Starting phenix.real_space_refine on Tue Jul 29 19:12:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sh5_10194/07_2025/6sh5_10194.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sh5_10194/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6sh5_10194/07_2025/6sh5_10194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sh5_10194/07_2025/6sh5_10194.map" model { file = "/net/cci-nas-00/data/ceres_data/6sh5_10194/07_2025/6sh5_10194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sh5_10194/07_2025/6sh5_10194.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'ARG:plan': 14, 'TYR:plan': 14, 'ASN:plan1': 16, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 16, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 556 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 4.96, per 1000 atoms: 0.43 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: 3.53 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.20 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: 4.17 Time building geometry restraints manager: 4.01 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } 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: 1.260 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 30.400 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.21824 ( 755) hydrogen bonds : angle 6.84749 ( 2160) covalent geometry : bond 0.00492 (11494) covalent geometry : angle 0.97121 (15939) *********************** 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 : 0.192 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0261 time to fit residues: 0.7909 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 : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 30.0000 chunk 175 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 181 optimal weight: 20.0000 chunk 70 optimal weight: 40.0000 chunk 110 optimal weight: 30.0000 chunk 134 optimal weight: 20.0000 chunk 209 optimal weight: 40.0000 overall best weight: 14.0000 ------------------------------------------------------------------------------- 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 = 0.3119 r_free = 0.3119 target = 0.061469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.045790 restraints weight = 13500.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.045379 restraints weight = 10611.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.045514 restraints weight = 9319.860| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.5537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 11494 Z= 0.410 Angle : 0.818 5.818 15939 Z= 0.513 Chirality : 0.045 0.180 2177 Planarity : 0.005 0.014 2303 Dihedral : 7.078 26.780 2303 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2268 helix: -0.84 (0.15), residues: 917 sheet: -2.75 (0.19), residues: 525 loop : -2.15 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.05569 ( 755) hydrogen bonds : angle 6.35091 ( 2160) covalent geometry : bond 0.00570 (11494) covalent geometry : angle 0.81816 (15939) *********************** 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 : 0.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0177 time to fit residues: 0.6245 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 : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 199 optimal weight: 10.0000 chunk 174 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 149 optimal weight: 10.0000 chunk 228 optimal weight: 20.0000 chunk 204 optimal weight: 40.0000 chunk 78 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 128 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 overall best weight: 6.5192 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.061073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.045611 restraints weight = 13203.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.045048 restraints weight = 10755.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.045203 restraints weight = 9690.358| |-----------------------------------------------------------------------------| r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 11494 Z= 0.198 Angle : 0.516 6.138 15939 Z= 0.310 Chirality : 0.042 0.155 2177 Planarity : 0.002 0.009 2303 Dihedral : 4.914 23.165 2303 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.18), residues: 2268 helix: 0.65 (0.17), residues: 938 sheet: -2.31 (0.23), residues: 448 loop : -2.33 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 755) hydrogen bonds : angle 4.54681 ( 2160) covalent geometry : bond 0.00274 (11494) covalent geometry : angle 0.51619 (15939) *********************** 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 : 0.205 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0201 time to fit residues: 0.7202 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 : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 230 optimal weight: 30.0000 chunk 78 optimal weight: 0.2980 chunk 171 optimal weight: 40.0000 chunk 195 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 182 optimal weight: 20.0000 chunk 189 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 chunk 65 optimal weight: 30.0000 chunk 93 optimal weight: 0.0270 chunk 5 optimal weight: 30.0000 overall best weight: 8.2046 ------------------------------------------------------------------------------- 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 = 0.3072 r_free = 0.3072 target = 0.059022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.042834 restraints weight = 12949.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.043314 restraints weight = 10237.