Starting phenix.real_space_refine on Fri Jun 13 07:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uc7_42116/06_2025/8uc7_42116_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uc7_42116/06_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_42116/06_2025/8uc7_42116.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uc7_42116/06_2025/8uc7_42116.map" model { file = "/net/cci-nas-00/data/ceres_data/8uc7_42116/06_2025/8uc7_42116_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uc7_42116/06_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-5710/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: 8.91, per 1000 atoms: 0.60 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: 3.93 Conformation dependent library (CDL) restraints added in 2.1 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: 1.61 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: 4.64 Time building geometry restraints manager: 4.50 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: 0.12 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.220 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: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.180 Set scattering table: 0.180 Process input model: 35.550 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.160 ------------------------------------------------------------------------------- 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 : 1.586 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: 1.3295 time to fit residues: 543.7606 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 : 1.701 ------------------------------------------------------------------------------- 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 = 0.162802 restraints weight = 15185.501| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.16 r_work: 0.3612 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 1.790 Fit side-chains REVERT: D 101 MET cc_start: 0.7270 (mmt) cc_final: 0.6927 (mtt) REVERT: D 191 ILE cc_start: 0.8035 (pp) cc_final: 0.7773 (mt) REVERT: D 238 ILE cc_start: 0.7514 (tp) cc_final: 0.7056 (tp) REVERT: D 283 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7176 (mm-30) REVERT: D 398 GLN cc_start: 0.8278 (mt0) cc_final: 0.8024 (mt0) REVERT: D 429 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7496 (mm-40) REVERT: D 448 ASN cc_start: 0.8262 (m-40) cc_final: 0.8000 (m-40) REVERT: D 460 GLU cc_start: 0.8194 (tt0) cc_final: 0.7979 (pt0) REVERT: D 494 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: A 101 MET cc_start: 0.7266 (mmt) cc_final: 0.6918 (mtt) REVERT: A 283 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7223 (mm-30) REVERT: A 285 PHE cc_start: 0.7832 (m-10) cc_final: 0.7612 (m-10) REVERT: A 398 GLN cc_start: 0.8297 (mt0) cc_final: 0.8024 (mt0) REVERT: A 460 GLU cc_start: 0.8289 (tt0) cc_final: 0.7925 (pt0) REVERT: A 494 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: A 554 ARG cc_start: 0.8349 (ptm-80) cc_final: 0.8082 (ptm160) REVERT: B 101 MET cc_start: 0.7337 (mmt) cc_final: 0.6980 (mtt) REVERT: B 283 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7220 (mm-30) REVERT: B 460 GLU cc_start: 0.8297 (tt0) cc_final: 0.7899 (pt0) REVERT: B 494 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: C 101 MET cc_start: 0.7233 (mmt) cc_final: 0.6898 (mtt) REVERT: C 238 ILE cc_start: 0.7520 (tp) cc_final: 0.7038 (tp) REVERT: C 256 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7914 (mm) REVERT: C 283 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7214 (mm-30) REVERT: C 429 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7464 (mm-40) REVERT: C 448 ASN cc_start: 0.8283 (m-40) cc_final: 0.8004 (m-40) REVERT: C 460 GLU cc_start: 0.8252 (tt0) cc_final: 0.7899 (pt0) REVERT: C 494 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7949 (mt-10) outliers start: 22 outliers final: 4 residues processed: 264 average time/residue: 1.4099 time to fit residues: 412.4055 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 : 1.667 ------------------------------------------------------------------------------- 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: 0.9980 chunk 66 optimal weight: 0.0020 chunk 49 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 