Starting phenix.real_space_refine on Thu Mar 5 09:57:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q3h_13792/03_2026/7q3h_13792.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 45 5.16 5 C 13920 2.51 5 N 3585 2.21 5 O 4070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21620 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 559, 4324 Classifications: {'peptide': 559} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 532} Chain breaks: 4 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 52 Restraints were copied for chains: E, D, C, B Time building chain proxies: 3.60, per 1000 atoms: 0.17 Number of scatterers: 21620 At special positions: 0 Unit cell: (139.4, 136.94, 148.42, 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 45 16.00 O 4070 8.00 N 3585 7.00 C 13920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.1 seconds 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5170 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 28.3% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 89 through 100 removed outlier: 4.268A pdb=" N GLY A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 114 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 372 removed outlier: 4.200A pdb=" N CYS A 371 " --> pdb=" O SER A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.482A pdb=" N ALA A 440 " --> pdb=" O ASP A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 522 removed outlier: 3.701A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 536 removed outlier: 3.616A pdb=" N SER A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 539 No H-bonds generated for 'chain 'A' and resid 537 through 539' Processing helix chain 'A' and resid 541 through 563 Processing helix chain 'A' and resid 574 through 604 Processing helix chain 'A' and resid 605 through 637 removed outlier: 3.622A pdb=" N VAL A 618 " --> pdb=" O THR A 614 " (cutoff:3.500A) Proline residue: A 621 - end of helix removed outlier: 3.752A pdb=" N THR A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 removed outlier: 4.268A pdb=" N GLY E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 114 Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 372 removed outlier: 4.199A pdb=" N CYS E 371 " --> pdb=" O SER E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 437 through 441 removed outlier: 4.481A pdb=" N ALA E 440 " --> pdb=" O ASP E 437 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR E 441 " --> pdb=" O PHE E 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 437 through 441' Processing helix chain 'E' and resid 514 through 522 removed outlier: 3.701A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 536 removed outlier: 3.614A pdb=" N SER E 533 " --> pdb=" O ILE E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 539 No H-bonds generated for 'chain 'E' and resid 537 through 539' Processing helix chain 'E' and resid 541 through 563 Processing helix chain 'E' and resid 574 through 604 Processing helix chain 'E' and resid 605 through 637 removed outlier: 3.622A pdb=" N VAL E 618 " --> pdb=" O THR E 614 " (cutoff:3.500A) Proline residue: E 621 - end of helix removed outlier: 3.750A pdb=" N THR E 637 " --> pdb=" O LEU E 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 100 removed outlier: 4.268A pdb=" N GLY D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 372 removed outlier: 4.199A pdb=" N CYS D 371 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 437 through 441 removed outlier: 4.481A pdb=" N ALA D 440 " --> pdb=" O ASP D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 522 removed outlier: 3.701A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 removed outlier: 3.615A pdb=" N SER D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 539 No H-bonds generated for 'chain 'D' and resid 537 through 539' Processing helix chain 'D' and resid 541 through 563 Processing helix chain 'D' and resid 574 through 604 Processing helix chain 'D' and resid 605 through 637 removed outlier: 3.622A pdb=" N VAL D 618 " --> pdb=" O THR D 614 " (cutoff:3.500A) Proline residue: D 621 - end of helix removed outlier: 3.751A pdb=" N THR D 637 " --> pdb=" O LEU D 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 100 removed outlier: 4.267A pdb=" N GLY C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.200A pdb=" N CYS C 371 " --> pdb=" O SER C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 437 through 441 removed outlier: 4.481A pdb=" N ALA C 440 " --> pdb=" O ASP C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 522 removed outlier: 3.701A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 536 removed outlier: 3.615A pdb=" N SER C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 539 No H-bonds generated for 'chain 'C' and resid 537 through 539' Processing helix chain 'C' and resid 541 through 563 Processing helix chain 'C' and resid 574 through 604 Processing helix chain 'C' and resid 605 through 637 removed outlier: 3.622A pdb=" N VAL C 618 " --> pdb=" O THR C 614 " (cutoff:3.500A) Proline residue: C 621 - end of helix removed outlier: 3.750A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 4.267A pdb=" N GLY B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 