Starting phenix.real_space_refine on Fri Aug 22 18:26:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osh_17153/08_2025/8osh_17153.map" } resolution = 4.9 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 4026 2.51 5 N 1372 2.21 5 O 1372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6770 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 1431 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 16, 'TRANS': 273} Chain breaks: 5 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 889 Unresolved non-hydrogen angles: 1138 Unresolved non-hydrogen dihedrals: 710 Unresolved non-hydrogen chiralities: 99 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 9, 'GLU:plan': 23, 'ASN:plan1': 10, 'ASP:plan': 20, 'ARG:plan': 20, 'TYR:plan': 5, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 453 Chain: "B" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1564 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 276} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 961 Unresolved non-hydrogen angles: 1227 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 103 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 10, 'GLU:plan': 27, 'ASN:plan1': 10, 'ASP:plan': 24, 'ARG:plan': 22, 'TYR:plan': 5, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 495 Chain: "C" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1554 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 274} Link IDs: {'PTRANS': 17, 'TRANS': 297} Chain breaks: 3 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 954 Unresolved non-hydrogen angles: 1218 Unresolved non-hydrogen dihedrals: 761 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 10, 'GLU:plan': 26, 'ASN:plan1': 10, 'ASP:plan': 26, 'ARG:plan': 22, 'TYR:plan': 5, 'HIS:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 497 Chain: "D" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1135 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 199} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 6 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 704 Unresolved non-hydrogen angles: 901 Unresolved non-hydrogen dihedrals: 558 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'PHE:plan': 7, 'GLN:plan1': 8, 'GLU:plan': 17, 'ASN:plan1': 8, 'ASP:plan': 16, 'ARG:plan': 18, 'TYR:plan': 4, 'HIS:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 361 Chain: "E" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1086 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 189} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 8 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 679 Unresolved non-hydrogen angles: 866 Unresolved non-hydrogen dihedrals: 545 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 14, 'ASN:plan1': 5, 'ASP:plan': 17, 'ARG:plan': 18, 'TYR:plan': 5, 'HIS:plan': 5, 'TRP:plan': 1, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 349 Time building chain proxies: 2.61, per 1000 atoms: 0.39 Number of scatterers: 6770 At special positions: 0 Unit cell: (134.904, 130.284, 85.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1372 8.00 N 1372 7.00 C 4026 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: 0.71 Conformation dependent library (CDL) restraints added in 546.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 53.4% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.603A pdb=" N LEU A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 removed outlier: 5.602A pdb=" N LEU A 60 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA A 61 " --> pdb=" O ILE A 57 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 141 through 144 removed outlier: 3.712A pdb=" N LYS A 144 " --> pdb=" O LEU A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 144' Processing helix chain 'A' and resid 166 through 170 removed outlier: 3.930A pdb=" N ALA A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 4.102A pdb=" N ARG A 210 " --> pdb=" O LEU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 239 removed outlier: 3.630A pdb=" N ASN A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.979A pdb=" N TYR A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 264 removed outlier: 3.770A pdb=" N GLN A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 268 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.681A pdb=" N GLU A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY A 308 " --> pdb=" O THR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 326 removed outlier: 5.775A pdb=" N THR A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 329 No H-bonds generated for 'chain 'A' and resid 327 through 329' Processing helix chain 'A' and resid 340 through 352 Processing helix chain 'B' and resid 24 through 37 Processing helix chain 'B' and resid 49 through 62 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.759A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASN B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 265 removed outlier: 4.097A pdb=" N TYR B 247 " --> pdb=" O PHE B 243 " (cutoff:3.500A) Proline residue: B 249 - end of helix removed outlier: 3.898A pdb=" N LEU B 254 " --> pdb=" O GLU B 250 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS B 263 " --> pdb=" O VAL B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 282 removed outlier: 3.719A pdb=" N SER B 279 " --> pdb=" O ARG B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 285 No H-bonds generated for 'chain 'B' and resid 283 through 285' Processing helix chain 'B' and resid 290 through 308 removed outlier: 3.744A pdb=" N VAL B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN B 297 