156 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- 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 = 0.4238 r_free = 0.4238 target = 0.192041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157202 restraints weight = 15295.680| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.04 r_work: 0.3564 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15192 Z= 0.120 Angle : 0.478 5.146 20580 Z= 0.259 Chirality : 0.041 0.154 2276 Planarity : 0.004 0.041 2604 Dihedral : 8.663 63.817 2292 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.19 % Allowed : 12.57 % Favored : 86.24 % 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: 1.87 (0.19), residues: 1920 helix: 1.55 (0.15), residues: 1312 sheet: 0.09 (0.56), residues: 88 loop : 0.92 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 281 HIS 0.004 0.001 HIS A 437 PHE 0.014 0.001 PHE B 514 TYR 0.012 0.001 TYR D 411 ARG 0.005 0.001 ARG D 504 Details of bonding type rmsd hydrogen bonds : bond 0.04298 ( 1005) hydrogen bonds : angle 4.14169 ( 2931) covalent geometry : bond 0.00259 (15192) covalent geometry : angle 0.47784 (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 259 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 243 time to evaluate : 1.463 Fit side-chains REVERT: D 101 MET cc_start: 0.7288 (mmt) cc_final: 0.6922 (mtt) REVERT: D 238 ILE cc_start: 0.7543 (tp) cc_final: 0.7072 (tp) REVERT: D 283 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7201 (mm-30) REVERT: D 336 MET cc_start: 0.8601 (ptp) cc_final: 0.8359 (ptm) REVERT: D 448 ASN cc_start: 0.8383 (m-40) cc_final: 0.8066 (m-40) REVERT: D 460 GLU cc_start: 0.8445 (tt0) cc_final: 0.8036 (pt0) REVERT: D 494 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: A 101 MET cc_start: 0.7334 (mmt) cc_final: 0.6962 (mtt) REVERT: A 283 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7229 (mm-30) REVERT: A 460 GLU cc_start: 0.8444 (tt0) cc_final: 0.8003 (pt0) REVERT: A 494 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7891 (mt-10) REVERT: A 554 ARG cc_start: 0.8407 (ptm-80) cc_final: 0.8095 (ptm160) REVERT: B 101 MET cc_start: 0.7321 (mmt) cc_final: 0.6948 (mtt) REVERT: B 238 ILE cc_start: 0.7603 (tp) cc_final: 0.7078 (tp) REVERT: B 283 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7278 (mm-30) REVERT: B 460 GLU cc_start: 0.8448 (tt0) cc_final: 0.7951 (pt0) REVERT: B 484 VAL cc_start: 0.7648 (t) cc_final: 0.7439 (t) REVERT: B 494 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7922 (mt-10) REVERT: C 101 MET cc_start: 0.7340 (mmt) cc_final: 0.6982 (mtt) REVERT: C 238 ILE cc_start: 0.7544 (tp) cc_final: 0.7084 (tp) REVERT: C 283 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7224 (mm-30) REVERT: C 336 MET cc_start: 0.8642 (ptp) cc_final: 0.8410 (ptm) REVERT: C 448 ASN cc_start: 0.8373 (m-40) cc_final: 0.8100 (m-40) REVERT: C 460 GLU cc_start: 0.8392 (tt0) cc_final: 0.7963 (pt0) REVERT: C 494 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7947 (mt-10) outliers start: 16 outliers final: 5 residues processed: 250 average time/residue: 1.2740 time to fit residues: 351.3092 Evaluate side-chains 211 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 ASP Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 176 ILE 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: 0.0000 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 140 optimal weight: 30.0000 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 74 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN B 448 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156369 restraints weight = 15264.193| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 1.06 r_work: 0.3536 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15192 Z= 0.161 Angle : 0.521 5.524 20580 Z= 0.276 Chirality : 0.043 0.171 2276 Planarity : 0.004 0.048 2604 Dihedral : 8.406 62.919 2292 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.56 % Allowed : 13.76 % Favored : 84.67 % 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: 1.83 (0.19), residues: 1920 helix: 1.53 (0.14), residues: 1320 sheet: 0.10 (0.58), residues: 88 loop : 0.84 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 281 HIS 0.004 0.002 HIS C 437 PHE 0.022 0.002 