114 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 372 removed outlier: 4.200A pdb=" N CYS B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 437 through 441 removed outlier: 4.481A pdb=" N ALA B 440 " --> pdb=" O ASP B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 522 removed outlier: 3.701A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 536 removed outlier: 3.615A pdb=" N SER B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 541 through 563 Processing helix chain 'B' and resid 574 through 604 Processing helix chain 'B' and resid 605 through 637 removed outlier: 3.622A pdb=" N VAL B 618 " --> pdb=" O THR B 614 " (cutoff:3.500A) Proline residue: B 621 - end of helix removed outlier: 3.751A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.912A pdb=" N ILE A 45 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLY A 166 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN A 169 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ASN A 70 " --> pdb=" O GLN A 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 212 removed outlier: 3.903A pdb=" N VAL A 236 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 270 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 261 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 218 through 222 removed outlier: 6.758A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.549A pdb=" N THR A 430 " --> pdb=" O GLN A 403 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN A 405 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR A 428 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP A 407 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ARG A 426 " --> pdb=" O TRP A 407 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN A 409 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N PHE A 424 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN A 411 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N SER A 422 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 9.803A pdb=" N ILE A 413 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ARG A 420 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN A 348 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY A 341 " --> pdb=" O ASN A 348 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 350 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE A 339 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL A 352 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A 360 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU A 329 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 399 removed outlier: 4.971A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 486 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 512 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL A 484 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 41 through 45 removed outlier: 3.912A pdb=" N ILE E 45 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY E 166 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN E 169 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN E 70 " --> pdb=" O GLN E 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 204 through 212 removed outlier: 3.903A pdb=" N VAL E 236 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU E 270 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 261 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 218 through 222 removed outlier: 6.757A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.549A pdb=" N THR E 430 " --> pdb=" O GLN E 403 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN E 405 " --> pdb=" O THR E 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR E 428 " --> pdb=" O ASN E 405 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP E 407 " --> pdb=" O ARG E 426 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG E 426 " --> pdb=" O TRP E 407 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN E 409 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE E 424 " --> pdb=" O GLN E 409 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN E 411 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N SER E 422 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N ILE E 413 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ARG E 420 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN E 348 " --> pdb=" O GLY E 341 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY E 341 " --> pdb=" O ASN E 348 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER E 350 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE E 339 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL E 352 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS E 360 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N LEU E 329 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 397 through 399 removed outlier: 4.971A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 486 " --> pdb=" O LEU E 510 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS E 512 " --> pdb=" O VAL E 484 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL E 484 " --> pdb=" O LYS E 512 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 41 through 45 removed outlier: 3.912A pdb=" N ILE D 45 