Starting phenix.real_space_refine on Fri May 16 19:57:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc7_42116/05_2025/8uc7_42116_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc7_42116/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uc7_42116/05_2025/8uc7_42116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc7_42116/05_2025/8uc7_42116.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc7_42116/05_2025/8uc7_42116_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc7_42116/05_2025/8uc7_42116_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14840 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" 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: {'GLN:plan1': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 3, 'GLU:plan': 13, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 170 Chain: "A" 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: C, B, D Time building chain proxies: 7.80, per 1000 atoms: 0.53 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: 3.28 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.82 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: 4.77 Time building geometry restraints manager: 3.85 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 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: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 32.590 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:12.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.780 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (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 TRP 0.185 0.023 TRP B 281 HIS 0.009 0.003 HIS B 437 PHE 0.047 0.008 PHE B 186 TYR 0.115 0.016 TYR A 347 ARG 0.010 0.002 ARG C 428 Details of bonding type rmsd hydrogen bonds : bond 0.18882 ( 1005) hydrogen bonds : angle 7.04143 ( 2931) covalent geometry : bond 0.01456 (15192) covalent geometry : angle 1.75033 (20580) *********************** 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 : 1.526 Fit side-chains REVERT: D 101 MET cc_start: 0.7005 (mmt) cc_final: 0.6574 (mtt) REVERT: D 121 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6330 (mm-30) REVERT: D 189 ASP cc_start: 0.8439 (t70) cc_final: 0.8148 (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: 0.6863 (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: 0.7828 (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: 0.6510 (mtt) REVERT: A 121 GLU cc_start: 0.6648 (mt-10) cc_final: 0.6307 (mm-30) REVERT: A 189 ASP cc_start: 0.8441 (t70) cc_final: 0.8115 (t70) REVERT: A 238 ILE cc_start: 0.7331 (tp) cc_final: 0.7126 (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: 0.6836 (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: 0.7419 (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: 0.6574 (mtt) REVERT: B 121 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6296 (mm-30) REVERT: B 189 ASP cc_start: 0.8407 (t70) cc_final: 0.8119 (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: 0.6919 (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: 0.6923 (mm110) REVERT: B 433 ASP cc_start: 0.7511 (t70) cc_final: 0.6919 (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: 0.6549 (mtt) REVERT: C 121 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6266 (mm-30) REVERT: C 189 ASP cc_start: 0.8433 (t70) cc_final: 0.8208 (t70) REVERT: C 287 MET cc_start: 0.6515 (mmm) cc_final: 0.6017 (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: 0.6872 (mm110) REVERT: C 433 ASP cc_start: 0.7589 (t70) cc_final: 0.6990 (m-30) REVERT: C 451 ASN cc_start: 0.8174 (m-40) cc_final: 0.7864 (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: 1.2052 time to fit residues: 492.5267 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 : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.0770 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 = 0.4240 r_free = 0.4240 target = 0.192135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.162804 restraints weight = 15185.510| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.16 r_work: 0.3614 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15192 Z= 0.151 Angle : 0.545 5.542 20580 Z= 0.297 Chirality : 0.043 0.133 2276 Planarity : 0.004 0.036 2604 Dihedral : 9.825 76.056 2292 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.64 % Allowed : 10.19 % Favored : 88.17 % 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: 1.32 (0.19), residues: 1920 helix: 1.09 (0.14), residues: 1312 sheet: 0.10 (0.48), residues: 112 loop : 0.84 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 281 HIS 0.006 0.001 HIS A 437 PHE 0.016 