Starting phenix.real_space_refine on Fri Sep 11 20:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2026/6sh5_10194.map" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6853 2.51 5 N 2338 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11529 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1647 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 293} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 1077 Unresolved non-hydrogen angles: 1379 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'ASP:plan': 24, 'GLU:plan': 16, 'GLN:plan1': 7, 'TYR:plan': 14, 'TRP:plan': 5, 'PHE:plan': 16, 'HIS:plan': 7, 'ARG:plan': 14, 'ASN:plan1': 16} Unresolved non-hydrogen planarities: 556 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 1.57, per 1000 atoms: 0.14 Number of scatterers: 11529 At special positions: 0 Unit cell: (150.378, 149.319, 86.838, 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 2338 8.00 N 2338 7.00 C 6853 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: 1.03 Conformation dependent library (CDL) restraints added in 568.3 milliseconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4354 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 21 sheets defined 42.5% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 198 " --> pdb=" O ILE A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 239 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 246 Processing helix chain 'A' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA A 324 " --> pdb=" O ILE A 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 321 through 324' Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 410 " --> pdb=" O THR A 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A 415 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 434 Processing helix chain 'A' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS A 444 " --> pdb=" O HIS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 449 No H-bonds generated for 'chain 'A' and resid 447 through 449' Processing helix chain 'B' and resid 96 through 105 Processing helix chain 'B' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP B 186 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR B 198 " --> pdb=" O ILE B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.692A pdb=" N ARG B 255 " --> pdb=" O TRP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA B 324 " --> pdb=" O ILE B 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 321 through 324' Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.524A pdb=" N GLU B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS B 409 " --> pdb=" O GLU B 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER B 415 " --> pdb=" O LYS B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 434 Processing helix chain 'B' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'C' and resid 96 through 105 Processing helix chain 'C' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP C 186 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR C 198 " --> pdb=" O ILE C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.680A pdb=" N ILE C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 246 Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG C 255 " --> pdb=" O TRP C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 284 Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.641A pdb=" N ASN C 304 " --> pdb=" O ASP C 300 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N HIS C 305 " --> pdb=" O ASP C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA C 324 " --> pdb=" O ILE C 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 321 through 324' Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 390 through 402 removed outlier: 3.524A pdb=" N GLU C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS C 410 " --> pdb=" O THR C 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER C 415 " --> pdb=" O LYS C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 434 Processing helix chain 'C' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS C 444 " --> pdb=" O HIS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'D' and resid 96 through 105 Processing helix chain 'D' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP D 186 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR D 198 " --> pdb=" O ILE D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.680A pdb=" N ILE D 238 " --> pdb=" O ILE D 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG D 255 " --> pdb=" O TRP D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 284 Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN D 304 " --> pdb=" O ASP D 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA D 324 " --> pdb=" O ILE D 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 321 through 324' Processing helix chain 'D' and resid 342 through 351 Processing helix chain 'D' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU D 395 " --> pdb=" O PRO D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER D 415 " --> pdb=" O LYS D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 434 Processing helix chain 'D' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS D 444 " --> pdb=" O HIS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'E' and resid 96 through 105 Processing helix chain 'E' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP E 186 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR E 198 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU E 239 " --> pdb=" O LYS E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.692A pdb=" N ARG E 255 " --> pdb=" O TRP E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 284 Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN E 304 " --> pdb=" O ASP E 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA E 324 " --> pdb=" O ILE E 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU E 395 " --> pdb=" O PRO E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS E 409 " --> pdb=" O GLU E 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER E 415 " --> pdb=" O LYS E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 434 Processing helix chain 'E' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing helix chain 'F' and resid 96 through 105 