Starting phenix.real_space_refine on Fri Mar 6 17:38:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215.map" model { file = "/net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xjv_22215/03_2026/6xjv_22215_neut.cif" } resolution = 4.17 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4093 atoms to isotropic. 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 130 5.16 5 C 19302 2.51 5 N 5092 2.21 5 O 5397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29921 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 416 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "Q" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2189 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 5, 'TRANS': 263} Chain breaks: 3 Chain: "R" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2423 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 3, 'TRANS': 287} Chain breaks: 2 Chain: "I" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "J" Number of atoms: 416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 416 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "K" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "L" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "N" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "O" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "P" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "S" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2198 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 5, 'TRANS': 264} Chain breaks: 3 Chain: "T" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2423 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 3, 'TRANS': 287} Chain breaks: 2 Time building chain proxies: 6.81, per 1000 atoms: 0.23 Number of scatterers: 29921 At special positions: 0 Unit cell: (120.785, 199.087, 182.427, 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 130 16.00 O 5397 8.00 N 5092 7.00 C 19302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 872.8 milliseconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6966 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 18 sheets defined 67.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.830A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 172 through 191 Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.617A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 256 removed outlier: 4.111A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 285 Processing helix chain 'A' and resid 290 through 310 removed outlier: 3.718A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 4.523A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'B' and resid 65 through 95 Proline residue: B 76 - end of helix removed outlier: 3.824A pdb=" N HIS B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 140 through 146 Processing helix chain 'C' and resid 171 through 190 removed outlier: 3.642A pdb=" N THR C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 215 removed outlier: 3.797A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 255 removed outlier: 3.820A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 removed outlier: 4.414A pdb=" N MET C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) Proline residue: C 265 - end of helix Processing helix chain 'C' and resid 291 through 311 removed outlier: 4.094A pdb=" N ARG C 297 " --> pdb=" O GLU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.671A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 95 removed outlier: 3.634A pdb=" N ILE D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.663A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.543A pdb=" N PHE E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 169 through 190 Processing helix chain 'E' and resid 191 through 256 removed outlier: 3.739A pdb=" N HIS E 195 " --> pdb=" O CYS E 191 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.793A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP E 255 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 285 removed outlier: 3.752A pdb=" N MET E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) Proline residue: E 265 - end of helix removed outlier: 3.650A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 311 Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.743A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 95 removed outlier: 3.589A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 3.512A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N HIS F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 119 removed outlier: 3.862A pdb=" N ASP G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 178 through 191 removed outlier: 3.575A pdb=" N LEU G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 257 removed outlier: 3.709A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.782A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 286 removed outlier: 4.190A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 310 Processing helix chain 'G' and resid 313 through 334 Processing helix chain 'H' and resid 65 through 93 removed outlier: 3.527A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.682A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 122 removed outlier: 3.717A pdb=" N TYR Q 121 " --> pdb=" O ARG Q 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'Q' and resid 148 through 157 Processing helix chain 'Q' and resid 194 through 199 Processing helix chain 'Q' and resid 206 through 217 removed outlier: 3.676A pdb=" N ILE Q 210 " --> pdb=" O PHE Q 206 " (cutoff:3.500A) Processing helix chain 'Q' and resid 219 through 231 Processing helix chain 'Q' and resid 239 through 252 removed outlier: 3.835A pdb=" N ILE Q 249 " --> pdb=" O GLN Q 245 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 283 removed outlier: 3.551A pdb=" N PHE Q 283 " --> pdb=" O THR Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 292 through 315 removed outlier: 3.800A pdb=" N PHE Q 296 " --> pdb=" O THR Q 292 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS Q 315 " --> pdb=" O GLU Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 323 through 336 Processing helix chain 'Q' and resid 340 through 353 removed outlier: 4.426A pdb=" N LYS Q 350 " --> pdb=" O GLN Q 346 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS Q 351 " --> pdb=" O ARG Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 3.927A pdb=" N ASN Q 373 " --> pdb=" O THR Q 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 386 removed outlier: 4.140A pdb=" N THR Q 379 " --> pdb=" O ASN Q 375 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA Q 380 " --> pdb=" O ASP Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 392 through 404 removed outlier: 3.742A pdb=" N MET Q 396 " --> pdb=" O ASP Q 392 " (cutoff:3.500A) Processing helix chain 'Q' and resid 409 through 421 Processing helix chain 'Q' and resid 433 through 443 Processing helix chain 'R' and resid 86 through 93 removed outlier: 3.609A pdb=" N PHE R 90 " --> pdb=" O ARG R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 115 Processing helix chain 'R' and resid 128 through 137 Processing helix chain 'R' and resid 138 through 142 Processing helix chain 'R' and resid 147 through 153 Processing helix chain 'R' and resid 159 through 172 Processing helix chain 'R' and resid 176 through 184 Processing helix chain 'R' and resid 193 through 208 removed outlier: 3.756A pdb=" N PHE R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 248 through 272 removed outlier: 3.568A pdb=" N PHE R 252 " --> pdb=" O HIS R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 288 Processing helix chain 'R' and resid 292 through 307 removed outlier: 3.527A pdb=" N LEU R 307 " --> pdb=" O VAL R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 325 removed outlier: 3.734A pdb=" N PHE R 318 " --> pdb=" O SER R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 341 removed outlier: 3.993A pdb=" N ILE R 333 " --> pdb=" O GLU R 329 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA R 334 " --> pdb=" O ASP R 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET R 335 " --> pdb=" O PHE R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 359 Processing helix chain 'R' and resid 363 through 375 Processing helix chain 'R' and resid 383 through 395 Processing helix chain 'I' and resid 107 through 119 removed outlier: 3.817A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 Processing helix chain 'I' and resid 172 through 191 removed outlier: 4.286A pdb=" N LEU I 176 " --> pdb=" O ASN I 172 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASP I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN I 184 " --> pdb=" O LYS I 180 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 256 removed outlier: 3.779A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN I 198 " --> pdb=" O GLN I 194 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 4.708A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG I 231 " --> pdb=" O LYS I 227 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET I 243 " --> pdb=" O GLY I 239 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU I 250 " --> pdb=" O GLN I 246 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG I 252 " --> pdb=" O GLY I 248 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU I 253 " --> pdb=" O ILE I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 262 Processing helix chain 'I' and resid 263 through 285 removed outlier: 3.833A pdb=" N PHE I 269 " --> pdb=" O PRO I 265 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 310 removed outlier: 4.122A pdb=" N LEU I 300 " --> pdb=" O ASP I 296 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 340 removed outlier: 3.586A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 65 through 95 removed outlier: 3.927A pdb=" N PHE J 71 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Proline residue: J 76 - end of helix removed outlier: 3.554A pdb=" N LYS J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 107 through 119 Processing helix chain 'K' and resid 140 through 146 Processing helix chain 'K' and resid 171 through 190 removed outlier: 3.908A pdb=" N THR K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 215 removed outlier: 3.820A pdb=" N HIS K 195 " --> pdb=" O CYS K 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU K 214 " --> pdb=" O LEU K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 255 removed outlier: 3.680A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE K 224 " --> pdb=" O VAL K 220 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET K 243 " --> pdb=" O GLY K 239 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU K 250 " --> pdb=" O GLN K 246 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP K 255 " --> pdb=" O ALA K 251 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 removed outlier: 3.785A pdb=" N MET K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) Proline residue: K 265 - end of helix removed outlier: 3.540A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 311 Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.559A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 95 removed outlier: 3.668A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Proline residue: L 76 - end of helix removed outlier: 3.593A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE L 88 " --> pdb=" O ILE L 84 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.523A pdb=" N PHE M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 169 through 190 Processing helix chain 'M' and resid 191 through 213 removed outlier: 3.600A pdb=" N HIS M 195 " --> pdb=" O CYS M 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU M 197 " --> pdb=" O GLU M 193 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU M 200 " --> pdb=" O GLN M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 256 removed outlier: 4.625A pdb=" N LEU M 217 " --> pdb=" O GLN M 213 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS M 219 " --> pdb=" O ALA M 215 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU M 223 " --> pdb=" O LYS M 219 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU M 253 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR M 254 " --> pdb=" O LEU M 250 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP M 255 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 285 removed outlier: 3.912A pdb=" N MET M 263 " --> pdb=" O SER M 259 " (cutoff:3.500A) Proline residue: M 265 - end of helix removed outlier: 3.971A pdb=" N THR M 271 " --> pdb=" O THR M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 311 removed outlier: 3.567A pdb=" N LEU M 300 " --> pdb=" O ASP M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 335 removed outlier: 3.794A pdb=" N LEU M 320 " --> pdb=" O LYS M 316 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA M 325 " --> pdb=" O LYS M 321 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 95 removed outlier: 3.915A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Proline residue: N 76 - end of helix removed outlier: 3.665A pdb=" N TYR N 79 " --> pdb=" O ILE N 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.944A pdb=" N ASP O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 145 Processing helix chain 'O' and resid 178 through 191 removed outlier: 3.667A pdb=" N THR O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU O 190 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS O 191 " --> pdb=" O TYR O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 257 removed outlier: 3.683A pdb=" N ARG O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.980A pdb=" N LYS O 219 " --> pdb=" O ALA O 215 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL O 220 " --> pdb=" O PRO O 216 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU O 234 " --> pdb=" O LYS O 230 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU O 240 " --> pdb=" O LEU O 236 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR O 254 " --> pdb=" O LEU O 250 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TRP O 255 " --> pdb=" O ALA O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 263 through 286 removed outlier: 3.673A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 310 Processing helix chain 'O' and resid 313 through 334 removed outlier: 3.761A pdb=" N GLN O 319 " --> pdb=" O GLU O 315 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG O 333 " --> pdb=" O MET O 329 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU O 334 " --> pdb=" O ASP O 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 93 removed outlier: 3.685A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.618A pdb=" N GLY P 81 " --> pdb=" O PHE P 77 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU P 91 " --> pdb=" O ASN P 87 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLU P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 122 removed outlier: 3.755A pdb=" N TYR S 114 " --> pdb=" O LYS S 110 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN S 116 " --> pdb=" O MET S 112 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG S 117 " --> pdb=" O GLU S 113 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE S 118 " --> pdb=" O TYR S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 132 removed outlier: 3.582A pdb=" N PHE S 131 " --> pdb=" O ILE S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 157 removed outlier: 3.643A pdb=" N ARG S 154 " --> pdb=" O GLU S 150 " (cutoff:3.500A) Processing helix chain 'S' and resid 194 through 199 removed outlier: 3.834A pdb=" N GLY S 199 " --> pdb=" O PHE S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 