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY D 166 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN D 169 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN D 70 " --> pdb=" O GLN D 169 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 204 through 212 removed outlier: 3.903A pdb=" N VAL D 236 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU D 270 " --> pdb=" O LEU D 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 261 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 218 through 222 removed outlier: 6.757A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.548A pdb=" N THR D 430 " --> pdb=" O GLN D 403 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N ASN D 405 " --> pdb=" O THR D 428 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR D 428 " --> pdb=" O ASN D 405 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP D 407 " --> pdb=" O ARG D 426 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG D 426 " --> pdb=" O TRP D 407 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLN D 409 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE D 424 " --> pdb=" O GLN D 409 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN D 411 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N SER D 422 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N ILE D 413 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N ARG D 420 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN D 348 " --> pdb=" O GLY D 341 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY D 341 " --> pdb=" O ASN D 348 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER D 350 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE D 339 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL D 352 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS D 360 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU D 329 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 397 through 399 removed outlier: 4.970A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER D 486 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS D 512 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL D 484 " --> pdb=" O LYS D 512 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 41 through 45 removed outlier: 3.912A pdb=" N ILE C 45 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY C 166 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN C 169 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN C 70 " --> pdb=" O GLN C 169 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 204 through 212 removed outlier: 3.904A pdb=" N VAL C 236 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 270 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 261 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 218 through 222 removed outlier: 6.757A pdb=" N LEU C 249 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.550A pdb=" N THR C 430 " --> pdb=" O GLN C 403 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN C 405 " --> pdb=" O THR C 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR C 428 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP C 407 " --> pdb=" O ARG C 426 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG C 426 " --> pdb=" O TRP C 407 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN C 409 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE C 424 " --> pdb=" O GLN C 409 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN C 411 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N SER C 422 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 9.802A pdb=" N ILE C 413 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 10.886A pdb=" N ARG C 420 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 397 through 399 removed outlier: 4.970A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 486 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS C 512 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N VAL C 484 " --> pdb=" O LYS C 512 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 41 through 45 removed outlier: 3.912A pdb=" N ILE B 45 " --> pdb=" O GLY B 166 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 166 " --> pdb=" O ILE B 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 169 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN B 70 " --> pdb=" O GLN B 169 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 204 through 212 removed outlier: 3.903A pdb=" N VAL B 236 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 270 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 261 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 218 through 222 removed outlier: 6.757A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.550A pdb=" N THR B 430 " --> pdb=" O GLN B 403 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ASN B 405 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N THR B 428 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP B 407 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ARG B 426 " --> pdb=" O TRP B 407 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN B 409 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE B 424 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLN B 411 