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B 298 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS B 301 " --> pdb=" O ASN B 297 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 326 Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'C' and resid 24 through 35 Processing helix chain 'C' and resid 52 through 58 removed outlier: 4.101A pdb=" N THR C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 88 through 93 removed outlier: 4.466A pdb=" N SER C 93 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 164 through 173 removed outlier: 3.678A pdb=" N ALA C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 222 through 239 removed outlier: 3.864A pdb=" N ASN C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.591A pdb=" N TYR C 247 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 265 removed outlier: 3.525A pdb=" N LEU C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 255 " --> pdb=" O GLN C 251 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS C 263 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 265 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.811A pdb=" N LYS C 277 " --> pdb=" O ASP C 273 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 280 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 287 removed outlier: 3.879A pdb=" N VAL C 287 " --> pdb=" O GLU C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 284 through 287' Processing helix chain 'C' and resid 289 through 307 removed outlier: 3.553A pdb=" N ASP C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG C 298 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA C 300 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS C 301 " --> pdb=" O ASN C 297 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 326 removed outlier: 4.402A pdb=" N THR C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LEU C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU C 325 " --> pdb=" O ILE C 321 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG C 326 " --> pdb=" O THR C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 4.053A pdb=" N ARG C 349 " --> pdb=" O LYS C 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.544A pdb=" N ILE D 21 " --> pdb=" O PHE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 34 removed outlier: 3.786A pdb=" N LYS D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.242A pdb=" N ASN D 146 " --> pdb=" O ALA D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 158 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.588A pdb=" N LEU D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 201 removed outlier: 3.538A pdb=" N GLY D 201 " --> pdb=" O PRO D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 223 through 238 removed outlier: 3.503A pdb=" N GLN D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 253 removed outlier: 3.869A pdb=" N GLU D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TYR D 247 " --> pdb=" O PHE D 243 " (cutoff:3.500A) Proline residue: D 249 - end of helix Processing helix chain 'D' and resid 271 through 279 removed outlier: 3.646A pdb=" N SER D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 304 removed outlier: 4.087A pdb=" N VAL D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA D 300 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N LYS D 301 " --> pdb=" O ASN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 322 removed outlier: 4.212A pdb=" N THR D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 330 removed outlier: 3.657A pdb=" N ARG D 328 " --> pdb=" O CYS D 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 36 removed outlier: 3.640A pdb=" N LYS E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ALA E 30 " --> pdb=" O GLU E 26 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 63 removed outlier: 3.529A pdb=" N LEU E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.821A pdb=" N ASN E 146 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG E 147 " --> pdb=" O LYS E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 169 Processing helix chain 'E' and resid 205 through 209 removed outlier: 3.653A pdb=" N ASP E 209 " --> pdb=" O PRO E 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 205 through 209' Processing helix chain 'E' and resid 222 through 238 Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 247 through 264 removed outlier: 3.526A pdb=" N GLN E 255 " --> pdb=" O GLN E 251 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS E 256 " --> pdb=" O THR E 252 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU E 264 " --> pdb=" O GLU E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 268 removed outlier: 4.030A pdb=" N VAL E 268 " --> pdb=" O LEU E 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 265 through 268' Processing helix chain 'E' and resid 271 through 285 removed outlier: 3.663A pdb=" N LYS E 277 " --> pdb=" O ASP E 273 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS E 282 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 303 removed outlier: 3.802A pdb=" N LYS E 301 " --> pdb=" O ASN E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 326 removed outlier: 3.850A pdb=" N ARG E 319 " --> pdb=" O ASP E 315 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR E 322 " --> pdb=" O ARG E 318 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 323 " --> pdb=" O ARG E 319 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 325 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.821A pdb=" N VAL A 43 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N MET A 44 " --> pdb=" O ALA