Starting phenix.real_space_refine on Wed Sep 17 21:46:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh5_10194/09_2025/6sh5_10194.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh5_10194/09_2025/6sh5_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_2025/6sh5_10194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2025/6sh5_10194.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2025/6sh5_10194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh5_10194/09_2025/6sh5_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-2.0-5805/lib/python3.9/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: 1.11, per 1000 atoms: 0.10 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: 1.16 Conformation dependent library (CDL) restraints added in 573.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.59 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: 1.97 Time building geometry restraints manager: 1.43 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: 0.06 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.880 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 aren 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 covalent geometry : bond 0.00492 (11494) covalent geometry : angle 0.97121 (15939) hydrogen bonds : bond 0.21824 ( 755) hydrogen bonds : angle 6.84749 ( 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 : 0.064 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0102 time to fit residues: 0.2896 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 : 0.063 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- 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: 0.8057 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 aren 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 covalent geometry : bond 0.00409 (11494) covalent geometry : angle 0.66982 (15939) hydrogen bonds : bond 0.04090 ( 755) hydrogen bonds : angle 5.34336 ( 2160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 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 : 0.059 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0084 time to fit residues: 0.2638 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 ------------------------------------------------------------------------------- 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: 7.9990 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: 15.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.058476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.043651 restraints weight = 13738.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.043078 restraints weight = 12454.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.043272 restraints weight = 10914.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.043314 restraints weight = 10087.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.043670 restraints weight = 9216.796| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.7340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11494 Z= 0.438 Angle : 0.804 5.869 15939 Z= 0.508 Chirality : 0.044 0.159 2177 Planarity : 0.005 0.013 2303 Dihedral : 7.217 24.717 2303 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.11 % Favored : 88.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.17), residues: 2268 helix: -0.29 (0.16), residues: 896 sheet: -2.52 (0.22), residues: 476 loop : -2.43 (0.21), 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 covalent geometry : bond 0.00611 (11494) covalent geometry : angle 0.80357 (15939) hydrogen bonds : bond 0.05541 ( 755) hydrogen bonds : angle 6.72336 ( 2160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 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: 0.0075 time to fit residues: 0.2515 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 : 0.062 ------------------------------------------------------------------------------- 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: 20.0000 chunk 29 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 114 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 11.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.039639 restraints weight = 14043.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.040055 restraints weight = 11019.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.040407 restraints weight = 9334.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.040407 restraints weight = 8205.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.040407 restraints weight = 8205.233| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.7932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 11494 Z= 0.318 Angle : 0.650 6.038 15939 Z= 0.404 Chirality : 0.043 0.155 2177 Planarity : 0.003 0.010 2303 Dihedral : 6.248 23.484 2303 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.18), residues: 2268 helix: 0.75 (0.17), residues: 847 sheet: -2.50 (0.23), residues: 427 loop : -2.63 (0.20), residues: 994 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 covalent geometry : bond 0.00442 (11494) covalent geometry : angle 0.65004 (15939) hydrogen bonds : bond 0.03953 ( 755) hydrogen bonds : angle 5.99942 ( 2160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 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: 0.2664 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 : 0.062 ------------------------------------------------------------------------------- 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: 0.0020 chunk 222 optimal weight: 0.2980 chunk 177 optimal weight: 30.0000 chunk 17 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 99 optimal weight: 50.0000 overall best weight: 10.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.057242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.040082 restraints weight = 13197.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.040465 restraints weight = 11038.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.040687 restraints weight = 9687.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.040926 restraints weight = 8860.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.041029 restraints weight = 8214.468| |-----------------------------------------------------------------------------| r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.8655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 11494 Z= 0.269 Angle : 0.593 6.015 15939 Z= 0.363 Chirality : 0.043 0.148 2177 Planarity : 0.003 0.009 2303 Dihedral : 5.682 21.158 2303 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.27 % Favored : 86.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.17), residues: 2268 helix: 0.45 (0.17), residues: 854 sheet: -2.67 (0.22), residues: 518 loop : -3.20 (0.19), 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 covalent geometry : bond 0.00374 (11494) covalent geometry : angle 0.59299 (15939) hydrogen bonds : bond 0.03872 ( 755) hydrogen bonds : angle 5.73612 ( 2160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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 : 0.062 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0084 time to fit residues: 0.2672 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 : 0.106 ------------------------------------------------------------------------------- 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: 7.9990 chunk 143 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 88 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 21 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 overall best weight: 17.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.055363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.038777 restraints weight = 13555.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.039111 restraints weight = 11466.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2571 r_free = 0.2571 target = 0.039299 restraints weight = 10114.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.039497 restraints weight = 9330.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.039532 restraints weight = 8719.401| |-----------------------------------------------------------------------------| r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 1.0004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 11494 Z= 0.458 Angle : 0.829 8.215 15939 Z= 0.521 Chirality : 0.045 0.141 2177 Planarity : 0.005 0.021 2303 Dihedral : 7.969 35.332 2303 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.93 % Allowed : 21.60 % Favored : 77.47 % 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 aren not related in a simple way. whole: -4.73 (0.15), residues: 2268 helix: -1.74 (0.15), residues: 847 sheet: -3.57 (0.22), residues: 448 loop : -4.20 (0.16), residues: 973 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 covalent geometry : bond 0.00641 (11494) covalent geometry : angle 0.82932 (15939) hydrogen bonds : bond 0.06023 ( 755) hydrogen bonds : angle 7.43067 ( 2160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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 : 0.048 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0082 time to fit residues: 0.2308 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 : 0.063 ------------------------------------------------------------------------------- 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: 40.0000 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: 10.0000 chunk 5 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 76 optimal weight: 30.0000 chunk 216 optimal weight: 3.9990 overall best weight: 14.