Starting phenix.real_space_refine on Tue Sep 24 04:01:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_17153.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_17153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_17153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_17153.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8osh_17153/09_2024/8osh_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-5461/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: 5.26, per 1000 atoms: 0.78 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: 1.83 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: 0.91 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: 1.78 Time building geometry restraints manager: 2.11 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: 1.770 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: 20.580 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.670 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.806 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0608 time to fit residues: 3.9439 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.734 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0565 time to fit residues: 3.7114 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 40.0000 chunk 38 optimal weight: 20.0000 chunk 102 optimal weight: 50.0000 chunk 84 optimal weight: 30.0000 chunk 34 optimal weight: 9.9990 chunk 123 optimal weight: 0.0040 chunk 133 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6740 Z= 0.180 Angle : 0.483 5.202 9334 Z= 0.304 Chirality : 0.042 0.121 1282 Planarity : 0.002 0.012 1342 Dihedral : 4.395 20.688 1342 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.48 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 (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: -1.10 (0.25), residues: 1312 helix: 0.78 (0.22), residues: 625 sheet: -3.57 (0.39), residues: 98 loop : -1.91 (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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.745 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0585 time to fit residues: 3.8632 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 93 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 30.0000 chunk 131 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6740 Z= 0.260 Angle : 0.562 6.070 9334 Z= 0.358 Chirality : 0.043 0.125 1282 Planarity : 0.003 0.015 1342 Dihedral : 5.023 19.298 1342 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.40 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 (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: 0.23 (0.21), residues: 616 sheet: -3.81 (0.37), residues: 98 loop : -2.04 (0.27), residues: 598 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.823 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0601 time to fit residues: 4.0401 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 40.0000 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 50.0000 chunk 54 optimal weight: 0.0670 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 overall best weight: 6.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3139 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= 0.208 Angle : 0.510 5.745 9334 Z= 0.322 Chirality : 0.042 0.124 1282 Planarity : 0.003 0.013 1342 Dihedral : 4.820 21.661 1342 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.19 % 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: -1.43 (0.24), residues: 1312 helix: 0.44 (0.21), residues: 614 sheet: -3.79 (0.37), residues: 98 loop : -1.94 (0.28), residues: 600 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.824 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0602 time to fit residues: 4.0117 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.0670 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 131 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 126 optimal weight: 9.9990 overall best weight: 7.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6740 Z= 0.242 Angle : 0.548 6.184 9334 Z= 0.348 Chirality : 0.042 0.123 1282 Planarity : 0.003 0.015 1342 Dihedral : 5.178 19.946 1342 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.93 % Favored : 84.07 % 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: -1.77 (0.24), residues: 1312 helix: 0.11 (0.21), residues: 614 sheet: -3.84 (0.38), residues: 99 loop : -2.06 (0.27), residues: 599 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.844 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0600 time to fit residues: 3.9694 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 9.9990 chunk 74 optimal weight: 40.0000 chunk 96 optimal weight: 30.0000 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 131 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6740 Z= 0.231 Angle : 0.531 6.125 9334 Z= 0.338 Chirality : 0.042 0.122 1282 Planarity : 0.003 0.015 1342 Dihedral : 5.099 22.550 1342 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % 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: -1.76 (0.24), residues: 1312 helix: 0.16 (0.21), residues: 615 sheet: -3.85 (0.39), residues: 99 loop : -2.12 (0.27), residues: 598 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.778 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0580 time to fit residues: 3.8374 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0970 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 125 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.009 6740 Z= 0.074 Angle : 0.413 5.200 9334 Z= 0.248 Chirality : 0.042 0.123 1282 Planarity : 0.002 0.010 1342 Dihedral : 4.107 21.643 1342 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % 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: -0.71 (0.25), residues: 1312 helix: 1.26 (0.22), residues: 642 sheet: -3.44 (0.41), residues: 99 loop : -1.99 (0.28), residues: 571 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.812 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0591 time to fit residues: 4.0248 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 40.0000 chunk 125 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 53 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 110 optimal weight: 20.0000 chunk 115 optimal weight: 10.0000 chunk 121 optimal weight: 50.0000 chunk 80 optimal weight: 10.0000 chunk 129 optimal weight: 40.0000 overall best weight: 5.2030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6740 Z= 0.184 Angle : 0.470 5.058 9334 Z= 0.297 Chirality : 0.042 0.120 1282 Planarity : 0.002 0.014 1342 Dihedral : 4.359 20.231 1342 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.48 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: -0.78 (0.25), residues: 1312 helix: 1.18 (0.22), residues: 627 sheet: -3.48 (0.42), residues: 99 loop : -1.91 (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 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.781 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0620 time to fit residues: 4.0337 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 40.0000 chunk 61 optimal weight: 8.9990 chunk 89 optimal weight: 0.0020 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 85 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6740 Z= 0.172 Angle : 0.471 5.198 9334 Z= 0.296 Chirality : 0.042 0.123 1282 Planarity : 0.002 0.013 1342 Dihedral : 4.491 21.061 1342 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % 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: -0.91 (0.25), residues: 1312 helix: 1.07 (0.22), residues: 630 sheet: -3.45 (0.43), residues: 99 loop : -2.02 (0.28), residues: 583 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.786 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0615 time to fit residues: 4.0422 Evaluate side-chains 25 residues out of total 1190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 chunk 45 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 19 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 0.0070 overall best weight: 5.0006 ------------------------------------------------------------------------------- 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 = 0.2736 r_free = 0.2736 target = 0.040396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.029731 restraints weight = 83479.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2414 r_free = 0.2414 target = 0.030095 restraints weight = 69518.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.030363 restraints weight = 59935.978| |-----------------------------------------------------------------------------| r_work (final): 0.2378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 6740 Z= 0.176 Angle : 0.472 5.190 9334 Z= 0.297 Chirality : 0.042 0.120 1282 Planarity : 0.002 0.014 1342 Dihedral : 4.472 20.046 1342 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.25 % Favored : 85.75 % 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: -0.91 (0.25), residues: 1312 helix: 1.06 (0.22), residues: 635 sheet: -3.45 (0.43), residues: 99 loop : -2.02 (0.28), 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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1097.47 seconds wall clock time: 19 minutes 59.80 seconds (1199.80 seconds total)