PHE D 186 TYR 0.017 0.002 TYR B 411 ARG 0.009 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 1005) hydrogen bonds : angle 4.15239 ( 2931) covalent geometry : bond 0.00384 (15192) covalent geometry : angle 0.52059 (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 230 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 209 time to evaluate : 1.725 Fit side-chains REVERT: D 101 MET cc_start: 0.7283 (mmt) cc_final: 0.6921 (mtt) REVERT: D 283 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7374 (mm-30) REVERT: D 448 ASN cc_start: 0.8389 (m-40) cc_final: 0.8095 (m-40) REVERT: D 460 GLU cc_start: 0.8521 (tt0) cc_final: 0.7969 (pt0) REVERT: D 494 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8062 (mt-10) REVERT: A 101 MET cc_start: 0.7342 (mmt) cc_final: 0.6957 (mtt) REVERT: A 283 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7405 (mm-30) REVERT: A 460 GLU cc_start: 0.8496 (tt0) cc_final: 0.7953 (pt0) REVERT: A 494 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: B 101 MET cc_start: 0.7319 (mmt) cc_final: 0.6958 (mtt) REVERT: B 238 ILE cc_start: 0.7676 (tp) cc_final: 0.7181 (tp) REVERT: B 283 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7424 (mm-30) REVERT: B 484 VAL cc_start: 0.7785 (t) cc_final: 0.7556 (t) REVERT: B 487 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: B 494 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: C 101 MET cc_start: 0.7283 (mmt) cc_final: 0.6926 (mtt) REVERT: C 238 ILE cc_start: 0.7612 (tp) cc_final: 0.7151 (tp) REVERT: C 283 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7408 (mm-30) REVERT: C 336 MET cc_start: 0.8612 (ptp) cc_final: 0.8412 (ptm) REVERT: C 448 ASN cc_start: 0.8424 (m-40) cc_final: 0.8143 (m-40) REVERT: C 460 GLU cc_start: 0.8498 (tt0) cc_final: 0.7926 (pt0) REVERT: C 494 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8058 (mt-10) outliers start: 21 outliers final: 8 residues processed: 224 average time/residue: 1.3511 time to fit residues: 333.4789 Evaluate side-chains 211 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 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 419 SER 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: 4.9990 chunk 127 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.188723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.153671 restraints weight = 15492.122| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 1.15 r_work: 0.3481 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3229 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= 0.141 Angle : 0.482 5.076 20580 Z= 0.256 Chirality : 0.041 0.149 2276 Planarity : 0.004 0.039 2604 Dihedral : 8.102 56.815 2292 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.64 % Allowed : 14.73 % Favored : 83.63 % 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: 1.98 (0.20), residues: 1920 helix: 1.66 (0.15), residues: 1320 sheet: 0.12 (0.58), residues: 88 loop : 0.84 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 281 HIS 0.003 0.001 HIS C 437 PHE 0.015 0.001 PHE B 186 TYR 0.016 0.002 TYR B 411 ARG 0.007 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1005) hydrogen bonds : angle 4.04074 ( 2931) covalent geometry : bond 0.00333 (15192) covalent geometry : angle 0.48238 (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 225 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 1.770 Fit side-chains REVERT: D 101 MET cc_start: 0.7259 (mmt) cc_final: 0.6905 (mtt) REVERT: D 283 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7341 (mm-30) REVERT: D 448 ASN cc_start: 0.8411 (m-40) cc_final: 0.8133 (m-40) REVERT: D 460 GLU cc_start: 0.8525 (tt0) cc_final: 0.7950 (pt0) REVERT: D 494 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: A 101 MET cc_start: 0.7321 (mmt) cc_final: 0.6927 (mtt) REVERT: A 283 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7341 (mm-30) REVERT: A 460 GLU cc_start: 0.8511 (tt0) cc_final: 0.7958 (pt0) REVERT: A 487 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7214 (ttm) REVERT: A 494 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: B 101 MET cc_start: 0.7265 (mmt) cc_final: 0.6901 (mtt) REVERT: B 283 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7360 (mm-30) REVERT: B 484 VAL