirality : 0.043 0.212 2201 Planarity : 0.004 0.055 2388 Dihedral : 4.687 58.034 1895 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.23 % Allowed : 20.04 % Favored : 76.72 % 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: -2.71 (0.19), residues: 1749 helix: -0.46 (0.19), residues: 822 sheet: -2.58 (0.36), residues: 178 loop : -3.17 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 265 TYR 0.011 0.001 TYR E 34 PHE 0.012 0.001 PHE D 260 TRP 0.008 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00275 (13629) covalent geometry : angle 0.60896 (18573) hydrogen bonds : bond 0.02922 ( 512) hydrogen bonds : angle 4.49989 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7520 (ttm110) REVERT: C 127 ASP cc_start: 0.7001 (p0) cc_final: 0.6677 (p0) REVERT: C 306 LEU cc_start: 0.6860 (mm) cc_final: 0.6636 (tt) REVERT: D 318 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8259 (pp) REVERT: A 168 ILE cc_start: 0.9278 (mm) cc_final: 0.9059 (mp) REVERT: A 208 TRP cc_start: 0.8119 (t60) cc_final: 0.7551 (t-100) REVERT: B 52 ILE cc_start: 0.8020 (OUTLIER) cc_final: 0.7726 (pt) REVERT: B 71 PHE cc_start: 0.8281 (t80) cc_final: 0.7231 (m-10) REVERT: B 115 MET cc_start: 0.8279 (mpp) cc_final: 0.7989 (ptp) REVERT: E 75 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8690 (mm) outliers start: 45 outliers final: 30 residues processed: 228 average time/residue: 0.1197 time to fit residues: 39.3618 Evaluate side-chains 217 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 80 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 126 optimal weight: 0.6980 chunk 86 optimal weight: 0.2980 chunk 121 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.186518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.154885 restraints weight = 18417.082| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.18 r_work: 0.3777 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3641 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13629 Z= 0.119 Angle : 0.610 9.179 18573 Z= 0.302 Chirality : 0.043 0.211 2201 Planarity : 0.004 0.054 2388 Dihedral : 4.612 57.695 1895 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.09 % Allowed : 20.19 % Favored : 76.72 % 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: -2.55 (0.20), residues: 1749 helix: -0.34 (0.19), residues: 821 sheet: -2.47 (0.36), residues: 180 loop : -3.08 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 265 TYR 0.013 0.001 TYR A 138 PHE 0.011 0.001 PHE D 260 TRP 0.008 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00287 (13629) covalent geometry : angle 0.61049 (18573) hydrogen bonds : bond 0.02932 ( 512) hydrogen bonds : angle 4.44913 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7419 (ttm110) REVERT: C 127 ASP cc_start: 0.6921 (p0) cc_final: 0.6598 (p0) REVERT: C 306 LEU cc_start: 0.6846 (mm) cc_final: 0.6467 (tt) REVERT: D 318 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8228 (pp) REVERT: A 168 ILE cc_start: 0.9285 (mm) cc_final: 0.9066 (mp) REVERT: A 208 TRP cc_start: 0.8122 (t60) cc_final: 0.7576 (t-100) REVERT: A 218 MET cc_start: 0.8785 (mtp) cc_final: 0.8583 (mtp) REVERT: B 52 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7731 (pt) REVERT: B 71 PHE cc_start: 0.8293 (t80) cc_final: 0.7252 (m-10) REVERT: B 115 MET cc_start: 0.8284 (mpp) cc_final: 0.8011 (ptp) REVERT: E 75 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8696 (mm) outliers start: 43 outliers final: 31 residues processed: 222 average time/residue: 0.1180 time to fit residues: 38.2971 Evaluate side-chains 219 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 80 optimal weight: 0.0070 chunk 155 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.9404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN D 232 ASN A 201 GLN E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.182883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.148697 restraints weight = 17929.590| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.41 r_work: 0.3759 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13629 Z= 0.129 Angle : 0.618 9.203 18573 Z= 0.305 Chirality : 0.043 0.212 2201 Planarity : 0.005 0.085 2388 Dihedral : 4.609 58.539 1895 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 3.23 % Allowed : 20.33 % Favored : 76.44 % 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: -2.43 (0.20), residues: 1749 helix: -0.25 (0.19), residues: 819 sheet: -2.36 (0.36), residues: 178 loop : -3.02 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 265 TYR 0.013 0.001 TYR E 34 PHE 0.022 0.001 PHE E 328 TRP 0.014 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00314 (13629) covalent geometry : angle 0.61781 (18573) hydrogen bonds : bond 0.02990 ( 512) hydrogen bonds : angle 4.41886 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7456 (ttm110) REVERT: C 115 ILE cc_start: 0.7612 (mm) cc_final: 0.7405 (mt) REVERT: C 127 ASP cc_start: 0.7004 (p0) cc_final: 0.6677 (p0) REVERT: D 318 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8235 (pp) REVERT: A 56 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 168 ILE cc_start: 0.9280 (mm) cc_final: 0.9065 (mp) REVERT: A 208 TRP cc_start: 0.8158 (t60) cc_final: 0.7582 (t-100) REVERT: A 216 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 218 MET cc_start: 0.8835 (mtp) cc_final: 0.8618 (mtp) REVERT: B 52 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7743 (pt) REVERT: B 71 PHE cc_start: 0.8306 (t80) cc_final: 0.7219 (m-10) REVERT: B 115 MET cc_start: 0.8306 (mpp) cc_final: 0.8029 (ptp) REVERT: B 184 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8623 (ttm110) outliers start: 45 outliers final: 33 residues processed: 224 average time/residue: 0.1101 time to fit residues: 36.2761 Evaluate side-chains 218 