Starting phenix.real_space_refine on Tue Mar 11 23:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8osh_17153/03_2025/8osh_17153.cif Found real_map, /net/cci-nas-00/data/ceres_data/8osh_17153/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8osh_17153/03_2025/8osh_17153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8osh_17153/03_2025/8osh_17153.map" model { file = "/net/cci-nas-00/data/ceres_data/8osh_17153/03_2025/8osh_17153.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8osh_17153/03_2025/8osh_17153.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 9, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 23, 'ARG:plan': 20} 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: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 24, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 22} 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: {'GLN:plan1': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 1, 'ASP:plan': 26, 'PHE:plan': 11, 'GLU:plan': 26, 'ARG:plan': 22} 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: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 16, 'PHE:plan': 7, 'GLU:plan': 17, 'ARG:plan': 18} 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, 'HIS:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 14, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 349 Time building chain proxies: 5.12, per 1000 atoms: 0.76 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: 1.87 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.94 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: 2.01 Time building geometry restraints manager: 2.23 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 21.940 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.610 ------------------------------------------------------------------------------- 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= 0.470 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.738 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0622 time to fit residues: 3.9499 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 : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 40.0000 chunk 69 optimal weight: 30.0000 chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 6.4188 ------------------------------------------------------------------------------- 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 = 0.2793 r_free = 0.2793 target = 0.042012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.031271 restraints weight = 81433.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.031631 restraints weight = 68632.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.031908 restraints weight = 59788.766| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6740 Z= 0.240 Angle : 0.542 5.384 9334 Z= 0.347 Chirality : 0.043 0.124 1282 Planarity : 0.003 0.015 1342 Dihedral : 4.571 18.465 1342 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1312 helix: 0.67 (0.21), residues: 606 sheet: -3.40 (0.43), residues: 91 loop : -1.90 (0.27), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.704 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0568 time to fit residues: 3.6963 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 : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 134 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 23 optimal weight: 0.0060 chunk 57 optimal weight: 20.0000 chunk 109 optimal weight: 40.0000 chunk 83 optimal weight: 7.9990 overall best weight: 3.5602 ------------------------------------------------------------------------------- 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 = 0.041294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.029797 restraints weight = 80712.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.030192 restraints weight = 68077.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.030405 restraints weight = 59158.132| |-----------------------------------------------------------------------------| r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 6740 Z= 0.134 Angle : 0.437 4.684 9334 Z= 0.271 Chirality : 0.042 0.124 1282 Planarity : 0.002 0.011 1342 Dihedral : 3.970 22.205 1342 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.25), residues: 1312 helix: 1.32 (0.22), residues: 625 sheet: -3.47 (0.39), residues: 98 loop : -1.77 (0.28), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.696 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0621 time to fit residues: 4.0312 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 : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 0.0870 chunk 124 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 87 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 overall best weight: 5.0166 ------------------------------------------------------------------------------- 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 = 0.2761 r_free = 0.2761 target = 0.041037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.030197 restraints weight = 85263.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.030589 restraints weight = 71348.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.030878 restraints weight = 61439.400| |-----------------------------------------------------------------------------| r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2776 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= 0.177 Angle : 0.483 5.475 9334 Z= 0.302 Chirality : 0.042 0.122 1282 Planarity : 0.002 0.014 1342 Dihedral : 4.419 19.135 1342 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1312 helix: 0.97 (0.22), residues: 634 sheet: -3.60 (0.38), residues: 98 loop : -1.85 (0.28), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.730 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0606 time to fit residues: 4.0231 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 : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 40.0000 chunk 86 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 66 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 112 optimal weight: 0.0060 chunk 80 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 overall best weight: 5.0004 ------------------------------------------------------------------------------- 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 = 0.040897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.030110 restraints weight = 83892.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.030426 restraints weight = 69884.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.030729 restraints weight = 61490.449| |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3061 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= 0.171 Angle : 0.474 5.358 9334 Z= 0.295 Chirality : 0.042 0.122 1282 Planarity : 0.002 0.014 1342 Dihedral : 4.410 22.353 1342 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.25), residues: 1312 helix: 1.05 (0.22), residues: 627 sheet: -3.44 (0.39), residues: 99 loop : -1.82 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.688 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0620 time to fit residues: 3.9560 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 : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 49 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 1 optimal weight: 10.0000 overall best weight: 3.7986 ------------------------------------------------------------------------------- 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 = 0.2755 r_free = 0.2755 target = 0.041011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2416 r_free = 0.2416 target = 0.030185 restraints weight = 83339.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.030557 restraints weight = 69426.