cc_start: 0.7617 (t) cc_final: 0.7393 (t) REVERT: B 487 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7408 (ttm) REVERT: B 494 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: C 101 MET cc_start: 0.7263 (mmt) cc_final: 0.6902 (mtt) REVERT: C 238 ILE cc_start: 0.7597 (tp) cc_final: 0.7114 (tp) REVERT: C 283 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7340 (mm-30) REVERT: C 336 MET cc_start: 0.8638 (ptp) cc_final: 0.8438 (ptm) REVERT: C 448 ASN cc_start: 0.8432 (m-40) cc_final: 0.8161 (m-40) REVERT: C 460 GLU cc_start: 0.8534 (tt0) cc_final: 0.7935 (pt0) REVERT: C 487 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7310 (ttm) REVERT: C 494 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8086 (mt-10) outliers start: 22 outliers final: 7 residues processed: 218 average time/residue: 1.5681 time to fit residues: 377.1754 Evaluate side-chains 208 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 487 MET 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 419 SER Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 25 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 172 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.190443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154247 restraints weight = 15446.430| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.03 r_work: 0.3531 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15192 Z= 0.103 Angle : 0.442 5.073 20580 Z= 0.235 Chirality : 0.039 0.137 2276 Planarity : 0.003 0.035 2604 Dihedral : 7.449 49.267 2292 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.34 % Allowed : 15.18 % Favored : 83.48 % 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: 2.30 (0.20), residues: 1920 helix: 1.93 (0.15), residues: 1316 sheet: 0.16 (0.58), residues: 88 loop : 0.92 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 281 HIS 0.003 0.001 HIS C 437 PHE 0.010 0.001 PHE A 186 TYR 0.014 0.001 TYR B 411 ARG 0.010 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 1005) hydrogen bonds : angle 3.87654 ( 2931) covalent geometry : bond 0.00220 (15192) covalent geometry : angle 0.44195 (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 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.965 Fit side-chains REVERT: D 101 MET cc_start: 0.7166 (mmt) cc_final: 0.6828 (mtt) REVERT: D 238 ILE cc_start: 0.7635 (tp) cc_final: 0.7155 (tp) REVERT: D 283 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7020 (mm-30) REVERT: D 448 ASN cc_start: 0.8381 (m-40) cc_final: 0.8119 (m-40) REVERT: D 460 GLU cc_start: 0.8327 (tt0) cc_final: 0.7906 (pt0) REVERT: D 487 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7205 (ttm) REVERT: A 101 MET cc_start: 0.7172 (mmt) cc_final: 0.6816 (mtt) REVERT: A 191 ILE cc_start: 0.8117 (pp) cc_final: 0.7811 (mt) REVERT: A 283 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7081 (mm-30) REVERT: A 460 GLU cc_start: 0.8334 (tt0) cc_final: 0.7885 (pt0) REVERT: A 487 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7244 (ttm) REVERT: B 101 MET cc_start: 0.7139 (mmt) cc_final: 0.6810 (mtt) REVERT: B 283 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7057 (mm-30) REVERT: B 484 VAL cc_start: 0.7510 (t) cc_final: 0.7273 (t) REVERT: B 487 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7413 (ttm) REVERT: C 101 MET cc_start: 0.7179 (mmt) cc_final: 0.6827 (mtt) REVERT: C 238 ILE cc_start: 0.7643 (tp) cc_final: 0.7156 (tp) REVERT: C 283 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7037 (mm-30) REVERT: C 448 ASN cc_start: 0.8389 (m-40) cc_final: 0.8128 (m-40) REVERT: C 460 GLU cc_start: 0.8345 (tt0) cc_final: 0.7908 (pt0) REVERT: C 487 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7284 (ttm) outliers start: 18 outliers final: 4 residues processed: 218 average time/residue: 1.3121 time to fit residues: 316.3651 Evaluate side-chains 200 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 192 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 401 ASP Chi-restraints excluded: chain B residue 487 MET Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 487 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 28 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4215 r_free = 0.4215 target = 