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.0070 chunk 146 optimal weight: 10.0000 chunk 151 optimal weight: 0.0670 chunk 134 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 127 optimal weight: 0.0570 overall best weight: 0.3854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN A 201 GLN ** E 375 ASN ** 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 = 0.4022 r_free = 0.4022 target = 0.174141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.148405 restraints weight = 17273.055| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.72 r_work: 0.3525 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13629 Z= 0.108 Angle : 0.615 9.308 18573 Z= 0.302 Chirality : 0.043 0.211 2201 Planarity : 0.005 0.065 2388 Dihedral : 4.473 55.721 1895 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.51 % Allowed : 21.62 % Favored : 75.86 % 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: -2.27 (0.20), residues: 1749 helix: -0.15 (0.19), residues: 822 sheet: -2.26 (0.37), residues: 178 loop : -2.91 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 265 TYR 0.016 0.001 TYR A 138 PHE 0.024 0.001 PHE E 328 TRP 0.012 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00249 (13629) covalent geometry : angle 0.61510 (18573) hydrogen bonds : bond 0.02833 ( 512) hydrogen bonds : angle 4.37451 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.7202 (ttm110) REVERT: C 115 ILE cc_start: 0.7621 (mm) cc_final: 0.7331 (mt) REVERT: C 127 ASP cc_start: 0.6634 (p0) cc_final: 0.6396 (p0) REVERT: D 318 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8176 (pp) REVERT: A 56 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8236 (tt) REVERT: A 168 ILE cc_start: 0.9202 (mm) cc_final: 0.8993 (mp) REVERT: A 208 TRP cc_start: 0.7976 (t60) cc_final: 0.7648 (t-100) REVERT: B 52 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7627 (pt) REVERT: B 71 PHE cc_start: 0.8029 (t80) cc_final: 0.7400 (m-10) REVERT: B 115 MET cc_start: 0.7890 (mpp) cc_final: 0.7686 (ptp) outliers start: 35 outliers final: 28 residues processed: 215 average time/residue: 0.1215 time to fit residues: 38.1040 Evaluate side-chains 215 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 37 ILE Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 156 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 232 ASN D 337 GLN A 60 HIS E 76 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.138228 restraints weight = 17305.119| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.67 r_work: 0.3489 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 13629 Z= 0.182 Angle : 0.679 9.443 18573 Z= 0.335 Chirality : 0.045 0.222 2201 Planarity : 0.005 0.063 2388 Dihedral : 4.844 64.843 1895 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 2.87 % Allowed : 21.26 % Favored : 75.86 % 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: -2.33 (0.20), residues: 1749 helix: -0.23 (0.19), residues: 824 sheet: -2.30 (0.37), residues: 178 loop : -2.90 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 265 TYR 0.018 0.001 TYR E 34 PHE 0.021 0.002 PHE E 328 TRP 0.019 0.001 TRP B 13 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00450 (13629) covalent geometry : angle 0.67887 (18573) hydrogen bonds : bond 0.03418 ( 512) hydrogen bonds : angle 4.48794 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3498 Ramachandran restraints generated. 1749 Oldfield, 0 Emsley, 1749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 8 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7602 (ttm110) REVERT: C 115 ILE cc_start: 0.7707 (mm) cc_final: 0.7445 (mt) REVERT: C 127 ASP cc_start: 0.6804 (p0) cc_final: 0.6531 (p0) REVERT: C 363 ARG cc_start: 0.8050 (ttp80) cc_final: 0.7824 (tpp-160) REVERT: D 318 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 208 TRP cc_start: 0.8086 (t60) cc_final: 0.7640 (t-100) REVERT: B 52 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7844 (pt) REVERT: B 71 PHE cc_start: 0.8208 (t80) cc_final: 0.7389 (m-10) REVERT: B 115 MET cc_start: 0.8256 (mpp) cc_final: 0.8032 (ptp) outliers start: 40 outliers final: 28 residues processed: 220 average time/residue: 0.1134 time to fit residues: 36.5811 Evaluate side-chains 212 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 8 ARG Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 222 THR Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 89 TYR Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 324 VAL Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 129 TRP Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 440 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 0.1980 chunk 90 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN B 220 GLN E 76 GLN E 264 GLN ** E 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.149706 restraints weight = 17236.895| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.55 r_work: 0.3534 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13629 Z= 0.121 Angle : 0.642 11.915 18573 Z= 0.315 Chirality : 0.043 0.206 2201 Planarity : 0.005 0.060 2388 Dihedral : 4.610 59.726 1895 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.51 % Allowed : 21.62 % Favored : 75.86 % 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: -2.12 (0.20), residues: 1749 helix: -0.07 (0.19), residues: 822 sheet: -2.17 (0.37), residues: 178 loop : -2.79 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 265 TYR 0.011 0.001 TYR E 34 PHE 0.022 0.001 PHE E 328 TRP 0.011 0.001 TRP B 13 HIS 0.004 0.001 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00288 (13629) covalent geometry : angle 0.64156 (18573) hydrogen bonds : bond 0.02921 ( 512) hydrogen bonds : angle 4.37594 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.29 seconds wall clock time: 59 minutes 55.52 seconds (3595.52 seconds total)