Starting phenix.real_space_refine on Sat Aug 23 21:26:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc7_42116/08_2025/8uc7_42116.map" } resolution = 2.9 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= 0.002 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 9748 2.51 5 N 2456 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14840 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 3633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3633 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 101} Link IDs: {'PTRANS': 16, 'TRANS': 467} Chain breaks: 1 Unresolved non-hydrogen bonds: 337 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 266 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'ARG:plan': 9, 'PHE:plan': 3, 'TRP:plan': 1, 'GLU:plan': 13, 'GLN:plan1': 1, 'ASP:plan': 11, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 77 Unusual residues: {'PCW': 3, 'PFL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 23 Restraints were copied for chains: A, B, C Time building chain proxies: 3.58, per 1000 atoms: 0.24 Number of scatterers: 14840 At special positions: 0 Unit cell: (114.915, 114.915, 115.73, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2528 8.00 N 2456 7.00 C 9748 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: 1.12 Conformation dependent library (CDL) restraints added in 750.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3688 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 8 sheets defined 73.6% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Proline residue: D 161 - end of helix removed outlier: 3.901A pdb=" N PHE D 167 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 195 " --> pdb=" O ILE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 221 removed outlier: 3.807A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER D 228 " --> pdb=" O VAL D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 268 No H-bonds generated for 'chain 'D' and resid 266 through 268' Processing helix chain 'D' and resid 269 through 290 removed outlier: 4.293A pdb=" N ARG D 273 " --> pdb=" O LEU D 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 4.504A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS D 468 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU D 469 " --> pdb=" O ASN D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN D 478 " --> pdb=" O PRO D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 543 Processing helix chain 'D' and resid 566 through 574 Processing helix chain 'D' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL D 586 " --> pdb=" O ALA D 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN A 103 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 100 through 103' Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.681A pdb=" N ARG A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 Processing helix chain 'A' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL A 158 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Proline residue: A 161 - end of helix removed outlier: 3.901A pdb=" N PHE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG A 195 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.806A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER A 228 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 290 removed outlier: 4.293A pdb=" N ARG A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 4.505A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 3.577A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS A 468 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 543 Processing helix chain 'A' and resid 566 through 574 Processing helix chain 'A' and resid 576 through 586 removed outlier: 3.984A pdb=" N VAL A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN B 103 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 103' Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 Processing helix chain 'B' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL B 158 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Proline residue: B 161 - end of helix removed outlier: 3.901A pdb=" N PHE B 167 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 196 removed outlier: 3.808A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 195 " --> pdb=" O ILE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 221 removed outlier: 3.808A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 268 No H-bonds generated for 'chain 'B' and resid 266 through 268' Processing helix chain 'B' and resid 269 through 290 removed outlier: 4.294A pdb=" N ARG