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 11.274A pdb=" N SER B 422 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 9.801A pdb=" N ILE B 413 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N ARG B 420 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASN B 348 " --> pdb=" O GLY B 341 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLY B 341 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N SER B 350 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE B 339 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 352 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 360 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N LEU B 329 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 397 through 399 removed outlier: 4.971A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 486 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS B 512 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N VAL B 484 " --> pdb=" O LYS B 512 " (cutoff:3.500A) 924 hydrogen bonds defined for protein. 2640 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: 3.45 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7074 1.34 - 1.46: 4597 1.46 - 1.58: 10379 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 22110 Sorted by residual: bond pdb=" CD2 PHE A 561 " pdb=" CE2 PHE A 561 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" CD2 PHE B 561 " pdb=" CE2 PHE B 561 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CD2 PHE E 561 " pdb=" CE2 PHE E 561 " ideal model delta sigma weight residual 1.382 1.347 0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" CD2 PHE D 561 " pdb=" CE2 PHE D 561 " ideal model delta sigma weight residual 1.382 1.348 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CD2 PHE C 561 " pdb=" CE2 PHE C 561 " ideal model delta sigma weight residual 1.382 1.348 0.034 3.00e-02 1.11e+03 1.31e+00 ... (remaining 22105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 28745 1.19 - 2.39: 1075 2.39 - 3.58: 245 3.58 - 4.77: 35 4.77 - 5.96: 25 Bond angle restraints: 30125 Sorted by residual: angle pdb=" N ILE E 390 " pdb=" CA ILE E 390 " pdb=" C ILE E 390 " ideal model delta sigma weight residual 112.96 109.43 3.53 1.00e+00 1.00e+00 1.24e+01 angle pdb=" N ILE C 390 " pdb=" CA ILE C 390 " pdb=" C ILE C 390 " ideal model delta sigma weight residual 112.96 109.45 3.51 1.00e+00 1.00e+00 1.24e+01 angle pdb=" N ILE B 390 " pdb=" CA ILE B 390 " pdb=" C ILE B 390 " ideal model delta sigma weight residual 112.96 109.47 3.49 1.00e+00 1.00e+00 1.22e+01 angle pdb=" N ILE D 390 " pdb=" CA ILE D 390 " pdb=" C ILE D 390 " ideal model delta sigma weight residual 112.96 109.49 3.47 1.00e+00 1.00e+00 1.21e+01 angle pdb=" N ILE A 390 " pdb=" CA ILE A 390 " pdb=" C ILE A 390 " ideal model delta sigma weight residual 112.96 109.49 3.47 1.00e+00 1.00e+00 1.20e+01 ... (remaining 30120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 11691 17.73 - 35.45: 964 35.45 - 53.18: 215 53.18 - 70.91: 45 70.91 - 88.64: 15 Dihedral angle restraints: 12930 sinusoidal: 4895 harmonic: 8035 Sorted by residual: dihedral pdb=" CA PHE C 427 " pdb=" C PHE C 427 " pdb=" N THR C 428 " pdb=" CA THR C 428 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE B 427 " pdb=" C PHE B 427 " pdb=" N THR B 428 " pdb=" CA THR B 428 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE A 427 " pdb=" C PHE A 427 " pdb=" N THR A 428 " pdb=" CA THR A 428 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 12927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2384 0.041 - 0.082: 830 0.082 - 0.123: 205 0.123 - 0.164: 26 0.164 - 0.205: 5 Chirality restraints: 3450 Sorted by residual: chirality pdb=" CB ILE D 536 " pdb=" CA ILE D 536 " pdb=" CG1 ILE D 536 " pdb=" CG2 ILE D 536 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE E 536 " pdb=" CA ILE E 536 " pdb=" CG1 ILE E 536 " pdb=" CG2 ILE E 536 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB ILE B 536 " pdb=" CA ILE B 536 " pdb=" CG1 ILE B 536 " pdb=" CG2 ILE B 536 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 3447 not shown) Planarity restraints: 3910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 561 " 0.012 2.00e-02 2.50e+03 1.15e-02 2.33e+00 pdb=" CG PHE C 561 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE C 561 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE C 561 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 561 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 561 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 561 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 561 " -0.011 2.00e-02 2.50e+03 1.14e-02 2.27e+00 pdb=" CG PHE B 561 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE B 561 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 561 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 561 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 561 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 561 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 561 " 0.012 2.00e-02 2.50e+03 1.13e-02 2.25e+00 pdb=" CG PHE D 561 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE D 561 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE D 561 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 