0.001 PHE B 514 TYR 0.014 0.002 TYR D 289 ARG 0.008 0.001 ARG D 504 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 1005) hydrogen bonds : angle 4.47127 ( 2931) covalent geometry : bond 0.00322 (15192) covalent geometry : angle 0.54508 (20580) *********************** 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 273 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.529 Fit side-chains REVERT: D 101 MET cc_start: 0.7287 (mmt) cc_final: 0.6940 (mtt) REVERT: D 191 ILE cc_start: 0.8037 (pp) cc_final: 0.7773 (mt) REVERT: D 238 ILE cc_start: 0.7515 (tp) cc_final: 0.7058 (tp) REVERT: D 283 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7172 (mm-30) REVERT: D 398 GLN cc_start: 0.8274 (mt0) cc_final: 0.8020 (mt0) REVERT: D 429 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7508 (mm-40) REVERT: D 448 ASN cc_start: 0.8272 (m-40) cc_final: 0.8010 (m-40) REVERT: D 460 GLU cc_start: 0.8202 (tt0) cc_final: 0.7984 (pt0) REVERT: D 494 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: A 101 MET cc_start: 0.7290 (mmt) cc_final: 0.6936 (mtt) REVERT: A 283 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7225 (mm-30) REVERT: A 285 PHE cc_start: 0.7839 (m-10) cc_final: 0.7624 (m-10) REVERT: A 398 GLN cc_start: 0.8290 (mt0) cc_final: 0.8018 (mt0) REVERT: A 460 GLU cc_start: 0.8298 (tt0) cc_final: 0.7930 (pt0) REVERT: A 494 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: A 554 ARG cc_start: 0.8354 (ptm-80) cc_final: 0.8087 (ptm160) REVERT: B 101 MET cc_start: 0.7359 (mmt) cc_final: 0.6997 (mtt) REVERT: B 283 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7224 (mm-30) REVERT: B 460 GLU cc_start: 0.8306 (tt0) cc_final: 0.7905 (pt0) REVERT: B 494 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 101 MET cc_start: 0.7256 (mmt) cc_final: 0.6914 (mtt) REVERT: C 238 ILE cc_start: 0.7520 (tp) cc_final: 0.7037 (tp) REVERT: C 256 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7916 (mm) REVERT: C 283 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7214 (mm-30) REVERT: C 429 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7477 (mm-40) REVERT: C 448 ASN cc_start: 0.8288 (m-40) cc_final: 0.8010 (m-40) REVERT: C 460 GLU cc_start: 0.8256 (tt0) cc_final: 0.7898 (pt0) REVERT: C 494 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7949 (mt-10) outliers start: 22 outliers final: 4 residues processed: 264 average time/residue: 1.1285 time to fit residues: 331.0420 Evaluate side-chains 232 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 223 time to evaluate : 1.487 ------------------------------------------------------------------------------- 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 A residue 494 GLU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL 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 91 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 185 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157475 restraints weight = 15224.726| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.07 r_work: 0.3559 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15192 Z= 0.145 Angle : 0.509 5.435 20580 Z= 0.273 Chirality : 0.042 0.161 2276 Planarity : 0.004 0.051 2604 Dihedral : 8.676 64.390 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.49 % Allowed : 12.05 % Favored : 86.46 % 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: 1.79 (0.19), residues: 1920 helix: 1.49 (0.14), residues: 1312 sheet: 0.10 (0.57), residues: 88 loop : 0.84 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 281 HIS 0.005 0.001 HIS B 437 PHE 0.015 0.001 PHE C 186 TYR 0.015 0.002 TYR A 347 ARG 0.006 0.001 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 1005) hydrogen bonds : angle 4.16679 ( 2931) covalent geometry : bond 0.00337 (15192) covalent geometry : angle 0.50917 (20580) *********************** 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 264 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 244 time to evaluate : 1.567 Fit side-chains REVERT: D 101 MET cc_start: 0.7248 (mmt) cc_final: 0.6895 (mtt) REVERT: D 238 ILE cc_start: 0.7601 (tp) cc_final: 0.7128 (tp) REVERT: D 283 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7234 (mm-30) REVERT: D 448 ASN cc_start: 0.8392 (m-40) cc_final: 0.8102 (m-40) REVERT: D 460 GLU cc_start: 0.8390 (tt0) cc_final: 0.7971 (pt0) REVERT: D 494 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7979 (mt-10) REVERT: A 101 MET cc_start: 0.7277 (mmt) cc_final: 0.6906 (mtt) REVERT: A 283 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7277 (mm-30) REVERT: A 445 ASP cc_start: 0.7745 (t0) cc_final: 0.7478 (t0) REVERT: A 448 ASN cc_start: 0.8284 (m110) cc_final: 0.7909 (m110) REVERT: A 460 GLU cc_start: 0.8417 (tt0) cc_final: 0.7940 (pt0) REVERT: A 494 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: B 101 MET cc_start: 0.7306 (mmt) cc_final: 0.6952 (mtt) REVERT: B 238 ILE cc_start: 0.7654 (tp) cc_final: 0.7162 (tp) REVERT: B 283 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7334 (mm-30) REVERT: B 448 ASN cc_start: 0.8276 (m110) cc_final: 0.7887 (m110) REVERT: B 460 GLU cc_start: 0.8421 (tt0) cc_final: 0.7914 (pt0) REVERT: B 484 VAL cc_start: 0.7723 (t) cc_final: 0.7511 (t) REVERT: B 494 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7962 (mt-10) REVERT: C 101 MET cc_start: 0.7246 (mmt) cc_final: 0.6891 (mtt) REVERT: C 238 ILE cc_start: 0.7616 (tp) cc_final: 0.7169 (tp) REVERT: C 283 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7255 (mm-30) REVERT: C 448 ASN cc_start: 0.8388 (m-40) cc_final: 0.8113 (m-40) REVERT: C 460 GLU cc_start: 0.8375 (tt0) cc_final: 0.7921 (pt0) REVERT: C 494 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7974 (mt-10) outliers start: 20 outliers final: 7 residues processed: 255 average time/residue: 1.1868 time to fit residues: 334.1162 Evaluate side-chains 217 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 1.600 ------------------------------------------------------------------------------- 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 494 GLU 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 166 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 30.0000 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.187825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.157343 restraints weight = 15298.859| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.20 r_work: 0.3526 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15192 Z= 0.172 Angle : 0.521 5.399 20580 Z= 0.277 Chirality : 0.043 0.161 2276 Planarity : 0.004 0.048 2604 Dihedral : 8.587 63.635 2292 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.34 % Allowed : 14.66 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 1920 helix: 1.49 (0.14), residues: 1316 sheet: 0.04 (0.58), residues: 88 loop : 0.79 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 281 HIS 0.005 0.002 HIS A 437 PHE 0.021 0.002 PHE A 186 TYR 0.017 0.002 TYR C 411 ARG 0.010 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04662 ( 1005) hydrogen bonds : angle 4.18279 ( 2931) covalent geometry : bond 0.00417 (15192) covalent geometry : angle 0.52122 (20580) *********************** 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 226 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 208 time to evaluate : 1.577 Fit side-chains REVERT: D 101 MET cc_start: 0.7214 (mmt) cc_final: 0.6870 (mtt) REVERT: D 283 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7354 (mm-30) REVERT: D 448 ASN cc_start: 0.8379 (m-40) cc_final: 0.8092 (m-40) REVERT: D 460 GLU cc_start: 0.8453 (tt0) cc_final: 0.7909 (pt0) REVERT: D 494 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: A 101 MET cc_start: 0.7290 (mmt) cc_final: 0.6925 (mtt) REVERT: A 283 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7349 (mm-30) REVERT: A 448 ASN cc_start: 0.8358 (m110) cc_final: 0.8119 (m-40) REVERT: A 494 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: B 101 MET cc_start: 0.7291 (mmt) cc_final: 0.6940 (mtt) REVERT: B 238 ILE cc_start: 0.7684 (tp) cc_final: 0.7182 (tp) REVERT: B 283 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7351 (mm-30) REVERT: B 484 VAL cc_start: 0.7778 (t) cc_final: 0.7544 (t) REVERT: B 487 MET cc_start: 0.8025 (OUTLIER) cc_final: 0.7330 (ttm) REVERT: B 494 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: C 101 MET cc_start: 0.7236 (mmt) cc_final: 0.6894 (mtt) REVERT: C 238 ILE cc_start: 0.7629 (tp) cc_final: 0.7169 (tp) REVERT: C 283 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7357 (mm-30) REVERT: C 448 ASN cc_start: 0.8394 (m-40) cc_final: 0.8111 (m-40) REVERT: C 494 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8055 (mt-10) outliers start: 18 outliers final: 8 residues processed: 221 average time/residue: 1.2056 time to fit residues: 294.0753 Evaluate side-chains 207 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 321 LEU 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 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 494 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 188 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN B 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.185758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150171 