B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 4.505A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 422 removed outlier: 3.748A pdb=" N VAL B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 471 removed outlier: 5.550A pdb=" N LYS B 468 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 469 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 removed outlier: 4.077A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 566 through 574 Processing helix chain 'B' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL B 586 " --> pdb=" O ALA B 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 100 through 103 removed outlier: 3.832A pdb=" N GLN C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 103' Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.680A pdb=" N ARG C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 Processing helix chain 'C' and resid 139 through 167 removed outlier: 3.676A pdb=" N VAL C 158 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Proline residue: C 161 - end of helix removed outlier: 3.901A pdb=" N PHE C 167 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 196 removed outlier: 3.809A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 195 " --> pdb=" O ILE C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 221 removed outlier: 3.807A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.697A pdb=" N SER C 228 " --> pdb=" O VAL C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 241 removed outlier: 3.580A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 265 removed outlier: 4.085A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 269 through 290 removed outlier: 4.292A pdb=" N ARG C 273 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 4.504A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 4.149A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 422 removed outlier: 3.747A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 3.578A pdb=" N GLU C 452 " --> pdb=" O ASN C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 471 removed outlier: 5.549A pdb=" N LYS C 468 " --> pdb=" O PHE C 464 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU C 469 " --> pdb=" O ASN C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.870A pdb=" N ASN C 478 " --> pdb=" O PRO C 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 4.076A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 543 Processing helix chain 'C' and resid 566 through 574 Processing helix chain 'C' and resid 576 through 586 removed outlier: 3.985A pdb=" N VAL C 586 " --> pdb=" O ALA C 582 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR D 501 " --> pdb=" O ALA D 555 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA D 555 " --> pdb=" O TYR D 501 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.699A pdb=" N TYR A 501 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A 555 " --> pdb=" O TYR A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.626A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR B 501 " --> pdb=" O ALA B 555 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA B 555 " --> pdb=" O TYR B 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.627A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.698A pdb=" N TYR C 501 " --> pdb=" O ALA C 555 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ALA C 555 " --> pdb=" O TYR C 501 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2296 1.27 - 1.41: 4126 1.41 - 1.54: 8379 1.54 - 1.68: 203 1.68 - 1.81: 188 Bond restraints: 15192 Sorted by residual: bond pdb=" C19 PCW C 704 " pdb=" C20 PCW C 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW B 704 " pdb=" C20 PCW B 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW A 704 " pdb=" C20 PCW A 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C19 PCW D 704 " pdb=" C20 PCW D 704 " ideal model delta sigma weight residual 1.333 1.535 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C18 PCW B 704 " pdb=" C19 PCW B 704 " ideal model delta sigma weight residual 1.497 1.333 0.164 2.00e-02 2.50e+03 6.75e+01 ... (remaining 15187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 16949 2.30 - 4.60: 3443 4.60 - 6.90: 143 6.90 - 9.21: 21 9.21 - 11.51: 24 Bond angle restraints: 20580 Sorted by residual: angle pdb=" N TYR C 513 " pdb=" CA TYR C 513 " pdb=" C TYR C 513 " ideal model delta sigma weight residual 109.52 121.03 -11.51 1.55e+00 4.16e-01 5.51e+01 angle pdb=" N TYR D 513 " pdb=" CA TYR D 513 " pdb=" C TYR D 513 " ideal model delta sigma weight residual 109.52 120.99 -11.47 1.55e+00 4.16e-01 5.48e+01 angle pdb=" N TYR B 513 " pdb=" CA