217 removed outlier: 3.608A pdb=" N ILE S 210 " --> pdb=" O PHE S 206 " (cutoff:3.500A) Processing helix chain 'S' and resid 219 through 231 removed outlier: 3.892A pdb=" N ILE S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 252 removed outlier: 3.504A pdb=" N PHE S 243 " --> pdb=" O ASP S 239 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE S 249 " --> pdb=" O GLN S 245 " (cutoff:3.500A) Processing helix chain 'S' and resid 278 through 283 Processing helix chain 'S' and resid 292 through 315 removed outlier: 3.729A pdb=" N PHE S 296 " --> pdb=" O THR S 292 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN S 300 " --> pdb=" O PHE S 296 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N HIS S 315 " --> pdb=" O GLU S 311 " (cutoff:3.500A) Processing helix chain 'S' and resid 323 through 336 Processing helix chain 'S' and resid 339 through 353 removed outlier: 3.512A pdb=" N ARG S 347 " --> pdb=" O THR S 343 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS S 350 " --> pdb=" O GLN S 346 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYS S 351 " --> pdb=" O ARG S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 361 through 373 removed outlier: 3.653A pdb=" N THR S 369 " --> pdb=" O GLU S 365 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN S 373 " --> pdb=" O THR S 369 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 386 removed outlier: 4.107A pdb=" N THR S 379 " --> pdb=" O ASN S 375 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ALA S 380 " --> pdb=" O ASP S 376 " (cutoff:3.500A) Processing helix chain 'S' and resid 392 through 403 removed outlier: 3.506A pdb=" N MET S 396 " --> pdb=" O ASP S 392 " (cutoff:3.500A) Processing helix chain 'S' and resid 409 through 421 Processing helix chain 'S' and resid 433 through 443 Processing helix chain 'T' and resid 86 through 93 removed outlier: 3.611A pdb=" N PHE T 90 " --> pdb=" O ARG T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 128 through 137 Processing helix chain 'T' and resid 138 through 142 Processing helix chain 'T' and resid 147 through 153 Processing helix chain 'T' and resid 159 through 172 Processing helix chain 'T' and resid 176 through 184 Processing helix chain 'T' and resid 193 through 208 removed outlier: 3.756A pdb=" N PHE T 197 " --> pdb=" O GLU T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 248 through 272 removed outlier: 3.569A pdb=" N PHE T 252 " --> pdb=" O HIS T 248 " (cutoff:3.500A) Processing helix chain 'T' and resid 279 through 288 Processing helix chain 'T' and resid 292 through 307 removed outlier: 3.527A pdb=" N LEU T 307 " --> pdb=" O VAL T 303 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 325 removed outlier: 3.733A pdb=" N PHE T 318 " --> pdb=" O SER T 314 " (cutoff:3.500A) Processing helix chain 'T' and resid 327 through 341 removed outlier: 3.993A pdb=" N ILE T 333 " --> pdb=" O GLU T 329 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA T 334 " --> pdb=" O ASP T 330 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N MET T 335 " --> pdb=" O PHE T 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 359 Processing helix chain 'T' and resid 363 through 375 Processing helix chain 'T' and resid 383 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.501A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG A 96 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE C 127 " --> pdb=" O VAL C 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 80 Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.650A pdb=" N ARG G 134 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 126 through 128 Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 78 removed outlier: 4.122A pdb=" N THR G 76 " --> pdb=" O SER G 87 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL G 78 " --> pdb=" O VAL G 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.576A pdb=" N TYR G 158 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 321 through 322 Processing sheet with id=AA9, first strand: chain 'R' and resid 101 through 103 removed outlier: 3.979A pdb=" N LEU R 96 " --> pdb=" O TYR R 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 76 through 80 removed outlier: 6.489A pdb=" N ARG I 96 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE K 127 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB4, first strand: chain 'M' and resid 76 through 80 removed outlier: 3.621A pdb=" N ARG O 134 " --> pdb=" O ARG M 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 126 through 128 removed outlier: 3.518A pdb=" N LEU M 156 " --> pdb=" O ILE M 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 76 through 78 removed outlier: 4.165A pdb=" N THR O 76 " --> pdb=" O SER O 87 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL O 78 " --> pdb=" O VAL O 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 126 through 128 removed outlier: 3.532A pdb=" N TYR O 158 " --> pdb=" O LEU O 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 321 through 322 Processing sheet with id=AB9, first strand: chain 'T' and resid 101 through 103 removed outlier: 3.979A pdb=" N LEU T 96 " --> pdb=" O TYR T 103 " (cutoff:3.500A) 1824 hydrogen bonds defined for protein. 5337 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: 4.59 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9308 1.34 - 1.46: 6538 1.46 - 1.58: 14451 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 30529 Sorted by residual: bond pdb=" C PRO C 162 " pdb=" N PRO C 163 " ideal model delta sigma weight residual 1.337 1.412 -0.075 9.80e-03 1.04e+04 5.87e+01 bond pdb=" C VAL J 99 " pdb=" N PRO J 100 " ideal model delta sigma weight residual 1.332 1.434 -0.102 1.34e-02 5.57e+03 5.79e+01 bond pdb=" C ILE L 75 " pdb=" N PRO L 76 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.85e+01 bond pdb=" C TYR I 291 " pdb=" N PRO I 292 " ideal model delta sigma weight residual 1.336 1.378 -0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" CA THR E 157 " pdb=" CB THR E 157 " ideal model delta sigma weight residual 1.524 1.488 0.036 1.33e-02 5.65e+03 7.35e+00 ... (remaining 30524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 40047 2.55 - 5.10: 919 5.10 - 7.65: 163 7.65 - 10.20: 48 10.20 - 12.75: 4 Bond angle restraints: 41181 Sorted by residual: angle pdb=" N ILE F 73 " pdb=" CA ILE F 73 " pdb=" C ILE F 73 " ideal model delta sigma weight residual 112.96 107.58 5.38 1.00e+00 1.00e+00 2.90e+01 angle pdb=" N PRO C 162 " pdb=" CA PRO C 162 " pdb=" C PRO C 162 " ideal model delta sigma weight residual 110.70 117.02 -6.32 1.22e+00 6.72e-01 2.68e+01 angle pdb=" CA PRO C 162 " pdb=" C PRO C 162 " pdb=" N PRO C 163 " ideal model delta sigma weight residual 117.93 124.15 -6.22 1.20e+00 6.94e-01 2.68e+01 angle pdb=" N ILE K 153 " pdb=" CA ILE K 153 " pdb=" C ILE K 153 " ideal model delta sigma weight residual 109.46 102.32 7.14 1.38e+00 5.25e-01 2.68e+01 angle pdb=" C ASN E 154 " pdb=" N ASP E 155 " pdb=" CA ASP E 155 " ideal model delta sigma weight residual 121.54 131.33 -9.79 1.91e+00 2.74e-01 2.63e+01 ... (remaining 41176 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 17409 15.89 - 31.78: 792 31.78 - 47.66: 252 47.66 - 63.55: 6 63.55 - 79.44: 24 Dihedral angle restraints: 18483 sinusoidal: 7752 harmonic: 10731 Sorted by residual: dihedral pdb=" CA PRO A 91 " pdb=" C PRO A 91 " pdb=" N SER A 92 " pdb=" CA SER A 92 " ideal model delta harmonic sigma weight residual -180.00 -135.94 -44.06 0 5.00e+00 4.00e-02 7.77e+01 dihedral pdb=" CA PRO I 91 " pdb=" C PRO I 91 " pdb=" N SER I 92 " pdb=" CA SER I 92 " ideal model delta harmonic sigma weight residual 180.00 -136.69 -43.31 0 5.00e+00 4.00e-02 7.50e+01 dihedral pdb=" CA ARG K 161 " pdb=" C ARG K 161 " pdb=" N PRO K 162 " pdb=" CA PRO K 162 " ideal model delta harmonic sigma