0.190303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3856 r_free = 0.3856 target = 0.153980 restraints weight = 15463.788| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.04 r_work: 0.3533 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15192 Z= 0.105 Angle : 0.446 6.178 20580 Z= 0.235 Chirality : 0.039 0.137 2276 Planarity : 0.003 0.035 2604 Dihedral : 7.154 51.440 2292 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.34 % Allowed : 15.85 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.41 (0.20), residues: 1920 helix: 2.02 (0.15), residues: 1316 sheet: 0.28 (0.59), residues: 88 loop : 0.92 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 281 HIS 0.003 0.001 HIS A 421 PHE 0.011 0.001 PHE B 186 TYR 0.014 0.001 TYR B 411 ARG 0.009 0.000 ARG B 504 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 1005) hydrogen bonds : angle 3.82421 ( 2931) covalent geometry : bond 0.00229 (15192) covalent geometry : angle 0.44640 (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 224 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 1.757 Fit side-chains REVERT: D 101 MET cc_start: 0.7162 (mmt) cc_final: 0.6822 (mtt) REVERT: D 283 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7095 (mm-30) REVERT: D 448 ASN cc_start: 0.8380 (m-40) cc_final: 0.8128 (m-40) REVERT: D 460 GLU cc_start: 0.8373 (tt0) cc_final: 0.7918 (pt0) REVERT: D 487 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7212 (ttm) REVERT: A 101 MET cc_start: 0.7161 (mmt) cc_final: 0.6796 (mtt) REVERT: A 191 ILE cc_start: 0.8100 (pp) cc_final: 0.7823 (mt) REVERT: A 238 ILE cc_start: 0.7679 (tp) cc_final: 0.7277 (tp) REVERT: A 283 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7108 (mm-30) REVERT: A 460 GLU cc_start: 0.8374 (tt0) cc_final: 0.7902 (pt0) REVERT: A 487 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7286 (ttm) REVERT: B 101 MET cc_start: 0.7199 (mmt) cc_final: 0.6826 (mtt) REVERT: B 283 GLU cc_start: 0.7635 (mt-10) cc_final: 0.7085 (mm-30) REVERT: B 484 VAL cc_start: 0.7515 (t) cc_final: 0.7274 (t) REVERT: B 487 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7440 (ttm) REVERT: C 101 MET cc_start: 0.7129 (mmt) cc_final: 0.6797 (mtt) REVERT: C 238 ILE cc_start: 0.7615 (tp) cc_final: 0.7111 (tp) REVERT: C 283 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7058 (mm-30) REVERT: C 448 ASN cc_start: 0.8379 (m-40) cc_final: 0.8141 (m-40) REVERT: C 460 GLU cc_start: 0.8384 (tt0) cc_final: 0.7925 (pt0) REVERT: C 487 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7267 (ttm) outliers start: 18 outliers final: 5 residues processed: 219 average time/residue: 1.1865 time to fit residues: 288.3384 Evaluate side-chains 207 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain A residue 487 MET 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 419 SER 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: 5.9990 chunk 94 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 139 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.183572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.149092 restraints weight = 15286.017| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.07 r_work: 0.3438 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 15192 Z= 0.351 Angle : 0.684 7.286 20580 Z= 0.355 Chirality : 0.050 0.255 2276 Planarity : 0.005 0.064 2604 Dihedral : 8.973 60.687 2292 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.01 % Allowed : 15.77 % Favored : 82.22 % 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: 1.27 (0.19), residues: 1920 helix: 1.17 (0.14), residues: 1316 sheet: 0.25 (0.59), residues: 88 loop : 0.34 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 281 HIS 0.007 0.002 HIS B 517 PHE 0.023 0.002 PHE A 186 TYR 0.022 0.003 TYR A 347 ARG 0.008 0.001 ARG D 504 Details of bonding type rmsd hydrogen bonds : bond 0.06087 ( 1005) hydrogen bonds : angle 4.42514 ( 2931) covalent geometry : bond 0.00880 (15192) covalent geometry : angle 0.68420 (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 233 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.964 Fit side-chains REVERT: D 101 MET cc_start: 0.7174 (mmt) cc_final: 0.6862 (mtt) REVERT: D 283 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7600 (mm-30) REVERT: D 448 ASN cc_start: 0.8445 (m-40) cc_final: 0.8136 (m-40) REVERT: D 487 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7622 (ttm) REVERT: D 494 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: A 101 MET cc_start: 0.7198 (mmt) cc_final: 0.6839 (mtt) REVERT: A 283 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7606 (mm-30) REVERT: A 487 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7724 (ttm) REVERT: A 494 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: B 101 MET cc_start: 0.7242 (mmt) cc_final: 0.6868 (mtt) REVERT: B 283 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7600 (mm-30) REVERT: B 484 VAL cc_start: 0.7766 (t) cc_final: 0.7526 (t) REVERT: B 487 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7796 (ttm) REVERT: B 494 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: C 101 MET cc_start: 0.7188 (mmt) cc_final: 0.6866 (mtt) REVERT: C 283 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7587 (mm-30) REVERT: C 285 PHE cc_start: 0.8133 (m-10) cc_final: 0.7901 (m-10) REVERT: C 448 ASN cc_start: 0.8461 (m-40) cc_final: 0.8055 (m110) REVERT: C 487 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7721 (ttm) REVERT: C 494 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8141 (mt-10) outliers start: 27 outliers final: 8 residues processed: 224 average time/residue: 1.6326 time to fit residues: 410.7650 Evaluate side-chains 212 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 199 VAL 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 487 MET 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 487 MET Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 487 MET Chi-restraints excluded: chain C residue 494 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 125 optimal weight: 0.9980 chunk 140 optimal weight: 30.0000 chunk 188 optimal weight: 30.0000 chunk 115 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 170 optimal weight: 0.4980 chunk 186 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.189164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.154221 restraints weight = 15148.430| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.16 r_work: 0.3495 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15192 Z= 0.115 Angle : 0.475 8.842 20580 Z= 0.252 Chirality : 0.040 0.134 2276 Planarity : 0.003 0.033 2604 Dihedral : 7.863 57.943 2292 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.82 % Allowed : 17.19 % 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: 1.90 (0.20), residues: 1920 helix: 1.63 (0.15), residues: 1324 sheet: 2.56 (0.69), residues: 48 loop : 0.37 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 281 HIS 0.003 0.001 HIS C 437 PHE 0.008 0.001 PHE D 514 TYR 0.015 0.001 TYR B 411 ARG 0.008 0.001 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04013 ( 1005) hydrogen bonds : angle 3.99742 ( 2931) covalent geometry : bond 0.00254 (15192) covalent geometry : angle 0.47455 (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 208 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.744 Fit side-chains REVERT: D 101 MET cc_start: 0.7299 (mmt) cc_final: 0.6975 (mtt) REVERT: D 283 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7397 (mm-30) REVERT: D 448 ASN cc_start: 0.8361 (m-40) cc_final: 0.7935 (m110) REVERT: D 487 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7579 (ttm) REVERT: A 101 MET cc_start: 0.7280 (mmt) cc_final: 0.6947 (mtt) REVERT: A 283 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7412 (mm-30) REVERT: A 487 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7641 (ttm) REVERT: B 101 MET cc_start: 0.7277 (mmt) cc_final: 0.6945 (mtt) REVERT: B 283 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7385 (mm-30) REVERT: B 484 VAL cc_start: 0.7699 (t) cc_final: 0.7447 (t) REVERT: B 504 ARG cc_start: 0.7665 (mmt90) cc_final: 0.7453 (mtt-85) REVERT: C 101 MET cc_start: 0.7278 (mmt) cc_final: 0.6958 (mtt) REVERT: C 283 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7332 (mm-30) REVERT: C 448 ASN cc_start: 0.8384 (m-40) cc_final: 0.8112 (m-40) REVERT: C 487 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7536 (ttm) outliers start: 11 outliers final: 2 residues processed: 203 average time/residue: 