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.043598 restraints weight = 8760.038| |-----------------------------------------------------------------------------| r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.7251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11494 Z= 0.250 Angle : 0.579 5.692 15939 Z= 0.356 Chirality : 0.043 0.161 2177 Planarity : 0.003 0.009 2303 Dihedral : 5.463 21.701 2303 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 2268 helix: 1.28 (0.18), residues: 861 sheet: -2.43 (0.22), residues: 476 loop : -1.80 (0.22), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 755) hydrogen bonds : angle 5.12859 ( 2160) covalent geometry : bond 0.00347 (11494) covalent geometry : angle 0.57881 (15939) *********************** REFINEMENT MACRO_CYCLE 4 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 : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0190 time to fit residues: 0.6908 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 124 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 126 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 chunk 104 optimal weight: 30.0000 chunk 168 optimal weight: 40.0000 chunk 34 optimal weight: 30.0000 chunk 135 optimal weight: 30.0000 overall best weight: 12.2110 ------------------------------------------------------------------------------- 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 = 0.3010 r_free = 0.3010 target = 0.057331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.040348 restraints weight = 13085.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.040676 restraints weight = 10972.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.040964 restraints weight = 9637.159| |-----------------------------------------------------------------------------| r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.8670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 11494 Z= 0.352 Angle : 0.689 6.596 15939 Z= 0.431 Chirality : 0.043 0.149 2177 Planarity : 0.004 0.012 2303 Dihedral : 6.346 22.594 2303 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.18), residues: 2268 helix: 0.31 (0.17), residues: 910 sheet: -2.85 (0.20), residues: 560 loop : -2.57 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 755) hydrogen bonds : angle 6.29889 ( 2160) covalent geometry : bond 0.00488 (11494) covalent geometry : angle 0.68930 (15939) *********************** REFINEMENT MACRO_CYCLE 5 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0199 time to fit residues: 0.7136 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 : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 30.0000 chunk 171 optimal weight: 50.0000 chunk 162 optimal weight: 30.0000 chunk 226 optimal weight: 30.0000 chunk 192 optimal weight: 20.0000 chunk 145 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 135 optimal weight: 40.0000 chunk 128 optimal weight: 10.0000 overall best weight: 13.9998 ------------------------------------------------------------------------------- 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 = 0.2991 r_free = 0.2991 target = 0.056209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.039625 restraints weight = 13410.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.039916 restraints weight = 11388.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.040011 restraints weight = 10170.911| |-----------------------------------------------------------------------------| r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.9564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 11494 Z= 0.366 Angle : 0.708 7.733 15939 Z= 0.441 Chirality : 0.044 0.150 2177 Planarity : 0.004 0.020 2303 Dihedral : 6.939 28.312 2303 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 15.74 % Favored : 83.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.16), residues: 2268 helix: -0.58 (0.15), residues: 889 sheet: -2.94 (0.21), residues: 469 loop : -3.57 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 755) hydrogen bonds : angle 6.27336 ( 2160) covalent geometry : bond 0.00511 (11494) covalent geometry : angle 0.70827 (15939) *********************** REFINEMENT MACRO_CYCLE 6 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 : 0.200 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0196 time to fit residues: 0.7069 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 : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 81 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 200 optimal weight: 30.0000 chunk 219 optimal weight: 20.0000 chunk 149 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 142 optimal weight: 30.0000 chunk 140 optimal weight: 50.0000 chunk 222 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 228 optimal weight: 30.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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 = 0.3012 r_free = 0.3012 target = 0.056495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.040617 restraints weight = 13742.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.041008 restraints weight = 11383.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.041247 restraints weight = 9983.952| |-----------------------------------------------------------------------------| r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.9655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 11494 Z= 0.255 Angle : 0.581 6.580 15939 Z= 0.354 Chirality : 0.042 0.136 2177 Planarity : 0.003 0.011 2303 Dihedral : 5.823 23.551 2303 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.80 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.17), residues: 2268 helix: -0.07 (0.17), residues: 868 sheet: -3.19 (0.21), residues: 448 loop : -3.35 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 755) hydrogen bonds : angle 5.80197 ( 2160) covalent geometry : bond 0.00355 (11494) covalent geometry : angle 0.58059 (15939) *********************** REFINEMENT MACRO_CYCLE 7 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 : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0184 time to fit residues: 0.6906 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 : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 2 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 61 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 210 optimal weight: 20.0000 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.055601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.041750 restraints weight = 13492.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.041403 restraints weight = 10490.