Processing helix chain 'F' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP F 186 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR F 198 " --> pdb=" O ILE F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE F 238 " --> pdb=" O ILE F 234 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU F 239 " --> pdb=" O LYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 248 through 255 removed outlier: 3.691A pdb=" N ARG F 255 " --> pdb=" O TRP F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 284 Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN F 304 " --> pdb=" O ASP F 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS F 305 " --> pdb=" O ASP F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 324 removed outlier: 3.720A pdb=" N ALA F 324 " --> pdb=" O ILE F 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 321 through 324' Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU F 395 " --> pdb=" O PRO F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS F 409 " --> pdb=" O GLU F 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS F 410 " --> pdb=" O THR F 406 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER F 415 " --> pdb=" O LYS F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 424 through 434 Processing helix chain 'F' and resid 438 through 446 removed outlier: 3.708A pdb=" N LYS F 444 " --> pdb=" O HIS F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 182 through 199 removed outlier: 4.107A pdb=" N ASP G 186 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR G 198 " --> pdb=" O ILE G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.681A pdb=" N ILE G 238 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU G 239 " --> pdb=" O LYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 246 Processing helix chain 'G' and resid 248 through 255 removed outlier: 3.690A pdb=" N ARG G 255 " --> pdb=" O TRP G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 284 Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.642A pdb=" N ASN G 304 " --> pdb=" O ASP G 300 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS G 305 " --> pdb=" O ASP G 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.721A pdb=" N ALA G 324 " --> pdb=" O ILE G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing helix chain 'G' and resid 342 through 351 Processing helix chain 'G' and resid 390 through 402 removed outlier: 3.525A pdb=" N GLU G 395 " --> pdb=" O PRO G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 417 removed outlier: 3.893A pdb=" N CYS G 409 " --> pdb=" O GLU G 405 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS G 410 " --> pdb=" O THR G 406 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N SER G 415 " --> pdb=" O LYS G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 424 through 434 Processing helix chain 'G' and resid 438 through 446 removed outlier: 3.707A pdb=" N LYS G 444 " --> pdb=" O HIS G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 449 No H-bonds generated for 'chain 'G' and resid 447 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE A 169 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR A 206 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN A 292 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER A 208 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN A 287 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 317 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS A 289 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU A 319 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU A 291 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 359 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 262 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 382 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE B 169 " --> pdb=" O SER B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 116 through 122 Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 216 removed outlier: 4.261A pdb=" N ILE B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR B 206 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN B 292 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 208 " --> pdb=" O ASN B 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 287 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 317 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS B 289 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU B 319 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU B 291 " --> pdb=" O GLU B 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE B 359 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 262 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 382 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE C 169 " --> pdb=" O SER C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 116 through 122 Processing sheet with id=AA9, first strand: chain 'C' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR C 206 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN C 292 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER C 208 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN C 287 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU C 317 " --> pdb=" O ASN C 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS C 289 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU C 319 " --> pdb=" O CYS C 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU C 291 " --> pdb=" O GLU C 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE C 359 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C 262 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR C 382 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 90 removed outlier: 4.693A pdb=" N PHE D 169 " --> pdb=" O SER D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 116 through 122 Processing sheet with id=AB3, first strand: chain 'D' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE D 205 " --> pdb=" O PHE D 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR D 206 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ASN D 292 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER D 208 " --> pdb=" O ASN D 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN D 287 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU D 317 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS D 289 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU D 319 " --> pdb=" O CYS D 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU D 291 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE D 359 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY D 262 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 382 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE E 169 " --> pdb=" O SER E 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 122 Processing sheet with id=AB6, first strand: chain 'E' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE E 205 " --> pdb=" O PHE E 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR E 206 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN E 292 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER E 208 " --> pdb=" O ASN E 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN E 287 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 317 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS E 289 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU E 319 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU E 291 " --> pdb=" O GLU E 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE E 359 " --> pdb=" O SER E 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY E 262 " --> pdb=" O ILE E 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR E 382 " --> pdb=" O GLY E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE F 169 " --> pdb=" O SER F 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 116 through 122 Processing sheet with id=AB9, first strand: chain 'F' and resid 213 through 216 removed outlier: 4.261A pdb=" N ILE F 205 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR F 206 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN F 292 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER F 208 " --> pdb=" O ASN F 292 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ASN F 287 " --> pdb=" O ILE F 315 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU F 317 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N CYS F 289 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N GLU F 319 " --> pdb=" O CYS F 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU F 291 " --> pdb=" O GLU F 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE F 359 " --> pdb=" O SER F 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY F 262 " --> pdb=" O ILE F 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 382 " --> pdb=" O GLY F 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 87 through 90 removed outlier: 4.692A pdb=" N PHE G 169 " --> pdb=" O SER G 157 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 116 through 122 Processing sheet with id=AC3, first strand: chain 'G' and resid 213 through 216 removed outlier: 4.260A pdb=" N ILE G 205 " --> pdb=" O PHE G 216 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR G 206 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N ASN G 292 " --> pdb=" O TYR G 206 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N SER G 208 " --> pdb=" O ASN G 292 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN G 287 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU G 317 " --> pdb=" O ASN G 287 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N CYS G 289 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N GLU G 319 " --> pdb=" O CYS G 289 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N LEU G 291 " --> pdb=" O GLU G 319 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ILE G 359 " --> pdb=" O SER G 314 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY G 262 " --> pdb=" O ILE G 380 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR G 382 " --> pdb=" O GLY G 262 " (cutoff:3.500A) 755 hydrogen bonds defined for protein. 2160 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: 1.86 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 2338 1.28 - 1.35: 2290 1.35 - 1.42: 13 1.42 - 1.48: 2317 1.48 - 1.55: 4536 Bond restraints: 11494 Sorted by residual: bond pdb=" N LEU C 177 " pdb=" CA LEU C 177 " ideal model delta sigma weight residual 1.456 1.502 -0.046 1.27e-02 6.20e+03 1.29e+01 bond pdb=" N LEU D 177 " pdb=" CA LEU D 177 " ideal model delta sigma weight residual 1.456 1.502 -0.045 1.27e-02 6.20e+03 1.28e+01 bond pdb=" N LEU F 177 " pdb=" CA LEU F 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.27e+01 bond pdb=" N LEU G 177 " pdb=" CA LEU G 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.26e+01 bond pdb=" N LEU B 177 " pdb=" CA LEU B 177 " ideal model delta sigma weight residual 1.456 1.501 -0.045 1.27e-02 6.20e+03 1.26e+01 ... (remaining 11489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 14955 1.70 - 3.41: 800 3.41 - 5.11: 107 5.11 - 6.82: 49 6.82 - 8.52: 28 Bond angle restraints: 15939 Sorted by residual: angle pdb=" N PRO F 403 " pdb=" CA PRO F 403 " pdb=" CB PRO F 403 " ideal model delta sigma weight residual 103.31 110.49 -7.18 8.90e-01 1.26e+00 6.50e+01 angle pdb=" N PRO G 403 " pdb=" CA PRO G 403 " pdb=" CB PRO G 403 " ideal model delta sigma weight residual 103.31 110.47 -7.16 8.90e-01 1.26e+00 6.48e+01 angle pdb=" N PRO B 403 " pdb=" CA PRO B 403 " pdb=" CB PRO B 403 " ideal model delta sigma weight residual 103.31 110.47 -7.16 8.90e-01 1.26e+00 6.47e+01 angle pdb=" N PRO A 403 " pdb=" CA PRO A 403 " pdb=" CB PRO A 403 " ideal model delta sigma weight residual 103.31 110.46 -7.15 8.90e-01 1.26e+00 6.45e+01 angle pdb=" N PRO D 403 " pdb=" CA PRO D 403 " pdb=" CB PRO D 403 " ideal model delta sigma weight residual 103.31 110.45 -7.14 8.90e-01 1.26e+00 6.43e+01 ... (remaining 15934 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.51: 5913 5.51 - 11.02: 639 11.02 - 16.52: 84 16.52 - 22.03: 14 22.03 - 27.54: 7 Dihedral angle restraints: 6657 sinusoidal: 0 harmonic: 6657 Sorted by residual: dihedral pdb=" CA GLN D 218 " pdb=" C GLN D 218 " pdb=" N PRO D 219 " pdb=" CA PRO D 219 " ideal model delta harmonic sigma weight residual -180.00 -152.46 -27.54 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN B 218 " pdb=" C GLN B 218 " pdb=" N PRO B 219 " pdb=" CA PRO B 219 " ideal model delta harmonic sigma weight residual -180.00 -152.48 -27.52 