weight residual 180.00 146.46 33.54 0 5.00e+00 4.00e-02 4.50e+01 ... (remaining 18480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3664 0.067 - 0.134: 832 0.134 - 0.202: 93 0.202 - 0.269: 21 0.269 - 0.336: 3 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CB VAL B 99 " pdb=" CA VAL B 99 " pdb=" CG1 VAL B 99 " pdb=" CG2 VAL B 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CB ILE J 97 " pdb=" CA ILE J 97 " pdb=" CG1 ILE J 97 " pdb=" CG2 ILE J 97 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE O 153 " pdb=" CA ILE O 153 " pdb=" CG1 ILE O 153 " pdb=" CG2 ILE O 153 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 4610 not shown) Planarity restraints: 5211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 161 " 0.074 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO K 162 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 99 " 0.061 5.00e-02 4.00e+02 9.14e-02 1.34e+01 pdb=" N PRO B 100 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO B 100 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 100 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 161 " 0.061 5.00e-02 4.00e+02 9.07e-02 1.32e+01 pdb=" N PRO C 162 " -0.157 5.00e-02 4.00e+02 pdb=" CA PRO C 162 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 162 " 0.050 5.00e-02 4.00e+02 ... (remaining 5208 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5669 2.77 - 3.30: 28497 3.30 - 3.84: 49754 3.84 - 4.37: 55133 4.37 - 4.90: 92909 Nonbonded interactions: 231962 Sorted by model distance: nonbonded pdb=" O PHE R 90 " pdb=" OG SER R 94 " model vdw 2.238 3.040 nonbonded pdb=" O PHE T 90 " pdb=" OG SER T 94 " model vdw 2.238 3.040 nonbonded pdb=" OG SER R 363 " pdb=" OD1 ASN R 365 " model vdw 2.267 3.040 nonbonded pdb=" OG SER T 363 " pdb=" OD1 ASN T 365 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR T 186 " pdb=" OE2 GLU T 196 " model vdw 2.283 3.040 ... (remaining 231957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'G' selection = (chain 'I' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 177 through 336)) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 49 through 95) selection = (chain 'D' and resid 49 through 95) selection = (chain 'F' and resid 49 through 95) selection = (chain 'H' and resid 49 through 95) selection = (chain 'J' and resid 49 through 95) selection = (chain 'L' and resid 49 through 95) selection = (chain 'N' and resid 49 through 95) selection = (chain 'P' and resid 49 through 95) } ncs_group { reference = chain 'Q' selection = (chain 'S' and (resid 108 through 134 or resid 145 through 443)) } ncs_group { reference = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.320 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 : 0.006 0.102 30529 Z= 0.282 Angle : 1.012 12.747 41181 Z= 0.539 Chirality : 0.056 0.336 4613 Planarity : 0.007 0.112 5211 Dihedral : 10.807 79.438 11517 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 0.27 % Allowed : 4.40 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.09 % 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: -3.26 (0.12), residues: 3585 helix: -1.94 (0.08), residues: 2323 sheet: -1.68 (0.37), residues: 172 loop : -2.30 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 134 TYR 0.030 0.002 TYR G 79 PHE 0.059 0.003 PHE Q 296 TRP 0.028 0.003 TRP E 255 HIS 0.016 0.002 HIS S 385 Details of bonding type rmsd covalent geometry : bond 0.00598 (30529) covalent geometry : angle 1.01247 (41181) hydrogen bonds : bond 0.15014 ( 1824) hydrogen bonds : angle 6.63201 ( 5337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 814 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7791 (tm-30) REVERT: A 246 GLN cc_start: 0.8564 (tm130) cc_final: 0.8350 (tp40) REVERT: A 296 ASP cc_start: 0.8645 (m-30) cc_final: 0.8310 (m-30) REVERT: B 79 TYR cc_start: 0.7573 (t80) cc_final: 0.7340 (t80) REVERT: B 97 ILE cc_start: 0.7493 (mt) cc_final: 0.7228 (mt) REVERT: C 290 VAL cc_start: 0.8886 (t) cc_final: 0.8599 (m) REVERT: D 67 LEU cc_start: 0.8162 (tm) cc_final: 0.6625 (pt) REVERT: D 79 TYR cc_start: 0.8068 (t80) cc_final: 0.7324 (m-10) REVERT: E 250 LEU cc_start: 0.8751 (mm) cc_final: 0.8297 (tp) REVERT: E 278 MET cc_start: 0.8440 (mtm) cc_final: 0.8208 (mpp) REVERT: E 298 GLN cc_start: 0.8368 (tp-100) cc_final: 0.7824 (tp-100) REVERT: F 71 PHE cc_start: 0.8470 (m-80) cc_final: 0.8245 (m-10) REVERT: F 75 ILE cc_start: 0.8967 (mm) cc_final: 0.8723 (pt) REVERT: G 127 ILE cc_start: 0.8708 (mt) cc_final: 0.8507 (mm) REVERT: H 88 PHE cc_start: 0.8159 (t80) cc_final: 0.7167 (t80) REVERT: Q 319 ASP cc_start: 0.8422 (m-30) cc_final: 0.8049 (p0) REVERT: Q 436 ILE cc_start: 0.8911 (mt) cc_final: 0.8671 (tp) REVERT: R 164 LEU cc_start: 0.9309 (mt) cc_final: 0.9040 (mt) REVERT: R 373 ILE cc_start: 0.9118 (mt) cc_final: 0.8731 (mt) REVERT: I 246 GLN cc_start: 0.8637 (tm130) cc_final: 0.8167 (tm-30) REVERT: I 256 TRP cc_start: 0.7598 (m-90) cc_final: 0.7174 (m-90) REVERT: I 296 ASP cc_start: 0.8577 (m-30) cc_final: 0.8227 (m-30) REVERT: J 79 TYR cc_start: 0.7184 (t80) cc_final: 0.6960 (t80) REVERT: K 284 MET cc_start: 0.8686 (mtp) cc_final: 0.8318 (ttm) REVERT: L 67 LEU cc_start: 0.8039 (tm) cc_final: 0.7419 (pp) REVERT: L 84 ILE cc_start: 0.9529 (tt) cc_final: 0.9200 (tp) REVERT: M 298 GLN cc_start: 0.8336 (tp-100) cc_final: 0.7809 (tp-100) REVERT: N 73 ILE cc_start: 0.8676 (mt) cc_final: 0.8447 (mt) REVERT: N 97 ILE cc_start: 0.8746 (mt) cc_final: 0.8525 (mm) REVERT: O 127 ILE cc_start: 0.8716 (mt) cc_final: 0.8470 (mm) REVERT: O 186 LEU cc_start: 0.8322 (tp) cc_final: 0.8088 (tt) REVERT: P 88 PHE cc_start: 0.8028 (t80) cc_final: 0.7137 (t80) REVERT: S 311 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7836 (tp30) REVERT: S 319 ASP cc_start: 0.8685 (m-30) cc_final: 0.8252 (p0) REVERT: S 322 ILE cc_start: 0.8385 (pt) cc_final: 0.7267 (pt) REVERT: T 373 ILE cc_start: 0.9121 (mt) cc_final: 0.8745 (mt) outliers start: 9 outliers final: 2 residues processed: 821 average time/residue: 0.2243 time to fit residues: 277.6168 Evaluate side-chains 361 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 213 GLN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN D 95 HIS E 159 HIS E 172 ASN E 339 GLN Q 247 GLN Q 373 ASN R 295 ASN R 302 ASN R 323 HIS R 393 ASN I 195 HIS K 114 GLN ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 159 HIS M 172 ASN M 184 GLN M 196 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 339 GLN ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 247 GLN S 373 ASN T 295 ASN T 302 ASN T 323 HIS T 393 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.062042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.052901 restraints weight = 192192.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.053416 restraints weight = 130812.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.053896 restraints weight = 93186.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.054079 restraints weight = 81116.