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.041454 restraints weight = 10035.748| |-----------------------------------------------------------------------------| r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 1.0039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11494 Z= 0.319 Angle : 0.657 7.493 15939 Z= 0.404 Chirality : 0.043 0.143 2177 Planarity : 0.003 0.011 2303 Dihedral : 6.481 27.346 2303 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.37 % Favored : 79.63 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.16), residues: 2268 helix: -0.54 (0.16), residues: 868 sheet: -3.20 (0.21), residues: 434 loop : -3.74 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 755) hydrogen bonds : angle 6.16785 ( 2160) covalent geometry : bond 0.00448 (11494) covalent geometry : angle 0.65708 (15939) *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.176 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0185 time to fit residues: 0.6494 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 : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 67 optimal weight: 40.0000 chunk 83 optimal weight: 20.0000 chunk 200 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 chunk 131 optimal weight: 30.0000 chunk 225 optimal weight: 9.9990 chunk 54 optimal weight: 0.0010 chunk 167 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 overall best weight: 11.9998 ------------------------------------------------------------------------------- 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 = 0.2991 r_free = 0.2991 target = 0.055976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.042075 restraints weight = 13512.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.041571 restraints weight = 11077.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.041715 restraints weight = 10763.847| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 1.0258 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= 0.307 Angle : 0.638 6.842 15939 Z= 0.393 Chirality : 0.043 0.142 2177 Planarity : 0.003 0.012 2303 Dihedral : 6.279 25.345 2303 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.21 % Favored : 81.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.17), residues: 2268 helix: -0.39 (0.16), residues: 868 sheet: -3.36 (0.22), residues: 434 loop : -3.75 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04248 ( 755) hydrogen bonds : angle 6.22709 ( 2160) covalent geometry : bond 0.00429 (11494) covalent geometry : angle 0.63809 (15939) *********************** REFINEMENT MACRO_CYCLE 9 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 : 0.177 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0180 time to fit residues: 0.6386 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 : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 201 optimal weight: 40.0000 chunk 158 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 220 optimal weight: 0.6980 chunk 140 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 169 optimal weight: 40.0000 overall best weight: 14.1394 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.055553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2628 r_free = 0.2628 target = 0.041929 restraints weight = 14003.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.041349 restraints weight = 11692.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.041433 restraints weight = 10973.430| |-----------------------------------------------------------------------------| r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 1.0589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 11494 Z= 0.363 Angle : 0.714 7.758 15939 Z= 0.441 Chirality : 0.043 0.147 2177 Planarity : 0.004 0.013 2303 Dihedral : 6.920 27.522 2303 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 21.30 % Favored : 78.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.16), residues: 2268 helix: -0.94 (0.15), residues: 903 sheet: -3.58 (0.21), residues: 434 loop : -4.14 (0.18), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.04908 ( 755) hydrogen bonds : angle 6.69173 ( 2160) covalent geometry : bond 0.00509 (11494) covalent geometry : angle 0.71446 (15939) ********************** REFINEMENT MACRO_CYCLE 10 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 : 0.195 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0197 time to fit residues: 0.7020 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 : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 3.9990 chunk 166 optimal weight: 40.0000 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 50.0000 chunk 110 optimal weight: 20.0000 chunk 227 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 209 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- 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 = 0.2982 r_free = 0.2982 target = 0.054879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.038995 restraints weight = 13875.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.039312 restraints weight = 11492.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.039584 restraints weight = 10053.642| |-----------------------------------------------------------------------------| r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 1.0351 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= 0.172 Angle : 0.520 5.694 15939 Z= 0.308 Chirality : 0.042 0.144 2177 Planarity : 0.002 0.010 2303 Dihedral : 5.515 22.369 2303 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.17), residues: 2268 helix: 0.20 (0.16), residues: 882 sheet: -3.66 (0.21), residues: 448 loop : -3.57 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 98 PHE 0.000 0.000 PHE A 99 TYR 0.000 0.000 TYR A 96 Details of bonding type rmsd hydrogen bonds : bond 0.02990 ( 755) hydrogen bonds : angle 5.50968 ( 2160) covalent geometry : bond 0.00238 (11494) covalent geometry : angle 0.52029 (15939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1954.20 seconds wall clock time: 34 minutes 44.80 seconds (2084.80 seconds total)