TYR B 513 " pdb=" C TYR B 513 " ideal model delta sigma weight residual 109.52 120.99 -11.47 1.55e+00 4.16e-01 5.48e+01 angle pdb=" N TYR A 513 " pdb=" CA TYR A 513 " pdb=" C TYR A 513 " ideal model delta sigma weight residual 109.52 120.98 -11.46 1.55e+00 4.16e-01 5.47e+01 angle pdb=" CB HIS C 136 " pdb=" CG HIS C 136 " pdb=" CD2 HIS C 136 " ideal model delta sigma weight residual 131.20 125.33 5.87 1.30e+00 5.92e-01 2.04e+01 ... (remaining 20575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.76: 8504 21.76 - 43.53: 336 43.53 - 65.29: 68 65.29 - 87.05: 12 87.05 - 108.82: 4 Dihedral angle restraints: 8924 sinusoidal: 3220 harmonic: 5704 Sorted by residual: dihedral pdb=" CA TYR A 361 " pdb=" C TYR A 361 " pdb=" N GLY A 362 " pdb=" CA GLY A 362 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA TYR B 361 " pdb=" C TYR B 361 " pdb=" N GLY B 362 " pdb=" CA GLY B 362 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA TYR D 361 " pdb=" C TYR D 361 " pdb=" N GLY D 362 " pdb=" CA GLY D 362 " ideal model delta harmonic sigma weight residual -180.00 -157.24 -22.76 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 8921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1418 0.074 - 0.148: 686 0.148 - 0.222: 132 0.222 - 0.296: 31 0.296 - 0.369: 9 Chirality restraints: 2276 Sorted by residual: chirality pdb=" CA ASP C 290 " pdb=" N ASP C 290 " pdb=" C ASP C 290 " pdb=" CB ASP C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ASP B 290 " pdb=" N ASP B 290 " pdb=" C ASP B 290 " pdb=" CB ASP B 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA ASP D 290 " pdb=" N ASP D 290 " pdb=" C ASP D 290 " pdb=" CB ASP D 290 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.41e+00 ... (remaining 2273 not shown) Planarity restraints: 2604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 281 " 0.185 2.00e-02 2.50e+03 8.99e-02 2.02e+02 pdb=" CG TRP B 281 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP B 281 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP B 281 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP B 281 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP B 281 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP B 281 " -0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 281 " 0.109 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 281 " -0.047 2.00e-02 2.50e+03 pdb=" CH2 TRP B 281 " 0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 281 " -0.184 2.00e-02 2.50e+03 8.99e-02 2.02e+02 pdb=" CG TRP D 281 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 281 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP D 281 " 0.079 2.00e-02 2.50e+03 pdb=" NE1 TRP D 281 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP D 281 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 281 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 281 " -0.109 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 281 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP D 281 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " 0.184 2.00e-02 2.50e+03 8.98e-02 2.02e+02 pdb=" CG TRP C 281 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " -0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " 0.108 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " 0.085 2.00e-02 2.50e+03 ... (remaining 2601 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 7488 3.03 - 3.50: 15740 3.50 - 3.96: 22934 3.96 - 4.43: 25800 4.43 - 4.90: 42992 Nonbonded interactions: 114954 Sorted by model distance: nonbonded pdb=" OH TYR B 435 " pdb=" OE2 GLU C 452 " model vdw 2.560 3.040 nonbonded pdb=" OH TYR A 435 " pdb=" OE2 GLU B 452 " model vdw 2.563 3.040 nonbonded pdb=" OH TYR D 435 " pdb=" OE2 GLU A 452 " model vdw 2.564 3.040 nonbonded pdb=" OG SER D 419 " pdb=" NZ LYS A 442 " model vdw 2.566 3.120 nonbonded pdb=" OG SER B 419 " pdb=" NZ LYS C 442 " model vdw 2.567 3.120 ... (remaining 114949 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: 0.05 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.170 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 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 : 0.015 0.202 15192 Z= 0.859 Angle : 1.750 11.508 20580 Z= 1.175 Chirality : 0.087 0.369 2276 Planarity : 0.014 0.126 2604 Dihedral : 13.195 108.815 5236 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.22 % 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: -0.57 (0.19), residues: 1920 helix: -0.54 (0.13), residues: 1284 sheet: -1.61 (0.56), residues: 64 loop : 0.72 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 428 TYR 0.115 0.016 TYR A 347 PHE 0.047 0.008 