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.054171 restraints weight = 73435.717| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30529 Z= 0.146 Angle : 0.661 7.939 41181 Z= 0.342 Chirality : 0.042 0.176 4613 Planarity : 0.005 0.083 5211 Dihedral : 5.491 37.085 4021 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.07 % Rotamer: Outliers : 0.09 % Allowed : 2.75 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.13), residues: 3585 helix: -0.34 (0.10), residues: 2357 sheet: -1.40 (0.36), residues: 172 loop : -1.86 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG Q 129 TYR 0.033 0.001 TYR O 268 PHE 0.034 0.002 PHE R 252 TRP 0.016 0.001 TRP T 286 HIS 0.015 0.001 HIS R 248 Details of bonding type rmsd covalent geometry : bond 0.00308 (30529) covalent geometry : angle 0.66124 (41181) hydrogen bonds : bond 0.04493 ( 1824) hydrogen bonds : angle 4.88740 ( 5337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 519 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8562 (pp30) cc_final: 0.8221 (pp30) REVERT: A 246 GLN cc_start: 0.8529 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 79 TYR cc_start: 0.7571 (t80) cc_final: 0.7222 (t80) REVERT: C 263 MET cc_start: 0.7708 (mmm) cc_final: 0.7490 (mmt) REVERT: C 288 GLU cc_start: 0.8036 (tp30) cc_final: 0.7831 (tp30) REVERT: D 67 LEU cc_start: 0.8301 (tt) cc_final: 0.7457 (pt) REVERT: E 214 LEU cc_start: 0.8595 (tt) cc_final: 0.8223 (tt) REVERT: E 250 LEU cc_start: 0.8749 (mm) cc_final: 0.8302 (tp) REVERT: E 298 GLN cc_start: 0.8526 (tp-100) cc_final: 0.7910 (tp-100) REVERT: F 67 LEU cc_start: 0.8438 (tp) cc_final: 0.8199 (pt) REVERT: H 88 PHE cc_start: 0.8077 (t80) cc_final: 0.7131 (t80) REVERT: Q 334 TYR cc_start: 0.7271 (t80) cc_final: 0.6894 (t80) REVERT: Q 345 MET cc_start: 0.8584 (mtt) cc_final: 0.8360 (mtt) REVERT: R 335 MET cc_start: 0.7933 (mtp) cc_final: 0.7714 (mtp) REVERT: R 364 ASN cc_start: 0.8714 (t0) cc_final: 0.8265 (m110) REVERT: R 373 ILE cc_start: 0.9051 (mt) cc_final: 0.8597 (mt) REVERT: J 79 TYR cc_start: 0.7275 (t80) cc_final: 0.6887 (t80) REVERT: K 150 LYS cc_start: 0.8275 (mttt) cc_final: 0.8033 (mttp) REVERT: K 284 MET cc_start: 0.8639 (mtp) cc_final: 0.8288 (ttm) REVERT: K 288 GLU cc_start: 0.8228 (tp30) cc_final: 0.7903 (tp30) REVERT: K 290 VAL cc_start: 0.8819 (t) cc_final: 0.8290 (m) REVERT: K 312 PHE cc_start: 0.5582 (p90) cc_final: 0.5278 (p90) REVERT: M 298 GLN cc_start: 0.8493 (tp-100) cc_final: 0.7853 (tp-100) REVERT: O 127 ILE cc_start: 0.8710 (mt) cc_final: 0.8488 (mm) REVERT: O 186 LEU cc_start: 0.8361 (tp) cc_final: 0.8094 (tt) REVERT: O 284 MET cc_start: 0.8047 (ptm) cc_final: 0.7154 (tmm) REVERT: P 88 PHE cc_start: 0.7938 (t80) cc_final: 0.7054 (t80) REVERT: S 311 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7937 (tp30) REVERT: S 334 TYR cc_start: 0.7465 (t80) cc_final: 0.7192 (t80) REVERT: S 345 MET cc_start: 0.8569 (mtm) cc_final: 0.8124 (mtm) REVERT: S 368 PHE cc_start: 0.8277 (m-80) cc_final: 0.7996 (m-80) REVERT: S 384 TYR cc_start: 0.7265 (t80) cc_final: 0.7035 (t80) REVERT: S 390 SER cc_start: 0.8124 (m) cc_final: 0.7714 (p) REVERT: S 437 MET cc_start: 0.7539 (tpt) cc_final: 0.7068 (tpt) REVERT: T 364 ASN cc_start: 0.8714 (t0) cc_final: 0.8329 (m110) REVERT: T 373 ILE cc_start: 0.9124 (mt) cc_final: 0.8681 (mt) outliers start: 3 outliers final: 0 residues processed: 522 average time/residue: 0.1791 time to fit residues: 151.6175 Evaluate side-chains 328 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 350 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 345 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 334 optimal weight: 20.0000 chunk 330 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 195 HIS ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN E 196 GLN E 304 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 GLN Q 346 GLN Q 352 HIS ** R 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 304 HIS ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 315 HIS ** S 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 393 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.059096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.048881 restraints weight = 202537.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049811 restraints weight = 132293.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.050467 restraints weight = 95878.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.050931 restraints weight = 75082.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051265 restraints weight = 62320.900| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30529 Z= 0.253 Angle : 0.732 11.781 41181 Z= 0.382 Chirality : 0.045 0.173 4613 Planarity : 0.006 0.087 5211 Dihedral : 5.325 34.349 4021 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.08 % Favored : 94.87 % Rotamer: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.14), residues: 3585 helix: 0.25 (0.10), residues: 2373 sheet: -1.23 (0.35), residues: 178 loop : -1.86 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG T 254 TYR 0.025 0.002 TYR O 268 PHE 0.021 0.002 PHE Q 223 TRP 0.019 0.002 TRP R 286 HIS 0.006 0.002 HIS Q 385 Details of bonding type rmsd covalent geometry : bond 0.00545 (30529) covalent geometry : angle 0.73239 (41181) hydrogen bonds : bond 0.04493 ( 1824) hydrogen bonds : angle 4.80559 ( 5337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 415 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8789 (pp30) cc_final: 0.8312 (pp30) REVERT: A 263 MET cc_start: 0.9379 (mtp) cc_final: 0.8821 (mtt) REVERT: B 79 TYR cc_start: 0.7510 (t80) cc_final: 0.7221 (t80) REVERT: C 263 MET cc_start: 0.8291 (mmm) cc_final: 0.7836 (mmt) REVERT: C 288 GLU cc_start: 0.8295 (tp30) cc_final: 0.8015 (tp30) REVERT: D 67 LEU cc_start: 0.8188 (tt) cc_final: 0.7319 (pt) REVERT: E 250 LEU cc_start: 0.8720 (mm) cc_final: 0.8236 (tp) REVERT: H 88 PHE cc_start: 0.8138 (t80) cc_final: 0.7374 (t80) REVERT: Q 345 MET cc_start: 0.8803 (mtt) cc_final: 0.8445 (mtp) REVERT: Q 368 PHE cc_start: 0.8574 (m-80) cc_final: 0.8207 (m-80) REVERT: R 179 VAL cc_start: 0.9162 (m) cc_final: 0.8959 (p) REVERT: R 335 MET cc_start: 0.7926 (mtp) cc_final: 0.7694 (mtp) REVERT: I 296 ASP cc_start: 0.8919 (m-30) cc_final: 0.8696 (m-30) REVERT: J 79 TYR cc_start: 0.7319 (t80) cc_final: 0.6867 (t80) REVERT: K 284 MET cc_start: 0.8842 (mtp) cc_final: 0.8472 (ttm) REVERT: K 288 GLU cc_start: 0.8356 (tp30) cc_final: 0.8129 (tp30) REVERT: K 290 VAL cc_start: 0.9141 (t) cc_final: 0.8888 (m) REVERT: M 278 MET cc_start: 0.8748 (mtt) cc_final: 0.8402 (mpp) REVERT: M 298 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8210 (tp-100) REVERT: N 73 ILE cc_start: 0.8769 (mm) cc_final: 0.8538 (mm) REVERT: O 186 LEU cc_start: 0.8682 (tp) cc_final: 0.8411 (tt) REVERT: P 88 PHE cc_start: 0.7830 (t80) cc_final: 0.6836 (t80) REVERT: S 311 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8313 (mm-30) REVERT: S 334 TYR cc_start: 0.7776 (t80) cc_final: 0.7300 (t80) REVERT: S 345 MET cc_start: 0.8913 (mtm) cc_final: 0.8237 (ptp) REVERT: S 368 PHE cc_start: 0.8359 (m-80) cc_final: 0.8018 (m-80) outliers start: 5 outliers final: 0 residues processed: 420 average time/residue: 0.1774 time to fit residues: 121.4483 Evaluate side-chains 304 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 315 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 310 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 293 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 222 optimal weight: 10.0000 chunk 228 optimal weight: 9.9990 chunk 337 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN C 159 HIS C 177 ASN ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 116 ASN Q 295 ASN R 323 HIS ** K 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 HIS M 184 GLN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.059320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.049672 restraints weight = 194934.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050402 restraints weight = 136000.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051054 restraints weight = 91623.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051344 restraints weight = 72023.