A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.761A pdb=" N GLY B 196 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 109 through 110 removed outlier: 6.550A pdb=" N VAL B 109 " --> pdb=" O TYR B 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 122 through 123 Processing sheet with id=AA7, first strand: chain 'C' and resid 194 through 196 removed outlier: 6.182A pdb=" N VAL C 43 " --> pdb=" O GLY C 194 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLY C 196 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE C 45 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET C 44 " --> pdb=" O MET C 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 175 Processing sheet with id=AA9, first strand: chain 'D' and resid 44 through 45 removed outlier: 6.434A pdb=" N MET D 44 " --> pdb=" O ALA D 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 149 through 151 removed outlier: 6.028A pdb=" N LEU D 150 " --> pdb=" O VAL D 193 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 148 through 151 381 hydrogen bonds defined for protein. 1089 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: 0.96 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 1372 1.28 - 1.35: 1328 1.35 - 1.42: 14 1.42 - 1.48: 1205 1.48 - 1.55: 2821 Bond restraints: 6740 Sorted by residual: bond pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta sigma weight residual 1.458 1.488 -0.030 7.40e-03 1.83e+04 1.66e+01 bond pdb=" N VAL B 220 " pdb=" CA VAL B 220 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.18e+01 bond pdb=" N VAL C 177 " pdb=" CA VAL C 177 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.08e+01 bond pdb=" N ARG D 204 " pdb=" CA ARG D 204 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.11e-02 8.12e+03 1.06e+01 bond pdb=" N VAL D 220 " pdb=" CA VAL D 220 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.04e+01 ... (remaining 6735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 8367 1.54 - 3.07: 865 3.07 - 4.61: 87 4.61 - 6.15: 13 6.15 - 7.68: 2 Bond angle restraints: 9334 Sorted by residual: angle pdb=" C GLU C 267 " pdb=" CA GLU C 267 " pdb=" CB GLU C 267 " ideal model delta sigma weight residual 116.63 110.39 6.24 1.16e+00 7.43e-01 2.90e+01 angle pdb=" C GLY A 42 " pdb=" N VAL A 43 " pdb=" CA VAL A 43 " ideal model delta sigma weight residual 122.45 114.77 7.68 1.44e+00 4.82e-01 2.85e+01 angle pdb=" N ASP A 164 " pdb=" CA ASP A 164 " pdb=" C ASP A 164 " ideal model delta sigma weight residual 114.75 108.78 5.97 1.26e+00 6.30e-01 2.25e+01 angle pdb=" C LEU B 158 " pdb=" CA LEU B 158 " pdb=" CB LEU B 158 " ideal model delta sigma weight residual 116.54 111.12 5.42 1.15e+00 7.56e-01 2.22e+01 angle pdb=" CA GLY A 201 " pdb=" C GLY A 201 " pdb=" O GLY A 201 " ideal model delta sigma weight residual 122.24 118.23 4.01 8.70e-01 1.32e+00 2.13e+01 ... (remaining 9329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.67: 3583 3.67 - 7.34: 265 7.34 - 11.02: 50 11.02 - 14.69: 7 14.69 - 18.36: 1 Dihedral angle restraints: 3906 sinusoidal: 0 harmonic: 3906 Sorted by residual: dihedral pdb=" CA LEU C 203 " pdb=" C LEU C 203 " pdb=" N ARG C 204 " pdb=" CA ARG C 204 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA PRO B 68 " pdb=" C PRO B 68 " pdb=" N VAL B 69 " pdb=" CA VAL B 69 " ideal model delta harmonic sigma weight residual 180.00 166.01 13.99 0 5.00e+00 4.00e-02 7.83e+00 dihedral pdb=" CA ARG C 204 " pdb=" C ARG C 204 " pdb=" N PRO C 205 " pdb=" CA PRO C 205 " ideal model delta harmonic sigma weight residual -180.00 -166.74 -13.26 0 5.00e+00 4.00e-02 7.04e+00 ... (remaining 3903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 768 0.040 - 0.081: 316 0.081 - 0.121: 130 0.121 - 0.161: 41 0.161 - 0.201: 27 Chirality restraints: 1282 Sorted by residual: chirality pdb=" CA ILE D 57 " pdb=" N ILE D 57 " pdb=" C ILE D 57 " pdb=" CB ILE D 57 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ILE E 40 " pdb=" N ILE E 40 " pdb=" C ILE E 40 " pdb=" CB ILE E 40 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA ILE B 101 " pdb=" N ILE B 101 " pdb=" C ILE B 101 " pdb=" CB ILE B 101 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 1279 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 242 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C THR A 242 " -0.027 2.00e-02 2.50e+03 pdb=" O THR A 242 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE A 243 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 22 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C VAL C 22 " -0.024 2.00e-02 2.50e+03 pdb=" O VAL C 22 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 23 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 312 " 0.006 2.00e-02 2.50e+03 1.23e-02 1.51e+00 pdb=" C VAL B 312 " -0.021 2.00e-02 2.50e+03 pdb=" O VAL B 312 " 0.008 2.00e-02 2.50e+03 pdb=" N THR B 313 " 0.007 2.00e-02 2.50e+03 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.86: 2788 2.86 - 3.37: 6943 3.37 - 3.88: 9617 3.88 - 4.39: 9679 4.39 - 4.90: 14510 Nonbonded interactions: 43537 Sorted by model distance: nonbonded pdb=" O ILE A 45 " pdb=" N GLY A 196 " model vdw 2.344 3.120 nonbonded pdb=" N ARG C 147 " pdb=" O ARG C 189 " model vdw 2.359 3.120 nonbonded pdb=" O ASP B 118 " pdb=" N GLY B 122 " model vdw 2.367 3.120 nonbonded pdb=" O THR A 116 " pdb=" N VAL A 120 " model vdw 2.380 3.120 nonbonded pdb=" O ARG B 119 " pdb=" N LEU B 141 " model vdw 2.409 3.120 ... (remaining 43532 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 14 through 76 or resid 100 or resid 102 through 353)) selection = (chain 'B' and (resid 14 through 76 or resid 100 or resid 