PHE B 186 TRP 0.185 0.023 TRP B 281 HIS 0.009 0.003 HIS B 437 Details of bonding type rmsd covalent geometry : bond 0.01456 (15192) covalent geometry : angle 1.75033 (20580) hydrogen bonds : bond 0.18882 ( 1005) hydrogen bonds : angle 7.04143 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.613 Fit side-chains REVERT: D 101 MET cc_start: 0.7005 (mmt) cc_final: 0.6571 (mtt) REVERT: D 121 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6329 (mm-30) REVERT: D 189 ASP cc_start: 0.8439 (t70) cc_final: 0.8193 (t70) REVERT: D 287 MET cc_start: 0.6484 (mmm) cc_final: 0.5992 (mpp) REVERT: D 343 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7744 (mtmm) REVERT: D 408 GLN cc_start: 0.7349 (mm-40) cc_final: 0.6909 (mp10) REVERT: D 412 LYS cc_start: 0.7397 (mttm) cc_final: 0.6842 (mttp) REVERT: D 429 GLN cc_start: 0.7356 (mm-40) cc_final: 0.6864 (mm110) REVERT: D 433 ASP cc_start: 0.7567 (t70) cc_final: 0.7042 (m-30) REVERT: D 451 ASN cc_start: 0.8147 (m-40) cc_final: 0.7829 (m110) REVERT: D 460 GLU cc_start: 0.8124 (tt0) cc_final: 0.7753 (tt0) REVERT: A 101 MET cc_start: 0.6956 (mmt) cc_final: 0.6507 (mtt) REVERT: A 121 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6307 (mm-30) REVERT: A 149 MET cc_start: 0.7676 (mmp) cc_final: 0.7460 (mmm) REVERT: A 189 ASP cc_start: 0.8441 (t70) cc_final: 0.8160 (t70) REVERT: A 238 ILE cc_start: 0.7331 (tp) cc_final: 0.7127 (pp) REVERT: A 287 MET cc_start: 0.6397 (mmm) cc_final: 0.5950 (mpp) REVERT: A 343 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7780 (mtmm) REVERT: A 401 ASP cc_start: 0.6359 (p0) cc_final: 0.6133 (m-30) REVERT: A 408 GLN cc_start: 0.7324 (mm-40) cc_final: 0.6864 (mp10) REVERT: A 412 LYS cc_start: 0.7409 (mttm) cc_final: 0.6861 (mttp) REVERT: A 429 GLN cc_start: 0.7406 (mm-40) cc_final: 0.6837 (mm110) REVERT: A 433 ASP cc_start: 0.7515 (t70) cc_final: 0.6950 (m-30) REVERT: A 448 ASN cc_start: 0.7688 (t160) cc_final: 0.7420 (m110) REVERT: A 451 ASN cc_start: 0.8199 (m-40) cc_final: 0.7916 (m110) REVERT: A 460 GLU cc_start: 0.8128 (tt0) cc_final: 0.7848 (tt0) REVERT: B 101 MET cc_start: 0.7050 (mmt) cc_final: 0.6570 (mtt) REVERT: B 121 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6296 (mm-30) REVERT: B 149 MET cc_start: 0.7715 (mmp) cc_final: 0.7472 (mmm) REVERT: B 189 ASP cc_start: 0.8407 (t70) cc_final: 0.8162 (t70) REVERT: B 238 ILE cc_start: 0.7336 (tp) cc_final: 0.7113 (pp) REVERT: B 287 MET cc_start: 0.6526 (mmm) cc_final: 0.6068 (mpp) REVERT: B 343 LYS cc_start: 0.8136 (mtpt) cc_final: 0.7773 (mtmm) REVERT: B 408 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6918 (mp10) REVERT: B 412 LYS cc_start: 0.7414 (mttm) cc_final: 0.6898 (mttp) REVERT: B 429 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6924 (mm110) REVERT: B 433 ASP cc_start: 0.7511 (t70) cc_final: 0.6920 (m-30) REVERT: B 448 ASN cc_start: 0.7673 (t160) cc_final: 0.7386 (m110) REVERT: B 451 ASN cc_start: 0.8146 (m-40) cc_final: 0.7819 (m-40) REVERT: B 460 GLU cc_start: 0.8066 (tt0) cc_final: 0.7767 (tt0) REVERT: C 101 MET cc_start: 0.6985 (mmt) cc_final: 0.6546 (mtt) REVERT: C 121 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6265 (mm-30) REVERT: C 149 MET cc_start: 0.7683 (mmp) cc_final: 0.7465 (mmm) REVERT: C 287 MET cc_start: 0.6515 (mmm) cc_final: 0.6018 (mpp) REVERT: C 343 LYS cc_start: 0.8110 (mtpt) cc_final: 0.7764 (mtmm) REVERT: C 408 GLN cc_start: 0.7357 (mm-40) cc_final: 0.6935 (mp10) REVERT: C 412 LYS cc_start: 0.7471 (mttm) cc_final: 0.6934 (mttp) REVERT: C 429 GLN cc_start: 0.7373 (mm-40) cc_final: 0.6873 (mm110) REVERT: C 433 ASP cc_start: 0.7589 (t70) cc_final: 0.6991 (m-30) REVERT: C 451 ASN cc_start: 0.8174 (m-40) cc_final: 0.7865 (m110) REVERT: C 460 GLU cc_start: 0.8151 (tt0) cc_final: 0.7866 (tt0) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.6364 time to fit residues: 259.3237 Evaluate side-chains 244 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 117 GLN D 344 GLN A 344 GLN A 448 ASN B 344 GLN B 448 ASN C 344 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.193144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165028 restraints weight = 15191.365| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.20 r_work: 0.3619 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15192 Z= 0.139 Angle : 0.535 5.250 20580 Z= 0.293 Chirality : 0.043 0.132 2276 Planarity : 0.004 0.036 2604 Dihedral : 9.809 75.066 2292 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.34 % Allowed : 9.97 % Favored : 88.69 % 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: 1.35 (0.19), residues: 1920 helix: 1.11 (0.14), residues: 1312 sheet: 0.09 (0.48), residues: 112 loop : 0.87 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 504 TYR 0.015 0.002 TYR D 289 PHE 0.016 0.001 PHE B 514 TRP 0.025 0.002 TRP D 281 HIS 0.005 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00292 (15192) covalent geometry : angle 0.53454 (20580) hydrogen bonds : bond 0.04777 ( 1005) hydrogen bonds : angle 4.45070 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.591 Fit side-chains REVERT: D 101 MET cc_start: 0.7281 (mmt) cc_final: 0.6966 (mtt) REVERT: D 238 ILE cc_start: 0.7529 (tp) cc_final: 0.7068 (tp) REVERT: D 283 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7254 (mm-30) REVERT: D 429 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7512 (mm-40) REVERT: D 448 ASN cc_start: 0.8256 (m-40) cc_final: 0.7999 (m-40) REVERT: D 494 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7991 (mt-10) REVERT: D 554 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.7994 (ttt-90) REVERT: A 101 MET cc_start: 0.7287 (mmt) cc_final: 0.6946 (mtt) REVERT: A 283 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7307 (mm-30) REVERT: A 285 PHE cc_start: 0.7880 (m-10) cc_final: 0.7617 (m-10) REVERT: A 460 GLU cc_start: 0.8349 (tt0) cc_final: 0.8011 (pt0) REVERT: A 494 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: A 554 ARG cc_start: 0.8358 (ptm-80) cc_final: 0.8101 (ptm160) REVERT: B 101 MET cc_start: 0.7354 (mmt) cc_final: 0.7011 (mtt) REVERT: B 283 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7298 (mm-30) REVERT: B 460 GLU cc_start: 0.8312 (tt0) cc_final: 0.7947 (pt0) REVERT: B 494 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (mt-10) REVERT: C 101 MET cc_start: 0.7257 (mmt) cc_final: 0.6927 (mtt) REVERT: C 238 ILE cc_start: 0.7545 (tp) cc_final: 0.7067 (tp) REVERT: C 256 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7939 (mm) REVERT: C 283 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7295 (mm-30) REVERT: C 429 GLN cc_start: 0.7699 (mm-40) cc_final: 0.7497 (mm-40) REVERT: C 448 ASN cc_start: 0.8264 (m-40) cc_final: 0.8007 (m-40) REVERT: C 460 GLU cc_start: 0.8290 (tt0) cc_final: 0.7949 (pt0) REVERT: C 494 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7952 (mt-10) outliers start: 18 outliers final: 0 residues processed: 265 average time/residue: 0.5480 time to fit residues: 161.1744 Evaluate side-chains 223 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 218 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.188755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157329 restraints weight = 15395.280| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 1.07 r_work: 0.3542 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15192 Z= 0.185 Angle : 0.554 5.974 20580 Z= 0.295 Chirality : 0.044 0.160 2276 Planarity : 0.004 0.057 2604 Dihedral : 9.116 69.585 2292 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.64 % Allowed : 12.43 % Favored : 85.94 % 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: 1.56 (0.19), residues: 1920 helix: 1.31 (0.14), residues: 1316 sheet: 0.02 (0.56), residues: 88 loop : 0.80 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 504 TYR 0.018 0.002 TYR A 347 PHE 0.022 0.002 PHE D 186 TRP 0.025 0.002 TRP C 281 HIS 0.005 0.002 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00451 (15192) covalent geometry : angle 0.55368 (20580) hydrogen bonds : bond 0.05027 ( 1005) hydrogen bonds : angle 4.29176 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.616 Fit side-chains REVERT: D 101 MET cc_start: 0.7262 (mmt) cc_final: 0.6911 (mtt) REVERT: D 238 ILE cc_start: 0.7601 (tp) cc_final: 0.7121 (tp) REVERT: D 283 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7317 (mm-30) REVERT: D 448 ASN cc_start: 0.8419 (m-40) cc_final: 0.8140 (m-40) REVERT: D 494 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: A 101 MET cc_start: 0.7307 (mmt) cc_final: 0.6927 (mtt) REVERT: A 283 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7334 (mm-30) REVERT: A 445 ASP cc_start: 0.7766 (t0) cc_final: 0.7500 (t0) REVERT: A 448 ASN cc_start: 0.8354 (m110) cc_final: 0.8002 (m110) REVERT: A 460 GLU cc_start: 0.8456 (tt0) cc_final: 0.8077 (tt0) REVERT: A 494 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: A 554 ARG cc_start: 0.8421 (ptm-80) cc_final: 0.8103 (ptm160) REVERT: B 101 MET cc_start: 0.7312 (mmt) cc_final: 0.6963 (mtt) REVERT: B 238 ILE cc_start: 0.7668 (tp) cc_final: 0.7164 (tp) REVERT: B 283 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7385 (mm-30) REVERT: B 429 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: B 445 ASP