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.051394 restraints weight = 65168.045| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30529 Z= 0.207 Angle : 0.674 11.531 41181 Z= 0.348 Chirality : 0.043 0.170 4613 Planarity : 0.005 0.080 5211 Dihedral : 5.130 34.648 4021 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3585 helix: 0.63 (0.10), residues: 2373 sheet: -1.21 (0.36), residues: 182 loop : -1.76 (0.20), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 129 TYR 0.023 0.002 TYR S 130 PHE 0.025 0.002 PHE Q 223 TRP 0.020 0.002 TRP A 260 HIS 0.013 0.001 HIS Q 385 Details of bonding type rmsd covalent geometry : bond 0.00450 (30529) covalent geometry : angle 0.67410 (41181) hydrogen bonds : bond 0.04171 ( 1824) hydrogen bonds : angle 4.66072 ( 5337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8853 (pp30) cc_final: 0.8420 (pp30) REVERT: A 263 MET cc_start: 0.9408 (mtp) cc_final: 0.9031 (mtt) REVERT: A 296 ASP cc_start: 0.8857 (m-30) cc_final: 0.8651 (m-30) REVERT: A 329 MET cc_start: 0.8502 (tmm) cc_final: 0.8281 (tmm) REVERT: C 263 MET cc_start: 0.8230 (mmm) cc_final: 0.7729 (mmt) REVERT: D 67 LEU cc_start: 0.8118 (tt) cc_final: 0.7565 (pt) REVERT: H 88 PHE cc_start: 0.8279 (t80) cc_final: 0.7255 (t80) REVERT: Q 345 MET cc_start: 0.8900 (mtt) cc_final: 0.8409 (mtp) REVERT: Q 368 PHE cc_start: 0.8569 (m-80) cc_final: 0.8210 (m-80) REVERT: R 179 VAL cc_start: 0.9178 (m) cc_final: 0.8953 (p) REVERT: R 335 MET cc_start: 0.7944 (mtp) cc_final: 0.7692 (mtp) REVERT: I 296 ASP cc_start: 0.8875 (m-30) cc_final: 0.8666 (m-30) REVERT: J 79 TYR cc_start: 0.7370 (t80) cc_final: 0.6912 (t80) REVERT: K 284 MET cc_start: 0.8804 (mtp) cc_final: 0.8425 (ttm) REVERT: K 288 GLU cc_start: 0.8294 (tp30) cc_final: 0.8052 (tp30) REVERT: M 278 MET cc_start: 0.8749 (mtt) cc_final: 0.8407 (mpp) REVERT: N 73 ILE cc_start: 0.8712 (mm) cc_final: 0.8484 (mm) REVERT: O 127 ILE cc_start: 0.8971 (mt) cc_final: 0.8741 (mm) REVERT: O 186 LEU cc_start: 0.8653 (tp) cc_final: 0.8410 (tt) REVERT: O 284 MET cc_start: 0.8131 (ptt) cc_final: 0.7178 (tmm) REVERT: P 88 PHE cc_start: 0.7999 (t80) cc_final: 0.6979 (t80) REVERT: S 311 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8327 (mm-30) REVERT: S 345 MET cc_start: 0.8965 (mtm) cc_final: 0.8331 (ptp) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.1689 time to fit residues: 111.5464 Evaluate side-chains 281 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 272 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 273 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 336 optimal weight: 7.9990 chunk 91 optimal weight: 0.1980 chunk 253 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 295 ASN ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 177 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 295 ASN ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 323 HIS T 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050327 restraints weight = 195325.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051092 restraints weight = 141593.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.051651 restraints weight = 95037.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.051954 restraints weight = 75864.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.052037 restraints weight = 66483.182| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30529 Z= 0.140 Angle : 0.617 9.959 41181 Z= 0.317 Chirality : 0.042 0.172 4613 Planarity : 0.005 0.081 5211 Dihedral : 4.980 33.860 4021 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3585 helix: 0.95 (0.11), residues: 2370 sheet: -1.16 (0.35), residues: 182 loop : -1.77 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 251 TYR 0.029 0.001 TYR R 299 PHE 0.024 0.001 PHE Q 223 TRP 0.017 0.001 TRP R 286 HIS 0.013 0.001 HIS Q 385 Details of bonding type rmsd covalent geometry : bond 0.00307 (30529) covalent geometry : angle 0.61661 (41181) hydrogen bonds : bond 0.03933 ( 1824) hydrogen bonds : angle 4.45700 ( 5337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8273 (tp) cc_final: 0.7795 (tp) REVERT: A 263 MET cc_start: 0.9383 (mtp) cc_final: 0.9039 (mtt) REVERT: C 263 MET cc_start: 0.8055 (mmm) cc_final: 0.7609 (mmt) REVERT: E 250 LEU cc_start: 0.8859 (mm) cc_final: 0.8389 (tp) REVERT: H 88 PHE cc_start: 0.8219 (t80) cc_final: 0.7176 (t80) REVERT: Q 345 MET cc_start: 0.8820 (mtt) cc_final: 0.8342 (mtp) REVERT: Q 368 PHE cc_start: 0.8588 (m-80) cc_final: 0.8205 (m-80) REVERT: R 179 VAL cc_start: 0.9134 (m) cc_final: 0.8909 (p) REVERT: R 266 MET cc_start: 0.8268 (mmp) cc_final: 0.8007 (mmt) REVERT: R 335 MET cc_start: 0.7935 (mtp) cc_final: 0.7693 (mtp) REVERT: J 79 TYR cc_start: 0.7360 (t80) cc_final: 0.6897 (t80) REVERT: K 243 MET cc_start: 0.9446 (ttp) cc_final: 0.9046 (ttp) REVERT: K 284 MET cc_start: 0.8725 (mtp) cc_final: 0.8297 (ttm) REVERT: K 288 GLU cc_start: 0.8324 (tp30) cc_final: 0.8093 (tp30) REVERT: K 290 VAL cc_start: 0.9043 (t) cc_final: 0.8784 (m) REVERT: M 278 MET cc_start: 0.8651 (mtt) cc_final: 0.8386 (mpp) REVERT: N 73 ILE cc_start: 0.8725 (mm) cc_final: 0.8493 (mm) REVERT: O 127 ILE cc_start: 0.8923 (mt) cc_final: 0.8719 (mm) REVERT: O 186 LEU cc_start: 0.8583 (tp) cc_final: 0.8322 (tt) REVERT: O 284 MET cc_start: 0.8027 (ptt) cc_final: 0.7173 (tmm) REVERT: P 88 PHE cc_start: 0.7908 (t80) cc_final: 0.6912 (t80) REVERT: S 311 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8279 (mm-30) REVERT: S 345 MET cc_start: 0.8869 (mtm) cc_final: 0.8449 (mtp) REVERT: S 368 PHE cc_start: 0.8253 (m-80) cc_final: 0.7891 (m-80) REVERT: T 179 VAL cc_start: 0.9092 (m) cc_final: 0.8862 (p) REVERT: T 266 MET cc_start: 0.8274 (mmp) cc_final: 0.7989 (mmt) REVERT: T 335 MET cc_start: 0.7856 (mtp) cc_final: 0.7616 (mtp) outliers start: 0 outliers final: 0 residues processed: 393 average time/residue: 0.1645 time to fit residues: 109.7645 Evaluate side-chains 291 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 134 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 139 optimal weight: 0.0020 chunk 340 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 overall best weight: 2.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.050302 restraints weight = 194591.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.051133 restraints weight = 143874.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.051757 restraints weight = 94161.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.052181 restraints weight = 73688.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.052202 restraints weight = 64035.431| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30529 Z= 0.144 Angle : 0.607 11.029 41181 Z= 0.310 Chirality : 0.042 0.217 4613 Planarity : 0.004 0.077 5211 Dihedral : 4.817 32.859 4021 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.49 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.14), residues: 3585 helix: 1.07 (0.11), residues: 2376 sheet: -1.13 (0.35), residues: 182 loop : -1.71 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 252 TYR 0.019 0.001 TYR E 268 PHE 0.022 0.001 PHE Q 223 TRP 0.018 0.001 TRP R 286 HIS 0.014 0.001 HIS Q 385 Details of bonding type rmsd covalent geometry : bond 0.00316 (30529) covalent geometry : angle 0.60733 (41181) hydrogen bonds : bond 0.03800 ( 1824) hydrogen bonds : angle 4.36095 ( 5337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8818 (pp30) cc_final: 0.8568 (pp30) REVERT: A 145 LEU cc_start: 0.8315 (tp) cc_final: 0.7826 (tp) REVERT: A 263 MET cc_start: 0.9340 (mtp) cc_final: 0.8872 (mtt) REVERT: A 296 ASP cc_start: 0.8685 (m-30) cc_final: 0.8151 (p0) REVERT: C 263 MET cc_start: 0.7984 (mmm) cc_final: 0.7573 (mmt) REVERT: E 250 LEU cc_start: 0.8809 (mm) cc_final: 0.8326 (tp) REVERT: H 88 PHE cc_start: 0.8102 (t80) cc_final: 0.7049 (t80) REVERT: Q 345 MET cc_start: 0.8831 (mtt) cc_final: 0.8379 (mtp) REVERT: Q 368 PHE cc_start: 0.8576 (m-80) cc_final: 0.8189 (m-80) REVERT: R 179 VAL cc_start: 0.9118 (m) cc_final: 0.8900 (p) REVERT: R 335 MET cc_start: 0.7904 (mtp) cc_final: 0.7666 (mtp) REVERT: I 145 LEU cc_start: 0.8239 (tp) cc_final: 0.7679 (tp) REVERT: J 79 TYR cc_start: 0.7355 (t80) cc_final: 0.6899 (t80) REVERT: K 284 MET cc_start: 0.8675 (mtp) cc_final: 0.8242 (ttm) REVERT: M 243 MET cc_start: 0.8009 (ptp) cc_final: 