restraints weight = 15464.614| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 1.16 r_work: 0.3449 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15192 Z= 0.218 Angle : 0.565 5.878 20580 Z= 0.297 Chirality : 0.044 0.149 2276 Planarity : 0.004 0.062 2604 Dihedral : 8.964 62.656 2292 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.23 % Allowed : 14.51 % Favored : 83.26 % 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: 1.50 (0.19), residues: 1920 helix: 1.34 (0.14), residues: 1320 sheet: 0.10 (0.58), residues: 88 loop : 0.52 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 281 HIS 0.004 0.002 HIS A 517 PHE 0.022 0.002 PHE A 186 TYR 0.019 0.002 TYR D 347 ARG 0.007 0.001 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.05101 ( 1005) hydrogen bonds : angle 4.27850 ( 2931) covalent geometry : bond 0.00538 (15192) covalent geometry : angle 0.56527 (20580) *********************** 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 237 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.545 Fit side-chains REVERT: D 101 MET cc_start: 0.7199 (mmt) cc_final: 0.6831 (mtt) REVERT: D 283 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7475 (mm-30) REVERT: D 448 ASN cc_start: 0.8418 (m-40) cc_final: 0.7997 (m110) REVERT: D 487 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7485 (ttm) REVERT: D 494 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: A 101 MET cc_start: 0.7269 (mmt) cc_final: 0.6876 (mtt) REVERT: A 283 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7487 (mm-30) REVERT: A 448 ASN cc_start: 0.8434 (m110) cc_final: 0.8196 (m-40) REVERT: A 484 VAL cc_start: 0.7712 (t) cc_final: 0.7492 (p) REVERT: A 494 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8049 (mt-10) REVERT: B 101 MET cc_start: 0.7266 (mmt) cc_final: 0.6897 (mtt) REVERT: B 283 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7481 (mm-30) REVERT: B 484 VAL cc_start: 0.7698 (t) cc_final: 0.7459 (t) REVERT: B 487 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: B 494 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: C 101 MET cc_start: 0.7160 (mmt) cc_final: 0.6804 (mtt) REVERT: C 238 ILE cc_start: 0.7608 (tp) cc_final: 0.7110 (tp) REVERT: C 283 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7458 (mm-30) REVERT: C 448 ASN cc_start: 0.8398 (m-40) cc_final: 0.7968 (m110) REVERT: C 487 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7515 (ttm) REVERT: C 494 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.8051 (mt-10) outliers start: 30 outliers final: 12 residues processed: 226 average time/residue: 1.1114 time to fit residues: 278.7610 Evaluate side-chains 213 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 487 MET 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 459 GLU 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 459 GLU 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 459 GLU 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 25 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 158 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 172 optimal weight: 0.9990 chunk 117 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN A 103 GLN B 398 GLN C 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.153917 restraints weight = 15377.225| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.18 r_work: 0.3486 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15192 Z= 0.110 Angle : 0.461 5.458 20580 Z= 0.245 Chirality : 0.040 0.141 2276 Planarity : 0.003 0.036 2604 Dihedral : 8.166 59.118 2292 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.49 % Allowed : 15.48 % Favored : 83.04 % 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: 2.04 (0.20), residues: 1920 helix: 1.75 (0.15), residues: 1316 sheet: 2.15 (0.67), residues: 48 loop : 0.48 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 281 HIS 0.004 0.001 HIS B 437 PHE 0.009 0.001 PHE A 186 TYR 0.015 0.001 TYR A 411 ARG 0.008 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.03930 ( 1005) hydrogen bonds : angle 4.00474 ( 2931) covalent geometry : bond 0.00235 (15192) covalent geometry : angle 0.46067 (20580) *********************** 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 223 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 1.545 Fit side-chains REVERT: D 101 MET cc_start: 0.7192 (mmt) cc_final: 0.6863 (mtt) REVERT: D 283 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7324 (mm-30) REVERT: D 448 ASN cc_start: 0.8366 (m-40) cc_final: 0.8086 (m-40) REVERT: D 487 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7405 (ttm) REVERT: A 101 MET cc_start: 0.7284 (mmt) cc_final: 0.6893 (mtt) REVERT: A 283 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7324 (mm-30) REVERT: A 448 ASN cc_start: 0.8413 (m110) cc_final: 0.8162 (m-40) REVERT: B 101 MET cc_start: 0.7266 (mmt) cc_final: 0.6889 (mtt) REVERT: B 283 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7341 (mm-30) REVERT: B 484 VAL cc_start: 0.7583 (t) cc_final: 0.7351 (t) REVERT: B 487 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7502 (ttm) REVERT: C 101 MET cc_start: 0.7181 (mmt) cc_final: 0.6836 (mtt) REVERT: C 238 ILE cc_start: 0.7682 (tp) cc_final: 0.7188 (tp) REVERT: C 283 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7309 (mm-30) REVERT: C 448 ASN cc_start: 0.8369 (m-40) cc_final: 0.8084 (m-40) REVERT: C 487 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7434 (ttm) REVERT: C 554 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.8382 (ttt-90) outliers start: 20 outliers final: 1 residues processed: 216 average time/residue: 1.0981 time to fit residues: 264.4515 Evaluate side-chains 197 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 193 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET 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 28 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 GLN B 398 GLN C 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.189571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154065 restraints weight = 15417.592| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.21 r_work: 0.3504 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3512 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= 0.119 Angle : 0.463 5.508 20580 Z= 0.245 Chirality : 0.040 0.135 2276 Planarity : 0.003 0.034 2604 Dihedral : 7.626 59.718 2292 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.86 % Allowed : 15.48 % Favored : 82.66 % 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: 2.16 (0.20), residues: 1920 helix: 1.84 (0.15), residues: 1316 sheet: 2.27 (0.66), residues: 48 loop : 0.51 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 281 HIS 0.003 0.001 HIS C 437 PHE 0.013 0.001 PHE D 186 TYR 0.015 0.001 TYR A 411 ARG 0.006 0.000 ARG D 504 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 1005) hydrogen bonds : angle 3.93204 ( 2931) covalent geometry : bond 0.00272 (15192) covalent geometry : angle 0.46310 (20580) *********************** 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 231 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 1.492 Fit side-chains REVERT: D 101 MET cc_start: 0.7165 (mmt) cc_final: 0.6846 (mtt) REVERT: D 238 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7278 (tp) REVERT: D 283 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7195 (mm-30) REVERT: D 448 ASN cc_start: 0.8390 (m-40) cc_final: 0.8129 (m-40) REVERT: D 487 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7429 (ttm) REVERT: A 101 MET cc_start: 0.7256 (mmt) cc_final: 0.6901 (mtt) REVERT: A 283 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7254 (mm-30) REVERT: A 448 ASN cc_start: 0.8348 (m110) cc_final: 0.8078 (m-40) REVERT: B 101 MET cc_start: 0.7213 (mmt) cc_final: 0.6885 (mtt) REVERT: B 283 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7211 (mm-30) REVERT: B 484 VAL cc_start: 0.7700 (t) cc_final: 0.7443 (t) REVERT: B 487 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7512 (ttm) REVERT: C 101 MET cc_start: 0.7154 (mmt) cc_final: 0.6833 (mtt) REVERT: C 238 ILE cc_start: 0.7730 (tp) cc_final: 0.7215 (tp) REVERT: C 283 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7182 (mm-30) REVERT: C 448 ASN cc_start: 0.8386 (m-40) cc_final: 0.8113 (m-40) REVERT: C 487 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7376 (ttm) outliers start: 25 outliers final: 1 residues processed: 223 average time/residue: 1.0938 time to fit residues: 271.0678 Evaluate side-chains 203 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 198 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain C residue 487 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 7 optimal weight: 0.0980 chunk 37 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.187593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.152068 restraints weight = 15360.966| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 1.18 r_work: 0.3448 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15192 Z= 0.165 Angle : 0.507 6.660 20580 Z= 0.266 Chirality : 0.042 0.138 2276 Planarity : 0.004 0.033 2604 Dihedral : 7.761 59.978 2292 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.01 % Allowed : 15.62 % Favored : 82.37 % 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: 1.92 (0.20), residues: 1920 helix: 1.64 (0.15), residues: 1324 sheet: 2.54 (0.67), residues: 48 loop : 0.42 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 281 HIS 0.004 0.001 HIS C 437 PHE 0.016 0.001 PHE B 186 TYR 0.017 0.002 TYR B 411 ARG 0.007 0.001 ARG D 504 Details of bonding type rmsd hydrogen bonds : bond 0.04448 ( 1005) hydrogen bonds : angle 4.04847 ( 2931) covalent geometry : bond 0.00402 (15192) covalent geometry : angle 0.50654 (20580) *********************** REFINEMENT MACRO_CYCLE 8 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 236 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 1.740 Fit side-chains REVERT: D 101 MET cc_start: 0.7263 (mmt) cc_final: 0.6908 (mtt) REVERT: D 238 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7314 (tp) REVERT: D 283 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7427 (mm-30) REVERT: D 448 ASN cc_start: 0.8450 (m-40) cc_final: 0.8171 (m-40) REVERT: D 487 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7456 (ttm) REVERT: D 494 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: D 504 ARG cc_start: 0.7686 (mmt90) cc_final: 0.7461 (mtt-85) REVERT: A 101 MET cc_start: 0.7244 (mmt) cc_final: 0.6883 (mtt) REVERT: A 283 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7445 (mm-30) REVERT: A 448 ASN cc_start: 0.8425 (m110) cc_final: 0.8143 (m-40) REVERT: B 101 MET cc_start: 0.7243 (mmt) cc_final: 0.6878 (mtt) REVERT: B 283 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7442 (mm-30) REVERT: B 484 VAL cc_start: 0.7675 (t) cc_final: 0.7430 (t) REVERT: B 487 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7586 (ttm) REVERT: C 101 MET cc_start: 0.7214 (mmt) cc_final: 0.6866 (mtt) REVERT: C 283 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7407 (mm-30) REVERT: C 448 ASN cc_start: 0.8408 (m-40) cc_final: 0.8131 (m-40) REVERT: C 487 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7543 (ttm) outliers start: 27 outliers final: 6 residues processed: 232 average time/residue: 1.1681 time to fit residues: 301.5015 Evaluate side-chains 213 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 487 MET 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 C residue 199 VAL Chi-restraints excluded: chain C residue 487 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 2.9990 chunk 140 optimal weight: 50.0000 chunk 188 optimal weight: 50.0000 chunk 115 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 398 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.153553 restraints weight = 15253.420| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.15 r_work: 0.3477 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15192 Z= 0.134 Angle : 0.487 8.561 20580 Z= 0.255 Chirality : 0.041 0.143 2276 Planarity : 0.003 0.033 2604 Dihedral : 7.503 58.595 2292 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.12 % Allowed : 16.89 % Favored : 81.99 % 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: 2.03 (0.20), residues: 1920 helix: 1.72 (0.15), residues: 1324 sheet: 2.64 (0.69), residues: 48 loop : 0.45 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 281 HIS 0.003 0.001 HIS A 437 PHE 0.011 0.001 PHE D 186 TYR 0.016 0.001 TYR B 411 ARG 0.007 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 1005) hydrogen bonds : angle 3.99109 ( 2931) covalent geometry : bond 0.00315 (15192) covalent geometry : angle 0.48714 (20580) *********************** REFINEMENT MACRO_CYCLE 9 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 217 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 1.637 Fit side-chains REVERT: D 101 MET cc_start: 0.7160 (mmt) cc_final: 0.6835 (mtt) REVERT: D 238 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.7256 (tp) REVERT: D 283 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7236 (mm-30) REVERT: D 448 ASN cc_start: 0.8414 (m-40) cc_final: 0.8154 (m-40) REVERT: D 487 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7467 (ttm) REVERT: D 504 ARG cc_start: 0.7642 (mmt90) cc_final: 0.7424 (mtt-85) REVERT: A 101 MET cc_start: 0.7166 (mmt) cc_final: 0.6823 (mtt) REVERT: A 283 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7304 (mm-30) REVERT: A 448 ASN cc_start: 0.8397 (m110) cc_final: 0.8159 (m-40) REVERT: B 101 MET cc_start: 0.7164 (mmt) cc_final: 0.6819 (mtt) REVERT: B 283 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7241 (mm-30) REVERT: B 484 VAL cc_start: 0.7630 (t) cc_final: 0.7376 (t) REVERT: B 487 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7618 (ttm) REVERT: C 101 MET cc_start: 0.7148 (mmt) cc_final: 0.6818 (mtt) REVERT: C 283 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7204 (mm-30) REVERT: C 448 ASN cc_start: 0.8368 (m-40) cc_final: 0.8093 (m-40) REVERT: C 487 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7468 (ttm) outliers start: 15 outliers final: 3 residues processed: 213 average time/residue: 1.1510 time to fit residues: 271.5132 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 : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain C residue 487 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 68 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 173 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 437 HIS C 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.189932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.154222 restraints weight = 15394.888| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.22 r_work: 0.3480 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15192 Z= 0.110 Angle : 0.463 9.136 20580 Z= 0.242 Chirality : 0.040 0.132 2276 Planarity : 0.003 0.034 2604 Dihedral : 7.066 57.406 2292 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.67 % Allowed : 17.71 % Favored : 81.62 % 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: 2.21 (0.20), residues: 1920 helix: 1.86 (0.15), residues: 1324 sheet: 2.25 (0.69), residues: 48 loop : 0.56 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 281 HIS 0.004 0.001 HIS C 437 PHE 0.007 0.001 PHE D 186 TYR 0.014 0.001 TYR C 411 ARG 0.008 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 1005) hydrogen bonds : angle 3.89065 ( 2931) covalent geometry : bond 0.00244 (15192) covalent geometry : angle 0.46260 (20580) ********************** REFINEMENT MACRO_CYCLE 10 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 217 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 1.531 Fit side-chains REVERT: D 101 MET cc_start: 0.7110 (mmt) cc_final: 0.6782 (mtt) REVERT: D 283 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7171 (mm-30) REVERT: D 448 ASN cc_start: 0.8383 (m-40) cc_final: 0.8136 (m-40) REVERT: D 487 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7383 (ttm) REVERT: D 504 ARG cc_start: 0.7640 (mmt90) cc_final: 0.7425 (mtt-85) REVERT: A 101 MET cc_start: 0.7192 (mmt) cc_final: 0.6850 (mtt) REVERT: A 283 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7190 (mm-30) REVERT: A 448 ASN cc_start: 0.8384 (m110) cc_final: 0.8168 (m-40) REVERT: B 101 MET cc_start: 0.7176 (mmt) cc_final: 0.6833 (mtt) REVERT: B 283 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7203 (mm-30) REVERT: B 484 VAL cc_start: 0.7600 (t) cc_final: 0.7358 (t) REVERT: B 487 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7500 (ttm) REVERT: C 101 MET cc_start: 0.7113 (mmt) cc_final: 0.6785 (mtt) REVERT: C 283 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7167 (mm-30) REVERT: C 448 ASN cc_start: 0.8376 (m-40) cc_final: 0.8128 (m-40) REVERT: C 487 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7388 (ttm) outliers start: 9 outliers final: 2 residues processed: 213 average time/residue: 1.1165 time to fit residues: 264.1074 Evaluate side-chains 199 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 194 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain A 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 487 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 0.0040 chunk 178 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 HIS A 437 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.154090 restraints weight = 15306.483| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.15 r_work: 0.3485 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15192 Z= 0.120 Angle : 0.482 11.263 20580 Z= 0.250 Chirality : 0.040 0.154 2276 Planarity : 0.003 0.033 2604 Dihedral : 7.070 59.510 2292 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.67 % Allowed : 18.23 % Favored : 81.10 % 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: 2.19 (0.20), residues: 1920 helix: 1.84 (0.15), residues: 1328 sheet: 1.90 (0.68), residues: 48 loop : 0.60 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 281 HIS 0.004 0.001 HIS D 437 PHE 0.009 0.001 PHE D 186 TYR 0.015 0.001 TYR C 411 ARG 0.008 0.000 ARG C 504 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 1005) hydrogen bonds : angle 3.91259 ( 2931) covalent geometry : bond 0.00274 (15192) covalent geometry : angle 0.48185 (20580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8935.78 seconds wall clock time: 154 minutes 45.27 seconds (9285.27 seconds total)