cc_start: 0.7709 (t0) cc_final: 0.7438 (t0) REVERT: B 448 ASN cc_start: 0.8309 (m110) cc_final: 0.7933 (m110) REVERT: B 460 GLU cc_start: 0.8445 (tt0) cc_final: 0.8055 (tt0) REVERT: B 484 VAL cc_start: 0.7806 (t) cc_final: 0.7579 (t) REVERT: B 494 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: C 101 MET cc_start: 0.7259 (mmt) cc_final: 0.6908 (mtt) REVERT: C 238 ILE cc_start: 0.7593 (tp) cc_final: 0.7123 (tp) REVERT: C 283 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7357 (mm-30) REVERT: C 448 ASN cc_start: 0.8388 (m-40) cc_final: 0.8106 (m-40) REVERT: C 460 GLU cc_start: 0.8392 (tt0) cc_final: 0.8023 (tt0) REVERT: C 494 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7990 (mt-10) outliers start: 22 outliers final: 9 residues processed: 241 average time/residue: 0.5796 time to fit residues: 154.5184 Evaluate side-chains 219 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 429 GLN Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 59 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 188 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 138 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157001 restraints weight = 15369.622| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 1.08 r_work: 0.3562 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15192 Z= 0.123 Angle : 0.468 5.065 20580 Z= 0.251 Chirality : 0.041 0.161 2276 Planarity : 0.004 0.038 2604 Dihedral : 8.291 59.166 2292 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.26 % Allowed : 14.43 % Favored : 84.30 % 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: 1.96 (0.20), residues: 1920 helix: 1.63 (0.15), residues: 1316 sheet: 0.09 (0.57), residues: 88 loop : 0.89 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 504 TYR 0.015 0.001 TYR A 411 PHE 0.012 0.001 PHE B 514 TRP 0.026 0.002 TRP C 281 HIS 0.004 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00280 (15192) covalent geometry : angle 0.46842 (20580) hydrogen bonds : bond 0.04085 ( 1005) hydrogen bonds : angle 4.04608 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.604 Fit side-chains REVERT: D 101 MET cc_start: 0.7246 (mmt) cc_final: 0.6883 (mtt) REVERT: D 283 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7237 (mm-30) REVERT: D 285 PHE cc_start: 0.7862 (m-10) cc_final: 0.7658 (m-10) REVERT: D 448 ASN cc_start: 0.8354 (m-40) cc_final: 0.8076 (m-40) REVERT: D 494 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 101 MET cc_start: 0.7327 (mmt) cc_final: 0.6960 (mtt) REVERT: A 283 GLU cc_start: 0.7752 (mt-10) cc_final: 0.7212 (mm-30) REVERT: A 285 PHE cc_start: 0.7883 (m-10) cc_final: 0.7673 (m-10) REVERT: A 460 GLU cc_start: 0.8365 (tt0) cc_final: 0.7900 (pt0) REVERT: B 101 MET cc_start: 0.7305 (mmt) cc_final: 0.6933 (mtt) REVERT: B 238 ILE cc_start: 0.7663 (tp) cc_final: 0.7163 (tp) REVERT: B 283 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7233 (mm-30) REVERT: B 460 GLU cc_start: 0.8419 (tt0) cc_final: 0.7915 (pt0) REVERT: B 484 VAL cc_start: 0.7718 (t) cc_final: 0.7493 (t) REVERT: B 487 MET cc_start: 0.8007 (OUTLIER) cc_final: 0.7283 (ttm) REVERT: B 494 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7982 (mt-10) REVERT: C 101 MET cc_start: 0.7234 (mmt) cc_final: 0.6887 (mtt) REVERT: C 238 ILE cc_start: 0.7614 (tp) cc_final: 0.7132 (tp) REVERT: C 283 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7233 (mm-30) REVERT: C 448 ASN cc_start: 0.8366 (m-40) cc_final: 0.8087 (m-40) REVERT: C 460 GLU cc_start: 0.8378 (tt0) cc_final: 0.7912 (pt0) REVERT: C 494 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8001 (mt-10) outliers start: 17 outliers final: 5 residues processed: 223 average time/residue: 0.6253 time to fit residues: 153.1305 Evaluate side-chains 207 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 156 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 158 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 189 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 GLN A 448 ASN B 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.187887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156545 restraints weight = 15487.927| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.14 r_work: 0.3538 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15192 Z= 0.159 Angle : 0.505 5.184 20580 Z= 0.267 Chirality : 0.042 0.145 2276 Planarity : 0.004 0.042 2604 Dihedral : 8.319 58.665 2292 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.64 % Allowed : 15.03 % Favored : 83.33 % 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: 1.89 (0.20), residues: 1920 helix: 1.61 (0.15), residues: 