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.030801 restraints weight = 59987.063| |-----------------------------------------------------------------------------| r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 6740 Z= 0.134 Angle : 0.437 5.244 9334 Z= 0.270 Chirality : 0.042 0.122 1282 Planarity : 0.002 0.012 1342 Dihedral : 4.127 18.611 1342 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1312 helix: 1.33 (0.22), residues: 635 sheet: -3.40 (0.40), residues: 99 loop : -1.71 (0.29), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.718 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0587 time to fit residues: 3.7949 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 : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 17 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 76 optimal weight: 40.0000 chunk 20 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 122 optimal weight: 40.0000 chunk 117 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- 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 = 0.040531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.029784 restraints weight = 83887.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.030156 restraints weight = 70061.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.030398 restraints weight = 60320.876| |-----------------------------------------------------------------------------| r_work (final): 0.2379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3475 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= 0.196 Angle : 0.495 5.318 9334 Z= 0.312 Chirality : 0.042 0.121 1282 Planarity : 0.002 0.015 1342 Dihedral : 4.628 21.381 1342 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.25), residues: 1312 helix: 0.87 (0.22), residues: 636 sheet: -3.47 (0.41), residues: 99 loop : -1.93 (0.28), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.691 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0619 time to fit residues: 3.9931 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 : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 30 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 37 optimal weight: 0.0270 chunk 135 optimal weight: 5.9990 chunk 71 optimal weight: 40.0000 chunk 92 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 overall best weight: 6.0046 ------------------------------------------------------------------------------- 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 = 0.2734 r_free = 0.2734 target = 0.040334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.029599 restraints weight = 84578.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.029959 restraints weight = 70281.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.030234 restraints weight = 60604.050| |-----------------------------------------------------------------------------| r_work (final): 0.2373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6740 Z= 0.204 Angle : 0.498 5.513 9334 Z= 0.315 Chirality : 0.042 0.121 1282 Planarity : 0.002 0.014 1342 Dihedral : 4.666 18.946 1342 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.95 % Favored : 86.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.25), residues: 1312 helix: 0.72 (0.22), residues: 632 sheet: -3.44 (0.41), residues: 99 loop : -1.92 (0.28), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.762 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0648 time to fit residues: 4.2326 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 : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 130 optimal weight: 20.0000 chunk 114 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 58 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 97 optimal weight: 40.0000 chunk 78 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 = 0.2726 r_free = 0.2726 target = 0.040000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.029304 restraints weight = 85697.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2394 r_free = 0.2394 target = 0.029603 restraints weight = 71587.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.029908 restraints weight = 62877.502| |-----------------------------------------------------------------------------| r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6740 Z= 0.255 Angle : 0.552 6.268 9334 Z= 0.353 Chirality : 0.042 0.123 1282 Planarity : 0.003 0.016 1342 Dihedral : 5.136 21.677 1342 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.17 % Favored : 84.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1312 helix: 0.25 (0.21), residues: 622 sheet: -3.52 (0.42), residues: 99 loop : -2.13 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 *********************** 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 : 0.836 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0598 time to fit residues: 3.8485 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 : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 99 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 133 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 75 optimal weight: 50.0000 chunk 45 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 79 optimal weight: 9.9990 overall best weight: 10.1994 ------------------------------------------------------------------------------- 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 = 0.2706 r_free = 0.2706 target = 0.039360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2364 r_free = 0.2364 target = 0.028790 restraints weight = 87923.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2379 r_free = 0.2379 target = 0.029163 restraints weight = 73153.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2389 r_free = 0.2389 target = 0.029440 restraints weight = 62769.573| |-----------------------------------------------------------------------------| r_work (final): 0.2339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 6740 Z= 0.347 Angle : 0.646 7.361 9334 Z= 0.420 Chirality : 0.043 0.125 1282 Planarity : 0.004 0.017 1342 Dihedral : 5.937 24.966 1342 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.30 % Favored : 82.70 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1312 helix: -0.61 (0.20), residues: 605 sheet: -3.72 (0.41), residues: 99 loop : -2.40 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 ********************** 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 : 0.750 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0624 time to fit residues: 3.9454 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 : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 0.9980 chunk 113 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 124 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.2735 r_free = 0.2735 target = 0.040315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.029545 restraints weight = 84809.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.029903 restraints weight = 70829.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2417 r_free = 0.2417 target = 0.030159 restraints weight = 61153.784| |-----------------------------------------------------------------------------| r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 6740 Z= 0.135 Angle : 0.470 5.206 9334 Z= 0.291 Chirality : 0.042 0.121 1282 Planarity : 0.002 0.013 1342 Dihedral : 4.864 23.459 1342 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.11 % Favored : 86.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.24), residues: 1312 helix: 0.51 (0.22), residues: 628 sheet: -3.53 (0.43), residues: 93 loop : -2.25 (0.27), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 174 PHE 0.000 0.000 PHE A 16 TYR 0.000 0.000 TYR A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1706.87 seconds wall clock time: 30 minutes 8.25 seconds (1808.25 seconds total)