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA GLN E 218 " pdb=" C GLN E 218 " pdb=" N PRO E 219 " pdb=" CA PRO E 219 " ideal model delta harmonic sigma weight residual -180.00 -152.50 -27.50 0 5.00e+00 4.00e-02 3.03e+01 ... (remaining 6654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1358 0.038 - 0.076: 489 0.076 - 0.114: 234 0.114 - 0.153: 68 0.153 - 0.191: 28 Chirality restraints: 2177 Sorted by residual: chirality pdb=" CA PRO F 219 " pdb=" N PRO F 219 " pdb=" C PRO F 219 " pdb=" CB PRO F 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA PRO D 219 " pdb=" N PRO D 219 " pdb=" C PRO D 219 " pdb=" CB PRO D 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.92e-01 chirality pdb=" CA PRO A 219 " pdb=" N PRO A 219 " pdb=" C PRO A 219 " pdb=" CB PRO A 219 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 2174 not shown) Planarity restraints: 2303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 134 " -0.027 2.00e-02 2.50e+03 5.08e-02 2.59e+01 pdb=" C LEU A 134 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU A 134 " -0.032 2.00e-02 2.50e+03 pdb=" N VAL A 135 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 134 " 0.027 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C LEU G 134 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU G 134 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL G 135 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 134 " 0.027 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C LEU E 134 " -0.088 2.00e-02 2.50e+03 pdb=" O LEU E 134 " 0.032 2.00e-02 2.50e+03 pdb=" N VAL E 135 " 0.029 2.00e-02 2.50e+03 ... (remaining 2300 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 5755 2.96 - 3.45: 10927 3.45 - 3.93: 14513 3.93 - 4.42: 14813 4.42 - 4.90: 24141 Nonbonded interactions: 70149 Sorted by model distance: nonbonded pdb=" O SER B 115 " pdb=" N VAL B 135 " model vdw 2.477 3.120 nonbonded pdb=" O SER A 115 " pdb=" N VAL A 135 " model vdw 2.477 3.120 nonbonded pdb=" O SER F 115 " pdb=" N VAL F 135 " model vdw 2.477 3.120 nonbonded pdb=" O SER G 115 " pdb=" N VAL G 135 " model vdw 2.477 3.120 nonbonded pdb=" O SER E 115 " pdb=" N VAL E 135 " model vdw 2.477 3.120 ... (remaining 70144 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11494 Z= 0.354 Angle : 0.971 8.523 15939 Z= 0.625 Chirality : 0.053 0.191 2177 Planarity : 0.005 0.051 2303 Dihedral : 5.648 27.537 2303 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.63 (0.15), residues: 2268 helix: -1.55 (0.15), residues: 854 sheet: -3.04 (0.19), residues: 511 loop : -2.67 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.35 (11494) covalent geometry : angle 0.97121 / 0.62 (15939) hydrogen bonds : bond 0.21824 / 16.31 ( 755) hydrogen bonds : angle 6.84749 / 5.16 ( 2160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0098 time to fit residues: 0.2912 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 40.0000 chunk 200 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.063764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.045701 restraints weight = 12844.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.046245 restraints weight = 10223.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.046436 restraints weight = 8675.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.046882 restraints weight = 7901.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.047068 restraints weight = 7181.203| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11494 Z= 0.296 Angle : 0.670 5.239 15939 Z= 0.418 Chirality : 0.042 0.166 2177 Planarity : 0.004 0.013 2303 Dihedral : 5.972 23.812 2303 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.17), residues: 2268 helix: -0.18 (0.16), residues: 931 sheet: -2.45 (0.20), residues: 490 loop : -2.20 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.30 (11494) covalent geometry : angle 0.66982 / 0.42 (15939) hydrogen bonds : bond 0.04090 / 3.08 ( 755) hydrogen bonds : angle 5.34336 / 3.98 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.060 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0074 time to fit residues: 0.2280 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 171 optimal weight: 40.0000 chunk 138 optimal weight: 50.0000 chunk 120 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 215 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 6 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 32 optimal weight: 9.9990 chunk 195 optimal weight: 30.0000 overall best weight: 17.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.058409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.041166 restraints weight = 13500.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.041602 restraints weight = 10890.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.041957 restraints weight = 9441.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.042136 restraints weight = 8557.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.042183 restraints weight = 7961.812| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 11494 Z= 0.494 Angle : 0.845 5.889 15939 Z= 0.535 Chirality : 0.045 0.166 2177 Planarity : 0.006 0.017 2303 Dihedral : 7.478 26.111 2303 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.49 % Favored : 89.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.17), residues: 2268 helix: -0.36 (0.16), residues: 903 sheet: -2.38 (0.23), residues: 476 loop : -2.51 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.49 (11494) covalent geometry : angle 0.84508 / 0.54 (15939) hydrogen bonds : bond 0.05984 / 4.54 ( 755) hydrogen bonds : angle 6.92620 / 5.18 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.061 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0084 time to fit residues: 0.2680 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 137 optimal weight: 30.0000 chunk 180 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 114 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 12.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.055900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.039635 restraints weight = 14075.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.040081 restraints weight = 11162.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.040398 restraints weight = 9520.