1320 sheet: 0.11 (0.58), residues: 88 loop : 0.77 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 504 TYR 0.017 0.002 TYR C 411 PHE 0.019 0.001 PHE C 186 TRP 0.026 0.002 TRP C 281 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00384 (15192) covalent geometry : angle 0.50492 (20580) hydrogen bonds : bond 0.04492 ( 1005) hydrogen bonds : angle 4.08858 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.593 Fit side-chains REVERT: D 101 MET cc_start: 0.7206 (mmt) cc_final: 0.6875 (mtt) REVERT: D 283 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7252 (mm-30) REVERT: D 448 ASN cc_start: 0.8359 (m-40) cc_final: 0.8082 (m-40) REVERT: D 494 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: A 101 MET cc_start: 0.7242 (mmt) cc_final: 0.6886 (mtt) REVERT: A 283 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7254 (mm-30) REVERT: A 494 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8004 (mt-10) REVERT: B 101 MET cc_start: 0.7189 (mmt) cc_final: 0.6863 (mtt) REVERT: B 283 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7277 (mm-30) REVERT: B 484 VAL cc_start: 0.7766 (t) cc_final: 0.7538 (t) REVERT: B 487 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.7385 (ttm) REVERT: B 494 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: C 101 MET cc_start: 0.7144 (mmt) cc_final: 0.6833 (mtt) REVERT: C 238 ILE cc_start: 0.7677 (tp) cc_final: 0.7210 (tp) REVERT: C 283 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7250 (mm-30) REVERT: C 448 ASN cc_start: 0.8367 (m-40) cc_final: 0.8098 (m-40) REVERT: C 487 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7324 (ttm) REVERT: C 494 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8039 (mt-10) outliers start: 22 outliers final: 7 residues processed: 224 average time/residue: 0.5796 time to fit residues: 143.1581 Evaluate side-chains 209 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain D residue 494 GLU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 159 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 178 optimal weight: 0.0020 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 190 optimal weight: 5.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155985 restraints weight = 15378.414| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.17 r_work: 0.3535 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15192 Z= 0.113 Angle : 0.452 5.327 20580 Z= 0.241 Chirality : 0.040 0.140 2276 Planarity : 0.003 0.035 2604 Dihedral : 7.803 57.143 2292 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.26 % Allowed : 15.40 % Favored : 83.33 % 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: 2.18 (0.20), residues: 1920 helix: 1.85 (0.15), residues: 1316 sheet: 0.18 (0.58), residues: 88 loop : 0.82 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 504 TYR 0.015 0.001 TYR D 289 PHE 0.009 0.001 PHE B 186 TRP 0.025 0.002 TRP B 281 HIS 0.003 0.001 HIS A 437 Details of bonding type rmsd covalent geometry : bond 0.00251 (15192) covalent geometry : angle 0.45247 (20580) hydrogen bonds : bond 0.03875 ( 1005) hydrogen bonds : angle 3.91860 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 0.519 Fit side-chains REVERT: D 101 MET cc_start: 0.7170 (mmt) cc_final: 0.6840 (mtt) REVERT: D 283 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7251 (mm-30) REVERT: D 448 ASN cc_start: 0.8376 (m-40) cc_final: 0.8108 (m-40) REVERT: A 101 MET cc_start: 0.7209 (mmt) cc_final: 0.6856 (mtt) REVERT: A 283 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7275 (mm-30) REVERT: B 101 MET cc_start: 0.7187 (mmt) cc_final: 0.6836 (mtt) REVERT: B 283 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7293 (mm-30) REVERT: B 484 VAL cc_start: 0.7636 (t) cc_final: 0.7394 (t) REVERT: B 487 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7452 (ttm) REVERT: C 101 MET cc_start: 0.7163 (mmt) cc_final: 0.6824 (mtt) REVERT: C 238 ILE cc_start: 0.7721 (tp) cc_final: 0.7230 (tp) REVERT: C 283 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7216 (mm-30) REVERT: C 448 ASN cc_start: 0.8377 (m-40) cc_final: 0.8100 (m-40) REVERT: C 487 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7353 (ttm) REVERT: C 504 ARG cc_start: 0.7628 (mmt90) cc_final: 0.7374 (mtt-85) outliers start: 17 outliers final: 5 residues processed: 224 average time/residue: 0.5969 time to fit residues: 147.8278 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 487 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 398 GLN A 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.188798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.3847 