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.040214 restraints weight = 13459.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040619 restraints weight = 11090.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.040886 restraints weight = 9619.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.041114 restraints weight = 8704.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 14)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.041187 restraints weight = 8031.403| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 1.0131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 11494 Z= 0.373 Angle : 0.718 7.266 15939 Z= 0.445 Chirality : 0.044 0.148 2177 Planarity : 0.004 0.016 2303 Dihedral : 7.103 28.655 2303 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.31 % Allowed : 20.68 % Favored : 79.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.39 (0.15), residues: 2268 helix: -1.45 (0.15), residues: 889 sheet: -3.31 (0.22), residues: 392 loop : -4.17 (0.17), residues: 987 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 covalent geometry : bond 0.00521 (11494) covalent geometry : angle 0.71841 (15939) hydrogen bonds : bond 0.05035 ( 755) hydrogen bonds : angle 6.83947 ( 2160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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: 0.2692 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 : 0.051 ------------------------------------------------------------------------------- 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: 10.0000 chunk 180 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 89 optimal weight: 0.0970 chunk 32 optimal weight: 30.0000 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 132 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.056885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.041154 restraints weight = 13169.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.041353 restraints weight = 10676.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.041803 restraints weight = 9518.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.042072 restraints weight = 8379.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2649 r_free = 0.2649 target = 0.042072 restraints weight = 7514.322| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.9875 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= 0.169 Angle : 0.517 6.058 15939 Z= 0.304 Chirality : 0.043 0.141 2177 Planarity : 0.002 0.010 2303 Dihedral : 5.402 22.020 2303 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.26 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 aren not related in a simple way. whole: -3.27 (0.17), residues: 2268 helix: -0.14 (0.16), residues: 868 sheet: -3.41 (0.21), residues: 448 loop : -3.49 (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 covalent geometry : bond 0.00236 (11494) covalent geometry : angle 0.51705 (15939) hydrogen bonds : bond 0.02947 ( 755) hydrogen bonds : angle 5.36940 ( 2160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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: 0.0085 time to fit residues: 0.2712 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 : 0.063 ------------------------------------------------------------------------------- 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: 9.9990 chunk 109 optimal weight: 20.0000 chunk 163 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 199 optimal weight: 30.0000 chunk 184 optimal weight: 0.0670 chunk 165 optimal weight: 50.0000 chunk 20 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 overall best weight: 9.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.040244 restraints weight = 13640.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.040626 restraints weight = 11158.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.040863 restraints weight = 9699.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.040959 restraints weight = 8754.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.041262 restraints weight = 8310.444| |-----------------------------------------------------------------------------| r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 1.0070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 11494 Z= 0.243 Angle : 0.573 6.372 15939 Z= 0.347 Chirality : 0.042 0.140 2177 Planarity : 0.003 0.010 2303 Dihedral : 5.775 25.375 2303 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.75 % Favored : 79.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.17), residues: 2268 helix: -0.21 (0.16), residues: 868 sheet: -3.45 (0.21), residues: 448 loop : -3.63 (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 covalent geometry : bond 0.00339 (11494) covalent geometry : angle 0.57276 (15939) hydrogen bonds : bond 0.03642 ( 755) hydrogen bonds : angle 5.75458 ( 2160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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 : 0.046 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0069 time to fit residues: 0.2025 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 140 optimal weight: 50.0000 chunk 110 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 143 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 215 optimal weight: 0.0020 chunk 152 optimal weight: 30.0000 overall best weight: 10.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.042571 restraints weight = 13373.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.041737 restraints weight = 11632.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.041888 restraints weight = 11184.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.041930 restraints weight = 10385.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.042316 restraints weight = 9244.774| |-----------------------------------------------------------------------------| r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 1.0307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 11494 Z= 0.261 Angle : 0.594 6.511 15939 Z= 0.361 Chirality : 0.043 0.145 2177 Planarity : 0.003 0.010 2303 Dihedral : 5.896 23.078 2303 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.31 % Allowed : 19.75 % Favored : 79.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.17), residues: 2268 helix: -0.46 (0.16), residues: 875 sheet: -3.57 (0.22), residues: 448 loop : -3.76 (0.19), 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 covalent geometry : bond 0.00364 (11494) covalent geometry : angle 0.59428 (15939) hydrogen bonds : bond 0.03860 ( 755) hydrogen bonds : angle 5.87662 ( 2160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2592 Ramachandran restraints generated. 1296 Oldfield, 0 Emsley, 1296 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: 0.0086 time to fit residues: 0.2749 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 38 optimal weight: 40.0000 chunk 192 optimal weight: 9.9990 chunk 151 optimal weight: 10.0000 chunk 156 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 20.0000 chunk 228 optimal weight: 30.0000 chunk 96 optimal weight: 30.0000 chunk 198 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.042635 restraints weight = 13654.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.042107 restraints weight = 10128.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.042297 restraints weight = 9571.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.042480 restraints weight = 9051.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.042427 restraints weight = 8177.631| |-----------------------------------------------------------------------------| r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 1.0329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 11494 Z= 0.223 Angle : 0.552 6.088 15939 Z= 0.332 Chirality : 0.042 0.140 2177 Planarity : 0.003 0.010 2303 Dihedral : 5.557 22.681 2303 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.44 % Favored : 80.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.17), residues: 2268 helix: -0.20 (0.16), residues: 875 sheet: -3.58 (0.22), residues: 448 loop : -3.69 (0.19), 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 covalent geometry : bond 0.00310 (11494) covalent geometry : angle 0.55228 (15939) hydrogen bonds : bond 0.03407 ( 755) hydrogen bonds : angle 5.66674 ( 2160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 801.29 seconds wall clock time: 14 minutes 27.94 seconds (867.94 seconds total)