1.7795 time to fit residues: 402.8519 Evaluate side-chains 194 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain C residue 419 SER 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: 0.8980 chunk 166 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.4207 r_free = 0.4207 target = 0.189034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155452 restraints weight = 15378.849| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.25 r_work: 0.3515 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3655 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= 0.126 Angle : 0.485 10.538 20580 Z= 0.254 Chirality : 0.041 0.145 2276 Planarity : 0.003 0.034 2604 Dihedral : 7.434 58.470 2292 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.52 % Allowed : 17.41 % Favored : 82.07 % 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: 2.07 (0.20), residues: 1920 helix: 1.76 (0.15), residues: 1324 sheet: 2.40 (0.68), residues: 48 loop : 0.48 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 281 HIS 0.003 0.001 HIS C 437 PHE 0.012 0.001 PHE A 186 TYR 0.015 0.001 TYR C 411 ARG 0.008 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 1005) hydrogen bonds : angle 3.95175 ( 2931) covalent geometry : bond 0.00290 (15192) covalent geometry : angle 0.48475 (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 210 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 1.657 Fit side-chains REVERT: D 101 MET cc_start: 0.7214 (mmt) cc_final: 0.6886 (mtt) REVERT: D 283 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7216 (mm-30) REVERT: D 448 ASN cc_start: 0.8394 (m-40) cc_final: 0.8138 (m-40) REVERT: D 487 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7558 (ttm) REVERT: A 101 MET cc_start: 0.7217 (mmt) cc_final: 0.6869 (mtt) REVERT: A 283 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7197 (mm-30) REVERT: A 487 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7598 (ttm) REVERT: B 101 MET cc_start: 0.7247 (mmt) cc_final: 0.6903 (mtt) REVERT: B 283 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7187 (mm-30) REVERT: B 484 VAL cc_start: 0.7681 (t) cc_final: 0.7438 (t) REVERT: B 504 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7400 (mtt-85) REVERT: C 101 MET cc_start: 0.7226 (mmt) cc_final: 0.6894 (mtt) REVERT: C 283 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7192 (mm-30) REVERT: C 448 ASN cc_start: 0.8387 (m-40) cc_final: 0.8130 (m-40) REVERT: C 487 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7532 (ttm) outliers start: 7 outliers final: 1 residues processed: 205 average time/residue: 1.4871 time to fit residues: 337.3433 Evaluate side-chains 196 residues out of total 1748 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 2.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain A residue 487 MET Chi-restraints excluded: chain C residue 419 SER 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: 0.8980 chunk 21 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 44 optimal weight: 50.0000 chunk 41 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 HIS B 437 HIS C 437 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.189782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155863 restraints weight = 15254.790| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 1.25 r_work: 0.3509 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15192 Z= 0.113 Angle : 0.471 11.884 20580 Z= 0.246 Chirality : 0.040 0.147 2276 Planarity : 0.003 0.034 2604 Dihedral : 7.184 59.545 2292 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.82 % Allowed : 17.56 % 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: 2.17 (0.20), residues: 1920 helix: 1.84 (0.15), residues: 1328 sheet: 0.15 (0.58), residues: 88 loop : 0.78 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 281 HIS 0.004 0.001 HIS C 437 PHE 0.009 0.001 PHE A 186 TYR 0.014 0.001 TYR B 289 ARG 0.007 0.000 ARG A 504 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 1005) hydrogen bonds : angle 3.88511 ( 2931) covalent geometry : bond 0.00252 (15192) covalent geometry : angle 0.47133 (20580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10432.31 seconds wall clock time: 187 minutes 9.36 seconds (11229.36 seconds total)