r_free = 0.3847 target = 0.153035 restraints weight = 15348.478| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.03 r_work: 0.3507 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15192 Z= 0.130 Angle : 0.474 6.126 20580 Z= 0.250 Chirality : 0.041 0.139 2276 Planarity : 0.003 0.034 2604 Dihedral : 7.695 58.009 2292 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.86 % Allowed : 15.33 % Favored : 82.81 % 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: 2.14 (0.20), residues: 1920 helix: 1.82 (0.15), residues: 1320 sheet: 0.29 (0.59), residues: 88 loop : 0.76 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 504 TYR 0.015 0.001 TYR B 411 PHE 0.013 0.001 PHE C 186 TRP 0.025 0.002 TRP D 281 HIS 0.003 0.001 HIS C 437 Details of bonding type rmsd covalent geometry : bond 0.00302 (15192) covalent geometry : angle 0.47415 (20580) hydrogen bonds : bond 0.04082 ( 1005) hydrogen bonds : angle 3.93254 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 209 time to evaluate : 0.473 Fit side-chains REVERT: D 101 MET cc_start: 0.7190 (mmt) cc_final: 0.6865 (mtt) REVERT: D 283 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7233 (mm-30) REVERT: D 448 ASN cc_start: 0.8381 (m-40) cc_final: 0.8103 (m-40) REVERT: D 504 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7440 (mtt-85) REVERT: A 101 MET cc_start: 0.7272 (mmt) cc_final: 0.6890 (mtt) REVERT: A 283 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7213 (mm-30) REVERT: B 101 MET cc_start: 0.7197 (mmt) cc_final: 0.6845 (mtt) REVERT: B 283 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7237 (mm-30) REVERT: B 484 VAL cc_start: 0.7671 (t) cc_final: 0.7426 (t) REVERT: B 487 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7499 (ttm) REVERT: C 101 MET cc_start: 0.7202 (mmt) cc_final: 0.6854 (mtt) REVERT: C 238 ILE cc_start: 0.7712 (tp) cc_final: 0.7195 (tp) REVERT: C 283 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7164 (mm-30) REVERT: C 448 ASN cc_start: 0.8393 (m-40) cc_final: 0.8118 (m-40) REVERT: C 487 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7384 (ttm) REVERT: C 494 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (mt-10) outliers start: 25 outliers final: 5 residues processed: 232 average time/residue: 0.5665 time to fit residues: 145.8602 Evaluate side-chains 206 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 198 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.1313 > 50: distance: 24 - 31: 4.159 distance: 31 - 32: 6.195 distance: 31 - 241: 3.652 distance: 32 - 33: 6.659 distance: 32 - 35: 7.705 distance: 33 - 34: 4.027 distance: 34 - 238: 9.451 distance: 35 - 36: 4.625 distance: 36 - 37: 4.752 distance: 37 - 38: 6.251 distance: 39 - 40: 4.272 distance: 39 - 157: 7.630 distance: 40 - 41: 6.667 distance: 40 - 43: 4.750 distance: 41 - 42: 7.299 distance: 41 - 51: 3.873 distance: 42 - 154: 9.922 distance: 46 - 48: 3.941 distance: 47 - 49: 3.957 distance: 48 - 49: 3.052 distance: 49 - 50: 5.704 distance: 51 - 52: 4.402 distance: 51 - 226: 6.407 distance: 52 - 53: 6.506 distance: 52 - 55: 5.168 distance: 53 - 54: 20.103 distance: 53 - 62: 17.131 distance: 54 - 223: 18.821 distance: 55 - 56: 5.161 distance: 56 - 57: 3.814 distance: 56 - 58: 6.233 distance: 57 - 59: 9.510 distance: 58 - 60: 7.035 distance: 59 - 61: 4.606 distance: 60 - 61: 7.748 distance: 62 - 63: 12.431 distance: 63 - 64: 12.558 distance: 63 - 66: 20.409 distance: 64 - 65: 13.345 distance: 64 - 70: 7.331 distance: 66 - 67: 11.539 distance: 66 - 68: 34.785 distance: 67 - 69: 14.643 distance: 70 - 71: 12.541 distance: 70 - 210: 17.433 distance: 71 - 72: 6.603 distance: 71 - 74: 10.521 distance: 72 - 73: 9.048 distance: 72 - 79: 5.033 distance: 74 - 75: 8.363 distance: 75 - 76: 6.596 distance: 76 - 77: 7.257 distance: 76 - 78: 10.588 distance: 79 - 80: 3.014 distance: 80 - 81: 4.326 distance: 80 - 83: 5.718 distance: 81 - 82: 3.552 distance: 81 - 89: 6.789 distance: 83 - 84: 3.257 distance: 84 - 85: 5.031 distance: 84 - 86: 4.486 distance: 85 - 87: 6.314 distance: 86 - 88: 8.402 distance: 87 - 88: 5.621 distance: 90 - 91: 18.471 distance: 91 - 92: 17.456 distance: 91 - 93: 14.635 distance: 93 - 94: 4.544 distance: 94 - 95: 20.301 distance: 94 - 97: 17.058 distance: 95 - 96: 22.270 distance: 95 - 98: 12.334 distance: 98 - 99: 4.037 distance: 98 - 125: 4.764 distance: 99 - 100: 4.376 distance: 99 - 102: 8.535 distance: 100 - 101: 13.052 distance: 100 - 103: 4.907 distance: 101 - 122: 15.334 distance: 103 - 104: 5.418 distance: 103 - 184: 5.906 distance: 104 - 105: 9.239 distance: 105 - 106: 7.040 distance: 106 - 181: 9.946