0.7480 (ptm) REVERT: N 73 ILE cc_start: 0.8770 (mm) cc_final: 0.8544 (mm) REVERT: O 127 ILE cc_start: 0.8918 (mt) cc_final: 0.8717 (mm) REVERT: O 186 LEU cc_start: 0.8571 (tp) cc_final: 0.8329 (tt) REVERT: O 284 MET cc_start: 0.8043 (ptt) cc_final: 0.7198 (tmm) REVERT: P 88 PHE cc_start: 0.7894 (t80) cc_final: 0.6891 (t80) REVERT: S 311 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8285 (mm-30) REVERT: S 345 MET cc_start: 0.8825 (mtm) cc_final: 0.8354 (ptp) REVERT: T 179 VAL cc_start: 0.9091 (m) cc_final: 0.8840 (p) REVERT: T 256 MET cc_start: 0.8193 (ptt) cc_final: 0.7787 (ptt) REVERT: T 316 ASP cc_start: 0.8271 (p0) cc_final: 0.7830 (m-30) outliers start: 0 outliers final: 0 residues processed: 389 average time/residue: 0.1539 time to fit residues: 103.2947 Evaluate side-chains 289 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 291 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 258 optimal weight: 6.9990 chunk 209 optimal weight: 9.9990 chunk 299 optimal weight: 6.9990 chunk 303 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 214 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 chunk 356 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 ASN ** M 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.058178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048731 restraints weight = 198126.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.049357 restraints weight = 144533.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.049836 restraints weight = 97896.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.049937 restraints weight = 84028.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.050233 restraints weight = 76531.911| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 30529 Z= 0.245 Angle : 0.707 10.479 41181 Z= 0.364 Chirality : 0.044 0.225 4613 Planarity : 0.005 0.077 5211 Dihedral : 5.065 32.955 4021 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.14), residues: 3585 helix: 0.85 (0.11), residues: 2374 sheet: -0.99 (0.38), residues: 166 loop : -1.91 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 195 TYR 0.027 0.002 TYR E 268 PHE 0.027 0.002 PHE D 71 TRP 0.019 0.002 TRP R 286 HIS 0.011 0.001 HIS Q 385 Details of bonding type rmsd covalent geometry : bond 0.00529 (30529) covalent geometry : angle 0.70678 (41181) hydrogen bonds : bond 0.04169 ( 1824) hydrogen bonds : angle 4.61205 ( 5337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8409 (tp) cc_final: 0.7779 (tt) REVERT: A 263 MET cc_start: 0.9388 (mtp) cc_final: 0.9027 (mtt) REVERT: C 263 MET cc_start: 0.8106 (mmm) cc_final: 0.7545 (mmt) REVERT: H 88 PHE cc_start: 0.8153 (t80) cc_final: 0.7297 (t80) REVERT: Q 345 MET cc_start: 0.8974 (mtt) cc_final: 0.8509 (mtp) REVERT: Q 368 PHE cc_start: 0.8648 (m-80) cc_final: 0.8244 (m-80) REVERT: R 179 VAL cc_start: 0.9117 (m) cc_final: 0.8878 (p) REVERT: R 266 MET cc_start: 0.8440 (mmp) cc_final: 0.8163 (mmt) REVERT: R 335 MET cc_start: 0.7863 (mtp) cc_final: 0.7593 (mtp) REVERT: I 145 LEU cc_start: 0.8321 (tp) cc_final: 0.7718 (tp) REVERT: I 296 ASP cc_start: 0.8868 (m-30) cc_final: 0.8587 (m-30) REVERT: J 79 TYR cc_start: 0.7453 (t80) cc_final: 0.6925 (t80) REVERT: K 284 MET cc_start: 0.8690 (mtp) cc_final: 0.8199 (ttm) REVERT: K 290 VAL cc_start: 0.9088 (t) cc_final: 0.8844 (m) REVERT: M 243 MET cc_start: 0.8378 (ptp) cc_final: 0.7953 (ptm) REVERT: N 73 ILE cc_start: 0.8751 (mm) cc_final: 0.8520 (mm) REVERT: O 186 LEU cc_start: 0.8523 (tp) cc_final: 0.8273 (tt) REVERT: O 284 MET cc_start: 0.8074 (ptt) cc_final: 0.7252 (tmm) REVERT: P 88 PHE cc_start: 0.7965 (t80) cc_final: 0.6889 (t80) REVERT: S 130 TYR cc_start: 0.7285 (t80) cc_final: 0.7021 (t80) REVERT: S 311 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8279 (mm-30) REVERT: S 345 MET cc_start: 0.8866 (mtm) cc_final: 0.8472 (mtp) REVERT: T 179 VAL cc_start: 0.9119 (m) cc_final: 0.8861 (p) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1692 time to fit residues: 105.8299 Evaluate side-chains 280 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 312 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 282 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN R 393 ASN I 196 GLN M 287 GLN M 339 GLN S 295 ASN ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 364 ASN T 393 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.056862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.047588 restraints weight = 203063.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.048264 restraints weight = 138116.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.048760 restraints weight = 95706.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.048997 restraints weight = 78219.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.049109 restraints weight = 68592.845| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 30529 Z= 0.311 Angle : 0.800 11.547 41181 Z= 0.415 Chirality : 0.047 0.210 4613 Planarity : 0.006 0.079 5211 Dihedral : 5.450 33.851 4021 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.14), residues: 3585 helix: 0.44 (0.10), residues: 2358 sheet: -1.29 (0.37), residues: 166 loop : -2.12 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 226 TYR 0.034 0.002 TYR E 268 PHE 0.038 0.002 PHE G 269 TRP 0.022 0.002 TRP T 286 HIS 0.009 0.002 HIS R 342 Details of bonding type rmsd covalent geometry : bond 0.00669 (30529) covalent geometry : angle 0.80028 (41181) hydrogen bonds : bond 0.04614 ( 1824) hydrogen bonds : angle 4.94803 ( 5337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8910 (pp30) cc_final: 0.8710 (pp30) REVERT: A 145 LEU cc_start: 0.8435 (tp) cc_final: 0.7803 (tp) REVERT: A 263 MET cc_start: 0.9464 (mtp) cc_final: 0.9229 (mtm) REVERT: A 269 PHE cc_start: 0.8048 (m-80) cc_final: 0.7841 (m-10) REVERT: A 296 ASP cc_start: 0.8746 (m-30) cc_final: 0.8484 (p0) REVERT: B 93 GLU cc_start: 0.8540 (tp30) cc_final: 0.8294 (tp30) REVERT: C 263 MET cc_start: 0.8217 (mmm) cc_final: 0.7535 (mmt) REVERT: E 250 LEU cc_start: 0.8904 (mm) cc_final: 0.8383 (tp) REVERT: H 88 PHE cc_start: 0.8178 (t80) cc_final: 0.7283 (t80) REVERT: Q 345 MET cc_start: 0.9014 (mtt) cc_final: 0.8527 (mtp) REVERT: Q 368 PHE cc_start: 0.8636 (m-80) cc_final: 0.8302 (m-80) REVERT: R 118 MET cc_start: 0.5872 (mpp) cc_final: 0.5466 (tmm) REVERT: R 179 VAL cc_start: 0.9158 (m) cc_final: 0.8905 (p) REVERT: R 335 MET cc_start: 0.7902 (mtp) cc_final: 0.7635 (mtp) REVERT: I 296 ASP cc_start: 0.8940 (m-30) cc_final: 0.8657 (m-30) REVERT: K 263 MET cc_start: 0.8133 (mtm) cc_final: 0.7869 (mtt) REVERT: K 284 MET cc_start: 0.8687 (mtp) cc_final: 0.8077 (ttm) REVERT: K 290 VAL cc_start: 0.9168 (t) cc_final: 0.8858 (m) REVERT: N 73 ILE cc_start: 0.8809 (mm) cc_final: 0.8557 (mm) REVERT: O 186 LEU cc_start: 0.8620 (tp) cc_final: 0.8397 (tt) REVERT: O 284 MET cc_start: 0.8093 (ptt) cc_final: 0.7300 (tmm) REVERT: P 88 PHE cc_start: 0.7994 (t80) cc_final: 0.7099 (t80) REVERT: S 130 TYR cc_start: 0.7722 (t80) cc_final: 0.7349 (t80) REVERT: S 345 MET cc_start: 0.8936 (mtm) cc_final: 0.8505 (mtp) REVERT: S 393 LYS cc_start: 0.8754 (pptt) cc_final: 0.8246 (tmmt) REVERT: T 179 VAL cc_start: 0.9151 (m) cc_final: 0.8886 (p) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1670 time to fit residues: 99.7555 Evaluate side-chains 259 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 285 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 304 optimal weight: 20.0000 chunk 92 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 258 optimal weight: 10.0000 chunk 230 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 ASN ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 366 ASN T 302 ASN T 393 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048727 restraints weight = 199459.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.049390 restraints weight = 135625.