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.040665 restraints weight = 8494.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.040793 restraints weight = 7844.388| |-----------------------------------------------------------------------------| r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.7969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 11494 Z= 0.334 Angle : 0.666 6.168 15939 Z= 0.414 Chirality : 0.043 0.148 2177 Planarity : 0.004 0.012 2303 Dihedral : 6.258 24.246 2303 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.18), residues: 2268 helix: 0.75 (0.18), residues: 861 sheet: -2.58 (0.23), residues: 427 loop : -2.53 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.33 (11494) covalent geometry : angle 0.66570 / 0.41 (15939) hydrogen bonds : bond 0.04145 / 3.15 ( 755) hydrogen bonds : angle 5.91245 / 4.41 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.039 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0072 time to fit residues: 0.2219 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 145 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 190 optimal weight: 20.0000 chunk 116 optimal weight: 20.0000 chunk 216 optimal weight: 0.5980 chunk 222 optimal weight: 0.0770 chunk 177 optimal weight: 20.0000 chunk 17 optimal weight: 9.9990 chunk 202 optimal weight: 30.0000 chunk 99 optimal weight: 50.0000 overall best weight: 8.1348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.040818 restraints weight = 13840.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.041136 restraints weight = 10925.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.041587 restraints weight = 9336.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.041833 restraints weight = 8192.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.041986 restraints weight = 7508.721| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.8225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 11494 Z= 0.222 Angle : 0.543 5.914 15939 Z= 0.327 Chirality : 0.042 0.150 2177 Planarity : 0.003 0.009 2303 Dihedral : 5.372 23.421 2303 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.18), residues: 2268 helix: 1.34 (0.18), residues: 868 sheet: -2.36 (0.22), residues: 504 loop : -2.64 (0.20), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.22 (11494) covalent geometry : angle 0.54287 / 0.33 (15939) hydrogen bonds : bond 0.03294 / 2.50 ( 755) hydrogen bonds : angle 5.26384 / 3.92 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.074 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0102 time to fit residues: 0.3016 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 104 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 88 optimal weight: 8.9990 chunk 108 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 72 optimal weight: 50.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 162 optimal weight: 40.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.056467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.039641 restraints weight = 13178.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.039923 restraints weight = 11195.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.040192 restraints weight = 10029.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.040193 restraints weight = 9155.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.040193 restraints weight = 9153.933| |-----------------------------------------------------------------------------| r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.9200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 11494 Z= 0.408 Angle : 0.741 7.712 15939 Z= 0.465 Chirality : 0.044 0.162 2177 Planarity : 0.004 0.019 2303 Dihedral : 6.958 23.928 2303 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.98 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.16), residues: 2268 helix: -0.04 (0.16), residues: 903 sheet: -2.64 (0.22), residues: 483 loop : -3.62 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.41 (11494) covalent geometry : angle 0.74145 / 0.47 (15939) hydrogen bonds : bond 0.05123 / 3.90 ( 755) hydrogen bonds : angle 6.55626 / 4.89 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.069 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0092 time to fit residues: 0.2985 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 228 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 8 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 216 optimal weight: 9.9990 overall best weight: 15.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.039942 restraints weight = 13764.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040307 restraints weight = 11421.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.040573 restraints weight = 10059.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.040573 restraints weight = 9163.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.040573 restraints weight = 9163.460| |-----------------------------------------------------------------------------| r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 1.0029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 11494 Z= 0.403 Angle : 0.755 7.380 15939 Z= 0.472 Chirality : 0.044 0.133 2177 Planarity : 0.004 0.020 2303 Dihedral : 7.262 30.480 2303 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 16.05 % Favored : 83.64 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.54 (0.16), residues: 2268 helix: -0.62 (0.16), residues: 903 sheet: -3.17 (0.22), residues: 406 loop : -3.71 (0.17), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.40 (11494) covalent geometry : angle 0.75484 / 0.47 (15939) hydrogen bonds : bond 0.05320 / 4.05 ( 755) hydrogen bonds : angle 6.79746 / 5.07 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.066 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0086 time to fit residues: 0.2791 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 212 optimal weight: 0.2980 chunk 147 optimal weight: 10.0000 chunk 132 optimal weight: 50.0000 chunk 46 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 7.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.056510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.041085 restraints weight = 13264.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.041476 restraints weight = 10765.