102 through 113 or res \ id 116 through 176 or resid 184 through 353)) selection = (chain 'C' and (resid 14 through 76 or resid 82 or resid 102 through 113 or resi \ d 116 through 176 or resid 184 through 331 or resid 339 through 353)) } ncs_group { reference = (chain 'D' and (resid 20 through 46 or resid 49 through 65 or resid 142 through \ 153 or resid 159 through 174 or resid 189 through 194 or resid 204 through 214 o \ r resid 217 through 219 or resid 221 through 352)) selection = (chain 'E' and (resid 20 through 174 or resid 189 through 285 or resid 290 throu \ gh 310 or resid 314 through 330 or resid 349 through 352)) } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.580 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 0.040 6740 Z= 0.503 Angle : 0.942 7.685 9334 Z= 0.723 Chirality : 0.058 0.201 1282 Planarity : 0.002 0.016 1342 Dihedral : 3.379 18.359 1342 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.20 % Favored : 88.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.25), residues: 1312 helix: 1.93 (0.25), residues: 523 sheet: -3.13 (0.48), residues: 90 loop : -1.89 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00643 ( 6740) covalent geometry : angle 0.94170 ( 9334) hydrogen bonds : bond 0.27919 ( 381) hydrogen bonds : angle 7.47225 ( 1089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.256 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0307 time to fit residues: 1.7860 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 overall best weight: 4.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.042250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.030979 restraints weight = 80287.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.031257 restraints weight = 69613.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.031544 restraints weight = 61763.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.031821 restraints weight = 55475.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.031964 restraints weight = 51220.160| |-----------------------------------------------------------------------------| r_work (final): 0.2463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6740 Z= 0.179 Angle : 0.480 4.568 9334 Z= 0.304 Chirality : 0.043 0.121 1282 Planarity : 0.003 0.017 1342 Dihedral : 4.094 18.051 1342 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.25), residues: 1312 helix: 1.06 (0.22), residues: 619 sheet: -3.36 (0.43), residues: 90 loop : -1.80 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6740) covalent geometry : angle 0.47978 ( 9334) hydrogen bonds : bond 0.04505 ( 381) hydrogen bonds : angle 5.75358 ( 1089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.235 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0284 time to fit residues: 1.6355 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 40.0000 chunk 18 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 125 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 13 optimal weight: 50.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.040912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.030083 restraints weight = 84259.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.030453 restraints weight = 70522.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.030739 restraints weight = 60770.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.030948 restraints weight = 54155.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.031147 restraints weight = 49486.237| |-----------------------------------------------------------------------------| r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 6740 Z= 0.205 Angle : 0.524 5.796 9334 Z= 0.329 Chirality : 0.042 0.125 1282 Planarity : 0.003 0.014 1342 Dihedral : 4.822 21.144 1342 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.24), residues: 1312 helix: 0.46 (0.21), residues: 632 sheet: -3.65 (0.38), residues: 98 loop : -1.92 (0.28), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6740) covalent geometry : angle 0.52384 ( 9334) hydrogen bonds : bond 0.04207 ( 381) hydrogen bonds : angle 5.65970 ( 1089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0308 time to fit residues: 1.8294 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 55 optimal weight: 5.9990 chunk 102 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 131 optimal weight: 8.9990 chunk 84 optimal weight: 30.0000 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.0370 chunk 58 optimal weight: 6.9990 overall best weight: 5.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.040952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.030136 restraints weight = 84354.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.030449 restraints weight = 70136.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2442 r_free = 0.2442 target = 0.030764 restraints weight = 61632.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.030951 restraints weight = 54610.