561 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 561 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 561 " 0.020 2.00e-02 2.50e+03 ... (remaining 3907 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1603 2.74 - 3.28: 21837 3.28 - 3.82: 35214 3.82 - 4.36: 41216 4.36 - 4.90: 72012 Nonbonded interactions: 171882 Sorted by model distance: nonbonded pdb=" OG SER D 533 " pdb=" OD1 ASN D 552 " model vdw 2.195 3.040 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.195 3.040 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 552 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 533 " pdb=" OD1 ASN C 552 " model vdw 2.196 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.196 3.040 ... (remaining 171877 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'D' selection = chain 'C' selection = chain 'B' } 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: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.320 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 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 : 0.004 0.038 22110 Z= 0.159 Angle : 0.574 5.964 30125 Z= 0.307 Chirality : 0.043 0.205 3450 Planarity : 0.003 0.031 3910 Dihedral : 14.164 88.637 7760 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.16), residues: 2745 helix: 1.05 (0.21), residues: 645 sheet: 0.24 (0.20), residues: 730 loop : -1.62 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 155 TYR 0.020 0.002 TYR E 487 PHE 0.020 0.002 PHE C 561 TRP 0.006 0.001 TRP B 121 HIS 0.004 0.001 HIS A 285 Details of bonding type rmsd covalent geometry : bond 0.00370 (22110) covalent geometry : angle 0.57425 (30125) hydrogen bonds : bond 0.10939 ( 924) hydrogen bonds : angle 6.31028 ( 2640) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.6891 (ttp-110) REVERT: A 255 LYS cc_start: 0.6395 (ttmt) cc_final: 0.5704 (ttpt) REVERT: E 248 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.6913 (ttp-110) REVERT: E 255 LYS cc_start: 0.6377 (ttmt) cc_final: 0.5618 (ttmt) REVERT: E 638 ASP cc_start: 0.6399 (m-30) cc_final: 0.6182 (m-30) REVERT: D 159 PHE cc_start: 0.8022 (t80) cc_final: 0.7756 (t80) REVERT: D 248 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.7014 (ttp-110) REVERT: D 255 LYS cc_start: 0.6373 (ttmt) cc_final: 0.5585 (ttmt) REVERT: D 281 GLU cc_start: 0.6526 (mp0) cc_final: 0.6268 (mp0) REVERT: C 248 ARG cc_start: 0.7347 (mtm-85) cc_final: 0.6906 (ttp-110) REVERT: C 255 LYS cc_start: 0.6429 (ttmt) cc_final: 0.5964 (ttpt) REVERT: C 376 LYS cc_start: 0.7906 (tttt) cc_final: 0.7578 (ttmm) REVERT: B 248 ARG cc_start: 0.7399 (mtm-85) cc_final: 0.6855 (ttm170) REVERT: B 255 LYS cc_start: 0.6401 (ttmt) cc_final: 0.6087 (ttpt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.1522 time to fit residues: 76.4287 Evaluate side-chains 244 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 40.0000 chunk 111 optimal weight: 8.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 GLN A 307 ASN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN D 204 HIS D 292 GLN D 545 GLN D 597 GLN C 204 HIS C 292 GLN C 307 ASN B 204 HIS B 292 GLN B 360 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106382 restraints weight = 25173.233| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.11 r_work: 0.2912 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22110 Z= 0.301 Angle : 0.654 6.073 30125 Z= 0.344 Chirality : 0.046 0.161 3450 Planarity : 0.004 0.036 3910 Dihedral : 4.557 18.295 2995 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 1.48 % Allowed : 12.24 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2745 helix: 0.64 (0.20), residues: 660 sheet: 0.05 (0.19), residues: 700 loop : -1.62 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 246 TYR 0.016 0.002 TYR A 518 PHE 0.014 0.002 PHE D 561 TRP 0.010 0.001 TRP D 121 HIS 0.003 0.001 HIS E 204 Details of bonding type rmsd covalent geometry : bond 0.00732 (22110) covalent geometry : angle 0.65449 (30125) hydrogen bonds : bond 0.04663 ( 924) hydrogen bonds : angle 5.35470 ( 2640) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLU cc_start: 0.7140 (mp0) cc_final: 0.6890 (mp0) REVERT: A 248 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6464 (ttp-110) REVERT: A 326 GLU cc_start: 0.7785 (tp30) cc_final: 0.7157 (mt-10) REVERT: A 420 ARG cc_start: 0.7460 (mtm110) cc_final: 0.7102 (mtm110) REVERT: A 569 ARG cc_start: 0.7512 (mmt90) cc_final: 0.7153 (tpp-160) REVERT: E 45 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5514 (mm) REVERT: E 248 ARG cc_start: 0.6922 (mtm-85) cc_final: 0.6459 (ttp-110) REVERT: E 255 LYS cc_start: 0.5437 (ttmt) cc_final: 0.5153 (ttpt) REVERT: E 326 GLU cc_start: 0.7746 (tp30) cc_final: 0.7162 (mt-10) REVERT: E 569 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7163 (tpp-160) REVERT: D 45 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5437 (mm) REVERT: D 159 PHE cc_start: 0.8067 (t80) cc_final: 0.7683 (t80) REVERT: D 248 ARG cc_start: 0.6915 (mtm-85) cc_final: 0.6485 (ttp-110) REVERT: D 326 GLU cc_start: 0.7753 (tp30) cc_final: 0.7212 (mt-10) REVERT: D 569 ARG cc_start: 0.7431 (mmt90) cc_final: 0.6986 (mmt180) REVERT: C 248 ARG cc_start: 0.6978 (mtm-85) cc_final: 