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.049705 restraints weight = 95090.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.050099 restraints weight = 81978.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.050133 restraints weight = 70066.667| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30529 Z= 0.198 Angle : 0.688 10.754 41181 Z= 0.353 Chirality : 0.044 0.203 4613 Planarity : 0.005 0.077 5211 Dihedral : 5.215 33.694 4021 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.41 % Favored : 94.53 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3585 helix: 0.74 (0.11), residues: 2369 sheet: -1.59 (0.33), residues: 206 loop : -1.95 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 286 TYR 0.023 0.002 TYR F 79 PHE 0.036 0.002 PHE R 238 TRP 0.012 0.001 TRP I 255 HIS 0.005 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00433 (30529) covalent geometry : angle 0.68818 (41181) hydrogen bonds : bond 0.04197 ( 1824) hydrogen bonds : angle 4.66768 ( 5337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LEU cc_start: 0.8434 (tp) cc_final: 0.7806 (tp) REVERT: A 296 ASP cc_start: 0.8626 (m-30) cc_final: 0.8407 (p0) REVERT: A 329 MET cc_start: 0.8440 (tmm) cc_final: 0.8232 (tmm) REVERT: C 263 MET cc_start: 0.8169 (mmm) cc_final: 0.7662 (mmt) REVERT: H 88 PHE cc_start: 0.8068 (t80) cc_final: 0.7162 (t80) REVERT: Q 345 MET cc_start: 0.8974 (mtt) cc_final: 0.8504 (mtp) REVERT: Q 368 PHE cc_start: 0.8579 (m-80) cc_final: 0.8311 (m-80) REVERT: R 118 MET cc_start: 0.6018 (mpp) cc_final: 0.5452 (tmm) REVERT: R 179 VAL cc_start: 0.9090 (m) cc_final: 0.8834 (p) REVERT: R 335 MET cc_start: 0.7852 (mtp) cc_final: 0.7608 (mtp) REVERT: K 284 MET cc_start: 0.8590 (mtp) cc_final: 0.8062 (ttm) REVERT: K 290 VAL cc_start: 0.9103 (t) cc_final: 0.8802 (m) REVERT: M 243 MET cc_start: 0.8481 (ptp) cc_final: 0.8010 (ptt) REVERT: N 73 ILE cc_start: 0.8797 (mm) cc_final: 0.8536 (mm) REVERT: O 186 LEU cc_start: 0.8490 (tp) cc_final: 0.8220 (tt) REVERT: O 284 MET cc_start: 0.7993 (ptt) cc_final: 0.7148 (tmm) REVERT: P 88 PHE cc_start: 0.7878 (t80) cc_final: 0.6774 (t80) REVERT: S 130 TYR cc_start: 0.7868 (t80) cc_final: 0.7475 (t80) REVERT: S 334 TYR cc_start: 0.7437 (t80) cc_final: 0.7151 (t80) REVERT: S 345 MET cc_start: 0.8808 (mtm) cc_final: 0.8187 (ptp) REVERT: S 393 LYS cc_start: 0.8724 (pptt) cc_final: 0.8217 (tmmt) REVERT: T 118 MET cc_start: 0.6032 (mpp) cc_final: 0.5513 (tmm) REVERT: T 179 VAL cc_start: 0.9096 (m) cc_final: 0.8832 (p) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1611 time to fit residues: 97.1188 Evaluate side-chains 265 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 221 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 90 optimal weight: 0.5980 chunk 77 optimal weight: 8.9990 chunk 330 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 243 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 ASN R 393 ASN M 339 GLN ** S 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 364 ASN T 393 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.059058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.049745 restraints weight = 196687.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.050391 restraints weight = 145848.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.050916 restraints weight = 97227.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051101 restraints weight = 82232.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.051204 restraints weight = 73710.967| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30529 Z= 0.142 Angle : 0.651 10.198 41181 Z= 0.328 Chirality : 0.043 0.242 4613 Planarity : 0.005 0.132 5211 Dihedral : 4.945 32.290 4021 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.63 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3585 helix: 1.00 (0.11), residues: 2372 sheet: -1.35 (0.34), residues: 202 loop : -1.79 (0.21), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.022 0.001 TYR G 268 PHE 0.028 0.001 PHE R 238 TRP 0.010 0.001 TRP A 260 HIS 0.004 0.001 HIS E 304 Details of bonding type rmsd covalent geometry : bond 0.00316 (30529) covalent geometry : angle 0.65106 (41181) hydrogen bonds : bond 0.03890 ( 1824) hydrogen bonds : angle 4.43825 ( 5337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8829 (pp30) cc_final: 0.8428 (pp30) REVERT: A 263 MET cc_start: 0.8626 (mtm) cc_final: 0.8233 (mtm) REVERT: A 296 ASP cc_start: 0.8651 (m-30) cc_final: 0.8367 (p0) REVERT: A 329 MET cc_start: 0.8420 (tmm) cc_final: 0.8198 (tmm) REVERT: C 263 MET cc_start: 0.8153 (mmm) cc_final: 0.7866 (mmt) REVERT: E 250 LEU cc_start: 0.8786 (mm) cc_final: 0.8257 (tp) REVERT: H 88 PHE cc_start: 0.8082 (t80) cc_final: 0.7187 (t80) REVERT: Q 345 MET cc_start: 0.8928 (mtt) cc_final: 0.8507 (mtp) REVERT: Q 368 PHE cc_start: 0.8604 (m-80) cc_final: 0.8342 (m-80) REVERT: R 118 MET cc_start: 0.5950 (mpp) cc_final: 0.5470 (tmm) REVERT: R 179 VAL cc_start: 0.9073 (m) cc_final: 0.8835 (p) REVERT: R 299 TYR cc_start: 0.8639 (m-10) cc_final: 0.8295 (m-80) REVERT: I 256 TRP cc_start: 0.7941 (m-90) cc_final: 0.7502 (m-90) REVERT: J 79 TYR cc_start: 0.7710 (t80) cc_final: 0.6768 (t80) REVERT: K 284 MET cc_start: 0.8632 (mtp) cc_final: 0.8123 (ttm) REVERT: K 290 VAL cc_start: 0.9055 (t) cc_final: 0.8765 (m) REVERT: N 73 ILE cc_start: 0.8724 (mm) cc_final: 0.8474 (mm) REVERT: O 186 LEU cc_start: 0.8457 (tp) cc_final: 0.8211 (tt) REVERT: O 284 MET cc_start: 0.8020 (ptt) cc_final: 0.7331 (tmm) REVERT: P 88 PHE cc_start: 0.7988 (t80) cc_final: 0.6930 (t80) REVERT: S 130 TYR cc_start: 0.7892 (t80) cc_final: 0.7475 (t80) REVERT: S 345 MET cc_start: 0.8808 (mtm) cc_final: 0.8287 (ptp) REVERT: S 393 LYS cc_start: 0.8672 (pptt) cc_final: 0.8160 (tmmt) REVERT: T 118 MET cc_start: 0.5872 (mpp) cc_final: 0.5451 (tmm) REVERT: T 179 VAL cc_start: 0.9082 (m) cc_final: 0.8827 (p) REVERT: T 299 TYR cc_start: 0.8402 (m-10) cc_final: 0.7920 (m-80) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.1583 time to fit residues: 100.3148 Evaluate side-chains 277 residues out of total 3273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 325 optimal weight: 10.0000 chunk 211 optimal weight: 5.9990 chunk 301 optimal weight: 20.0000 chunk 246 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 356 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 320 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 159 HIS ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 393 ASN M 246 GLN S 300 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.059337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.050040 restraints weight = 197587.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050640 restraints weight = 144197.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.051248 restraints weight = 98466.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.051368 restraints weight = 83526.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.051446 restraints weight = 75212.606| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30529 Z= 0.133 Angle : 0.640 9.814 41181 Z= 0.321 Chirality : 0.042 0.213 4613 Planarity : 0.005 0.130 5211 Dihedral : 4.818 31.985 4021 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3585 helix: 1.16 (0.11), residues: 2373 sheet: -1.37 (0.34), residues: 202 loop : -1.72 (0.21), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 150 TYR 0.023 0.001 TYR E 268 PHE 0.023 0.001 PHE R 238 TRP 0.007 0.001 TRP C 255 HIS 0.008 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00294 (30529) covalent geometry : angle 0.64000 (41181) hydrogen bonds : bond 0.03786 ( 1824) hydrogen bonds : angle 4.32719 ( 5337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4608.85 seconds wall clock time: 81 minutes 0.54 seconds (4860.54 seconds total)