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.031159 restraints weight = 50013.814| |-----------------------------------------------------------------------------| r_work (final): 0.2411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 6740 Z= 0.170 Angle : 0.476 5.463 9334 Z= 0.297 Chirality : 0.042 0.122 1282 Planarity : 0.002 0.012 1342 Dihedral : 4.474 19.863 1342 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.59 % Favored : 88.41 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.25), residues: 1312 helix: 0.90 (0.22), residues: 621 sheet: -3.64 (0.37), residues: 98 loop : -1.82 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 6740) covalent geometry : angle 0.47580 ( 9334) hydrogen bonds : bond 0.03248 ( 381) hydrogen bonds : angle 5.13697 ( 1089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.267 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0304 time to fit residues: 1.7860 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 9 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 30.0000 chunk 135 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 123 optimal weight: 50.0000 chunk 130 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.040376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2397 r_free = 0.2397 target = 0.029650 restraints weight = 84745.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2412 r_free = 0.2412 target = 0.030029 restraints weight = 70724.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2422 r_free = 0.2422 target = 0.030286 restraints weight = 60571.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.030515 restraints weight = 54090.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.030642 restraints weight = 49194.908| |-----------------------------------------------------------------------------| r_work (final): 0.2388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6740 Z= 0.234 Angle : 0.538 5.913 9334 Z= 0.341 Chirality : 0.042 0.121 1282 Planarity : 0.003 0.016 1342 Dihedral : 4.968 20.915 1342 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.94 % Favored : 85.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.24), residues: 1312 helix: 0.39 (0.21), residues: 620 sheet: -3.69 (0.38), residues: 99 loop : -1.99 (0.28), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6740) covalent geometry : angle 0.53820 ( 9334) hydrogen bonds : bond 0.04104 ( 381) hydrogen bonds : angle 5.65796 ( 1089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.269 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0263 time to fit residues: 1.6039 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 125 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 34 optimal weight: 0.1980 chunk 78 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 overall best weight: 5.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.040575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.029759 restraints weight = 85342.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.030145 restraints weight = 71094.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.030427 restraints weight = 61095.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.030646 restraints weight = 54105.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2440 r_free = 0.2440 target = 0.030758 restraints weight = 49216.843| |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 6740 Z= 0.187 Angle : 0.488 5.409 9334 Z= 0.307 Chirality : 0.042 0.124 1282 Planarity : 0.002 0.013 1342 Dihedral : 4.620 20.855 1342 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.25), residues: 1312 helix: 0.67 (0.22), residues: 622 sheet: -3.64 (0.39), residues: 99 loop : -1.84 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6740) covalent geometry : angle 0.48751 ( 9334) hydrogen bonds : bond 0.03319 ( 381) hydrogen bonds : angle 5.26735 ( 1089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0299 time to fit residues: 1.8032 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 8.9990 chunk 8 optimal weight: 30.0000 chunk 12 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 91 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.039965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.029296 restraints weight = 84952.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.029593 restraints weight = 70514.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.029884 restraints weight = 61761.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.030118 restraints weight = 54801.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2421 r_free = 0.2421 target = 0.030269 restraints weight = 49676.314| |-----------------------------------------------------------------------------| r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6740 Z= 0.275 Angle : 0.573 6.655 9334 Z= 0.367 Chirality : 0.043 0.123 1282 Planarity : 0.003 0.017 1342 Dihedral : 5.302 20.640 1342 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.84 % Favored : 83.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.24), residues: 1312 helix: 0.04 (0.21), residues: 609 sheet: -3.83 (0.39), residues: 99 loop : -2.09 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 6740) covalent geometry : angle 0.57292 ( 9334) hydrogen bonds : bond 0.04530 ( 381) hydrogen bonds : angle 6.05971 ( 1089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.275 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0254 time to fit residues: 1.5342 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 40.0000 chunk 21 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 110 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.040198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.029452 restraints weight = 85356.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.029757 restraints weight = 71013.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.030064 restraints weight = 62289.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.030239 restraints weight = 55120.