0.6530 (ttp-110) REVERT: C 376 LYS cc_start: 0.7710 (tttt) cc_final: 0.7044 (ttmm) REVERT: C 569 ARG cc_start: 0.7412 (mmt90) cc_final: 0.7055 (tpp-160) REVERT: B 432 GLN cc_start: 0.8602 (tp40) cc_final: 0.8151 (tp40) REVERT: B 561 PHE cc_start: 0.8054 (p90) cc_final: 0.6972 (t80) REVERT: B 567 LEU cc_start: 0.7422 (tp) cc_final: 0.7222 (tt) REVERT: B 569 ARG cc_start: 0.7590 (mmt90) cc_final: 0.7126 (tpp-160) REVERT: B 606 GLN cc_start: 0.7395 (mm-40) cc_final: 0.6970 (mp10) outliers start: 34 outliers final: 21 residues processed: 243 average time/residue: 0.1702 time to fit residues: 61.2662 Evaluate side-chains 240 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 447 LYS Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 483 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 204 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 192 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 545 GLN A 597 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 GLN E 597 GLN C 545 GLN C 597 GLN B 545 GLN B 597 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.185722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111532 restraints weight = 25057.173| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.19 r_work: 0.2984 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22110 Z= 0.111 Angle : 0.511 5.441 30125 Z= 0.267 Chirality : 0.041 0.166 3450 Planarity : 0.003 0.031 3910 Dihedral : 3.979 16.749 2995 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 1.18 % Allowed : 15.64 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2745 helix: 0.65 (0.20), residues: 670 sheet: 0.11 (0.20), residues: 705 loop : -1.62 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 155 TYR 0.011 0.001 TYR D 620 PHE 0.016 0.001 PHE E 232 TRP 0.007 0.001 TRP B 359 HIS 0.004 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00248 (22110) covalent geometry : angle 0.51138 (30125) hydrogen bonds : bond 0.03466 ( 924) hydrogen bonds : angle 4.60162 ( 2640) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.3535 (ptm) cc_final: 0.3130 (ppp) REVERT: A 248 ARG cc_start: 0.6802 (mtm-85) cc_final: 0.6432 (ttp-110) REVERT: A 271 LEU cc_start: 0.7031 (tp) cc_final: 0.6722 (mp) REVERT: A 326 GLU cc_start: 0.7778 (tp30) cc_final: 0.7170 (mt-10) REVERT: A 420 ARG cc_start: 0.7332 (mtm110) cc_final: 0.6985 (mtm110) REVERT: A 569 ARG cc_start: 0.7376 (mmt90) cc_final: 0.7038 (tpp-160) REVERT: E 248 ARG cc_start: 0.6797 (mtm-85) cc_final: 0.6378 (ttp-110) REVERT: E 326 GLU cc_start: 0.7712 (tp30) cc_final: 0.7197 (mt-10) REVERT: E 569 ARG cc_start: 0.7341 (mmt90) cc_final: 0.6969 (tpp-160) REVERT: D 248 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6409 (ttp-110) REVERT: D 281 GLU cc_start: 0.5996 (mp0) cc_final: 0.5778 (mp0) REVERT: D 326 GLU cc_start: 0.7682 (tp30) cc_final: 0.7161 (mt-10) REVERT: D 370 GLN cc_start: 0.7956 (mp10) cc_final: 0.7707 (mp10) REVERT: D 561 PHE cc_start: 0.8245 (p90) cc_final: 0.7171 (t80) REVERT: D 569 ARG cc_start: 0.7205 (mmt90) cc_final: 0.6933 (tpp-160) REVERT: D 637 THR cc_start: 0.8160 (t) cc_final: 0.7946 (p) REVERT: C 232 PHE cc_start: 0.7532 (t80) cc_final: 0.7311 (t80) REVERT: C 248 ARG cc_start: 0.6841 (mtm-85) cc_final: 0.6588 (ttp-110) REVERT: C 376 LYS cc_start: 0.7723 (tttt) cc_final: 0.7095 (ttmm) REVERT: C 569 ARG cc_start: 0.7286 (mmt90) cc_final: 0.6909 (tpp-160) REVERT: C 637 THR cc_start: 0.8196 (t) cc_final: 0.7928 (p) REVERT: B 248 ARG cc_start: 0.6854 (ttm170) cc_final: 0.6513 (ttp-110) REVERT: B 356 LYS cc_start: 0.8624 (tttp) cc_final: 0.8377 (tttm) REVERT: B 376 LYS cc_start: 0.7862 (tttt) cc_final: 0.7324 (ttmm) REVERT: B 420 ARG cc_start: 0.7431 (mtm110) cc_final: 0.7134 (mtm110) REVERT: B 561 PHE cc_start: 0.8020 (p90) cc_final: 0.6989 (t80) REVERT: B 567 LEU cc_start: 0.7224 (tp) cc_final: 0.6978 (tt) REVERT: B 569 ARG cc_start: 0.7383 (mmt90) cc_final: 0.6964 (tpp-160) outliers start: 27 outliers final: 23 residues processed: 257 average time/residue: 0.1617 time to fit residues: 61.8598 Evaluate side-chains 249 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 13 optimal weight: 20.0000 chunk 122 optimal weight: 30.0000 chunk 6 optimal weight: 7.9990 chunk 223 optimal weight: 7.9990 chunk 188 optimal weight: 20.0000 chunk 175 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS D 545 GLN D 597 GLN C 360 HIS C 545 GLN C 597 GLN B 233 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.176733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100275 restraints weight = 25594.528| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.22 r_work: 0.2858 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 22110 Z= 0.338 Angle : 0.662 6.707 30125 Z= 0.349 Chirality : 0.047 0.171 3450 Planarity : 0.004 0.041 3910 Dihedral : 4.645 18.207 2995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.79 % Allowed : 17.69 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 2745 helix: 0.58 (0.20), residues: 655 sheet: 0.10 (0.20), residues: 700 loop : -1.72 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 246 TYR 0.020 0.002 TYR A 518 PHE 0.015 0.002 PHE C 523 TRP 0.010 0.001 TRP B 121 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00821 (22110) covalent geometry : angle 0.66249 (30125) hydrogen bonds : bond 0.04720 ( 924) hydrogen bonds : angle 5.25314 ( 2640) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 236 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6847 (mtm-85) cc_final: 0.6310 (ttp-110) REVERT: A 326 GLU cc_start: 0.7840 (tp30) cc_final: 0.7191 (mt-10) REVERT: A 420 ARG cc_start: 0.7437 (mtm110) cc_final: 0.7034 (mtm110) REVERT: A 569 ARG cc_start: 0.7633 (mmt90) cc_final: 0.7143 (tpp-160) REVERT: E 224 ARG cc_start: 0.6511 (ttm110) cc_final: 0.6150 (ttp-110) REVERT: E 248 ARG cc_start: 0.6658 (mtm-85) cc_final: 0.6454 (ttp-110) REVERT: E 271 LEU cc_start: 0.7493 (tp) cc_final: 0.7108 (mp) REVERT: E 326 GLU cc_start: 0.7748 (tp30) cc_final: 0.7166 (mt-10) REVERT: E 420 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7281 (mtm110) REVERT: E 432 GLN cc_start: 0.8702 (tp40) cc_final: 0.8260 (tp40) REVERT: E 569 ARG cc_start: 0.7509 (mmt90) cc_final: 0.7097 (tpp-160) REVERT: D 159 PHE cc_start: 0.8063 (t80) cc_final: 0.7763 (t80) REVERT: D 248 ARG cc_start: 0.6870 (mtm-85) cc_final: 0.6561 (ttp-110) REVERT: D 326 GLU cc_start: 0.7827 (tp30) cc_final: 0.7227 (mt-10) REVERT: D 490 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: D 569 ARG cc_start: 0.7457 (mmt90) cc_final: 0.7158 (tpp-160) REVERT: C 248 ARG cc_start: 0.6931 (mtm-85) cc_final: 0.6616 (ttp-110) REVERT: C 326 GLU cc_start: 0.7725 (tp30) cc_final: 0.7047 (mt-10) REVERT: C 376 LYS cc_start: 0.7755 (tttt) cc_final: 0.7150 (ttmm) REVERT: C 418 ASP cc_start: 0.8603 (m-30) cc_final: 0.8368 (m-30) REVERT: C 420 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7020 (mtm110) REVERT: C 569 ARG cc_start: 0.7477 (mmt90) cc_final: 0.7102 (tpp-160) REVERT: B 68 MET cc_start: 0.4996 (ppp) cc_final: 0.4772 (ppp) REVERT: B 248 ARG cc_start: 0.6661 (ttm170) cc_final: 0.6394 (ttp-110) REVERT: B 569 ARG cc_start: 0.7546 (mmt90) cc_final: 0.7145 (tpp-160) outliers start: 64 outliers final: 45 residues processed: 276 average time/residue: 0.1487 time to fit residues: 62.6498 Evaluate side-chains 270 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 371 CYS Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 356 LYS Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 96 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 0.0270 chunk 188 optimal weight: 40.0000 chunk 88 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 153 optimal weight: 0.9990 chunk 146 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN D 597 GLN C 545 GLN C 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.182238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.106826 restraints weight = 25230.004| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.21 r_work: 0.2980 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22110 Z= 0.105 Angle : 0.502 5.420 30125 Z= 0.262 Chirality : 0.041 0.146 3450 Planarity : 0.003 0.033 3910 Dihedral : 3.986 18.311 2995 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.61 % Allowed : 19.39 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 2745 helix: 0.59 (0.20), residues: 670 sheet: 0.15 (0.20), residues: 705 loop : -1.66 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 420 TYR 0.011 0.001 TYR D 620 PHE 0.015 0.001 PHE B 232 TRP 0.007 0.001 TRP D 359 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00227 (22110) covalent geometry : angle 0.50184 (30125) hydrogen bonds : bond 0.03348 ( 924) hydrogen bonds : angle 4.46617 ( 2640) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6568 (mtm-85) cc_final: 0.6319 (ttp-110) REVERT: A 326 GLU cc_start: 0.7838 (tp30) cc_final: 0.7211 (mt-10) REVERT: A 569 ARG cc_start: 0.7392 (mmt90) cc_final: 0.7039 (tpp-160) REVERT: E 248 ARG cc_start: 0.6754 (mtm-85) cc_final: 0.6549 (ttp-110) REVERT: E 326 GLU cc_start: 0.7748 (tp30) cc_final: 0.7186 (mt-10) REVERT: E 432 GLN cc_start: 0.8513 (tp40) cc_final: 0.8246 (tp40) REVERT: E 490 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7841 (tt0) REVERT: E 569 ARG cc_start: 0.7306 (mmt90) cc_final: 0.6919 (tpp-160) REVERT: D 224 ARG cc_start: 0.6256 (ttm-80) cc_final: 0.6023 (ttm110) REVERT: D 248 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.6465 (ttp-110) REVERT: D 432 GLN cc_start: 0.8515 (tp40) cc_final: 0.8186 (tp40) REVERT: D 490 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: D 561 PHE cc_start: 0.8181 (p90) cc_final: 0.7131 (t80) REVERT: D 569 ARG cc_start: 0.7218 (mmt90) cc_final: 0.6912 (tpp-160) REVERT: C 68 MET cc_start: 0.4407 (ppp) cc_final: 0.4147 (ppp) REVERT: C 232 PHE cc_start: 0.7438 (t80) cc_final: 0.7236 (t80) REVERT: C 248 ARG cc_start: 0.6772 (mtm-85) cc_final: 0.6545 (ttp-110) REVERT: C 376 LYS cc_start: 0.7644 (tttt) cc_final: 0.7058 (ttmm) REVERT: C 569 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6939 (tpp-160) REVERT: B 247 LEU cc_start: 0.6512 (tp) cc_final: 0.5886 (mt) REVERT: B 248 ARG cc_start: 0.6709 (ttm170) cc_final: 0.6426 (ttp-110) REVERT: B 561 PHE cc_start: 0.8112 (p90) cc_final: 0.7086 (t80) REVERT: B 569 ARG cc_start: 0.7407 (mmt90) cc_final: 0.6943 (tpp-160) outliers start: 37 outliers final: 27 residues processed: 260 average time/residue: 0.1536 time to fit residues: 60.2839 