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.041843 restraints weight = 9302.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.041899 restraints weight = 8282.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.042071 restraints weight = 7992.345| |-----------------------------------------------------------------------------| r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.9848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 11494 Z= 0.207 Angle : 0.564 6.879 15939 Z= 0.335 Chirality : 0.042 0.145 2177 Planarity : 0.003 0.009 2303 Dihedral : 5.913 22.686 2303 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.17), residues: 2268 helix: 0.50 (0.17), residues: 868 sheet: -3.14 (0.21), residues: 448 loop : -3.31 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.21 (11494) covalent geometry : angle 0.56355 / 0.34 (15939) hydrogen bonds : bond 0.03417 / 2.61 ( 755) hydrogen bonds : angle 5.68513 / 4.23 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0086 time to fit residues: 0.2784 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 22 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 16 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 163 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 199 optimal weight: 30.0000 chunk 184 optimal weight: 20.0000 chunk 165 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 overall best weight: 15.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.055725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.039998 restraints weight = 13925.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.040363 restraints weight = 11699.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.040580 restraints weight = 10359.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.040834 restraints weight = 9409.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.040929 restraints weight = 8722.744| |-----------------------------------------------------------------------------| r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 1.0324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 11494 Z= 0.390 Angle : 0.737 7.691 15939 Z= 0.459 Chirality : 0.044 0.144 2177 Planarity : 0.004 0.013 2303 Dihedral : 7.175 30.195 2303 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.31 % Allowed : 18.83 % Favored : 80.86 % 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 : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.17), residues: 2268 helix: -0.51 (0.16), residues: 896 sheet: -3.56 (0.20), residues: 504 loop : -3.45 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.39 (11494) covalent geometry : angle 0.73661 / 0.46 (15939) hydrogen bonds : bond 0.05144 / 3.93 ( 755) hydrogen bonds : angle 6.84601 / 5.10 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0087 time to fit residues: 0.2793 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 69 optimal weight: 40.0000 chunk 143 optimal weight: 30.0000 chunk 180 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 215 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 overall best weight: 11.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.056088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.042383 restraints weight = 13422.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.041831 restraints weight = 10866.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.041898 restraints weight = 10444.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.041965 restraints weight = 10120.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2631 r_free = 0.2631 target = 0.042106 restraints weight = 9327.978| |-----------------------------------------------------------------------------| r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 1.0315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 11494 Z= 0.312 Angle : 0.659 7.539 15939 Z= 0.403 Chirality : 0.043 0.150 2177 Planarity : 0.003 0.012 2303 Dihedral : 6.602 25.858 2303 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.12 % Favored : 84.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.33 (0.17), residues: 2268 helix: -0.23 (0.16), residues: 917 sheet: -3.29 (0.21), residues: 448 loop : -3.74 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.31 (11494) covalent geometry : angle 0.65880 / 0.40 (15939) hydrogen bonds : bond 0.04281 / 3.27 ( 755) hydrogen bonds : angle 6.30102 / 4.69 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.079 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0090 time to fit residues: 0.3010 Evaluate side-chains 12 residues out of total 293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 30.0000 chunk 192 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 156 optimal weight: 30.0000 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 228 optimal weight: 40.0000 chunk 96 optimal weight: 30.0000 chunk 198 optimal weight: 50.0000 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.056911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.041506 restraints weight = 13482.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.041891 restraints weight = 10930.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.042195 restraints weight = 9355.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.042296 restraints weight = 8297.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.042544 restraints weight = 7840.297| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 1.0164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 11494 Z= 0.170 Angle : 0.519 6.178 15939 Z= 0.306 Chirality : 0.042 0.143 2177 Planarity : 0.002 0.010 2303 Dihedral : 5.540 23.435 2303 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.18), residues: 2268 helix: 0.88 (0.17), residues: 875 sheet: -3.24 (0.22), residues: 448 loop : -3.31 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 96 PHE 0.000 0.000 PHE A 99 TRP 0.000 0.000 TRP A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.17 (11494) covalent geometry : angle 0.51896 / 0.31 (15939) hydrogen bonds : bond 0.03023 / 2.30 ( 755) hydrogen bonds : angle 5.40620 / 4.02 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 912.87 seconds wall clock time: 16 minutes 24.64 seconds (984.64 seconds total)