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.030453 restraints weight = 50388.723| |-----------------------------------------------------------------------------| r_work (final): 0.2380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6740 Z= 0.207 Angle : 0.517 5.995 9334 Z= 0.327 Chirality : 0.042 0.122 1282 Planarity : 0.003 0.014 1342 Dihedral : 5.027 21.496 1342 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.63 % Favored : 85.37 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.63 (0.24), residues: 1312 helix: 0.27 (0.21), residues: 620 sheet: -3.71 (0.40), residues: 99 loop : -2.08 (0.27), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6740) covalent geometry : angle 0.51719 ( 9334) hydrogen bonds : bond 0.03695 ( 381) hydrogen bonds : angle 5.65817 ( 1089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.187 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0297 time to fit residues: 1.7108 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 0.2980 chunk 58 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 0.0970 chunk 54 optimal weight: 8.9990 chunk 78 optimal weight: 40.0000 chunk 7 optimal weight: 30.0000 chunk 121 optimal weight: 40.0000 chunk 29 optimal weight: 9.9990 chunk 135 optimal weight: 5.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.041311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.030400 restraints weight = 83640.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.030691 restraints weight = 69834.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.031053 restraints weight = 60751.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.031305 restraints weight = 53662.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.031507 restraints weight = 47980.229| |-----------------------------------------------------------------------------| r_work (final): 0.2422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.008 6740 Z= 0.074 Angle : 0.408 4.736 9334 Z= 0.246 Chirality : 0.042 0.125 1282 Planarity : 0.002 0.010 1342 Dihedral : 3.958 21.570 1342 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.26), residues: 1312 helix: 1.45 (0.22), residues: 646 sheet: -3.28 (0.43), residues: 99 loop : -1.94 (0.28), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00102 ( 6740) covalent geometry : angle 0.40823 ( 9334) hydrogen bonds : bond 0.02157 ( 381) hydrogen bonds : angle 4.34798 ( 1089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.258 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0295 time to fit residues: 1.7536 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 14 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 37 optimal weight: 50.0000 chunk 118 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 93 optimal weight: 0.0270 chunk 3 optimal weight: 9.9990 overall best weight: 3.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.040877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.030064 restraints weight = 83510.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 17)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.030371 restraints weight = 69713.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.030695 restraints weight = 61467.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.030924 restraints weight = 54127.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.031105 restraints weight = 48721.432| |-----------------------------------------------------------------------------| r_work (final): 0.2409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 6740 Z= 0.117 Angle : 0.422 5.181 9334 Z= 0.260 Chirality : 0.042 0.123 1282 Planarity : 0.002 0.013 1342 Dihedral : 3.969 19.859 1342 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.04 % Favored : 87.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.26), residues: 1312 helix: 1.59 (0.22), residues: 641 sheet: -3.29 (0.43), residues: 99 loop : -1.90 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00161 ( 6740) covalent geometry : angle 0.42236 ( 9334) hydrogen bonds : bond 0.02489 ( 381) hydrogen bonds : angle 4.49053 ( 1089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0293 time to fit residues: 1.7119 Evaluate side-chains 25 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 127 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 121 optimal weight: 0.0170 chunk 2 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 overall best weight: 3.2142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.040966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.030116 restraints weight = 83865.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.030426 restraints weight = 70166.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.030720 restraints weight = 61831.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.030918 restraints weight = 54883.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.031127 restraints weight = 50014.718| |-----------------------------------------------------------------------------| r_work (final): 0.2408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 6740 Z= 0.112 Angle : 0.418 5.185 9334 Z= 0.257 Chirality : 0.042 0.121 1282 Planarity : 0.002 0.012 1342 Dihedral : 3.894 20.572 1342 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.26), residues: 1312 helix: 1.66 (0.22), residues: 648 sheet: -3.16 (0.44), residues: 99 loop : -1.90 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 151 PHE 0.000 0.000 PHE A 16 TRP 0.000 0.000 TRP A 174 Details of bonding type rmsd covalent geometry : bond 0.00154 ( 6740) covalent geometry : angle 0.41845 ( 9334) hydrogen bonds : bond 0.02344 ( 381) hydrogen bonds : angle 4.37848 ( 1089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1058.25 seconds wall clock time: 18 minutes 49.26 seconds (1129.26 seconds total)