Evaluate side-chains 249 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 50.0000 chunk 59 optimal weight: 9.9990 chunk 219 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 180 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 204 HIS D 360 HIS C 545 GLN C 597 GLN B 545 GLN B 597 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.183039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.108823 restraints weight = 25174.012| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.19 r_work: 0.2951 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22110 Z= 0.135 Angle : 0.513 5.472 30125 Z= 0.268 Chirality : 0.041 0.146 3450 Planarity : 0.003 0.037 3910 Dihedral : 3.931 17.941 2995 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.40 % Allowed : 19.52 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2745 helix: 0.65 (0.20), residues: 670 sheet: 0.23 (0.19), residues: 740 loop : -1.66 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.011 0.001 TYR C 627 PHE 0.016 0.001 PHE E 232 TRP 0.007 0.001 TRP B 359 HIS 0.005 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00318 (22110) covalent geometry : angle 0.51265 (30125) hydrogen bonds : bond 0.03524 ( 924) hydrogen bonds : angle 4.51419 ( 2640) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 236 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6578 (mtm-85) cc_final: 0.6359 (ttp-110) REVERT: A 326 GLU cc_start: 0.7912 (tp30) cc_final: 0.7250 (mt-10) REVERT: A 569 ARG cc_start: 0.7360 (mmt90) cc_final: 0.7023 (tpp-160) REVERT: E 224 ARG cc_start: 0.6364 (ttm-80) cc_final: 0.6045 (ttm110) REVERT: E 248 ARG cc_start: 0.6731 (mtm-85) cc_final: 0.6443 (ttp-110) REVERT: E 326 GLU cc_start: 0.7725 (tp30) cc_final: 0.7158 (mt-10) REVERT: E 432 GLN cc_start: 0.8579 (tp40) cc_final: 0.8204 (tp40) REVERT: E 490 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: E 569 ARG cc_start: 0.7340 (mmt90) cc_final: 0.6976 (tpp-160) REVERT: D 224 ARG cc_start: 0.6300 (ttm-80) cc_final: 0.6080 (ttm110) REVERT: D 248 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6447 (ttp-110) REVERT: D 251 ASP cc_start: 0.6468 (p0) cc_final: 0.6104 (p0) REVERT: D 420 ARG cc_start: 0.7416 (mtm110) cc_final: 0.6986 (mtm110) REVERT: D 490 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: D 569 ARG cc_start: 0.7265 (mmt90) cc_final: 0.6949 (tpp-160) REVERT: C 68 MET cc_start: 0.4560 (ppp) cc_final: 0.4299 (ppp) REVERT: C 232 PHE cc_start: 0.7455 (t80) cc_final: 0.7225 (t80) REVERT: C 248 ARG cc_start: 0.6752 (mtm-85) cc_final: 0.6525 (ttp-110) REVERT: C 376 LYS cc_start: 0.7590 (tttt) cc_final: 0.7004 (ttmm) REVERT: C 561 PHE cc_start: 0.8071 (p90) cc_final: 0.7775 (p90) REVERT: C 569 ARG cc_start: 0.7287 (mmt90) cc_final: 0.7059 (mmt180) REVERT: B 356 LYS cc_start: 0.8651 (tttp) cc_final: 0.8342 (tttm) REVERT: B 420 ARG cc_start: 0.7471 (mtm110) cc_final: 0.6894 (mtm110) REVERT: B 561 PHE cc_start: 0.8147 (p90) cc_final: 0.7114 (t80) REVERT: B 569 ARG cc_start: 0.7404 (mmt90) cc_final: 0.6972 (tpp-160) outliers start: 55 outliers final: 46 residues processed: 278 average time/residue: 0.1444 time to fit residues: 61.6410 Evaluate side-chains 275 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 265 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 55 optimal weight: 40.0000 chunk 87 optimal weight: 0.5980 chunk 244 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 chunk 183 optimal weight: 0.0970 chunk 3 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS C 597 GLN B 206 GLN B 225 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.106826 restraints weight = 25127.939| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.16 r_work: 0.2940 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22110 Z= 0.158 Angle : 0.528 5.652 30125 Z= 0.277 Chirality : 0.042 0.156 3450 Planarity : 0.003 0.041 3910 Dihedral : 4.002 18.074 2995 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.01 % Allowed : 19.96 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.15), residues: 2745 helix: 0.66 (0.20), residues: 670 sheet: 0.18 (0.19), residues: 740 loop : -1.65 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.011 0.001 TYR E 518 PHE 0.015 0.001 PHE B 232 TRP 0.007 0.001 TRP D 359 HIS 0.006 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00376 (22110) covalent geometry : angle 0.52846 (30125) hydrogen bonds : bond 0.03673 ( 924) hydrogen bonds : angle 4.58938 ( 2640) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 232 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.7911 (tp30) cc_final: 0.7247 (mt-10) REVERT: A 370 GLN cc_start: 0.8175 (pt0) cc_final: 0.7919 (pp30) REVERT: A 569 ARG cc_start: 0.7384 (mmt90) cc_final: 0.7024 (tpp-160) REVERT: E 248 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.6367 (ttp-110) REVERT: E 326 GLU cc_start: 0.7723 (tp30) cc_final: 0.7145 (mt-10) REVERT: E 432 GLN cc_start: 0.8594 (tp40) cc_final: 0.8175 (tp40) REVERT: E 490 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: E 569 ARG cc_start: 0.7397 (mmt90) cc_final: 0.7015 (tpp-160) REVERT: D 248 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6484 (ttp-110) REVERT: D 370 GLN cc_start: 0.8217 (pt0) cc_final: 0.7848 (pp30) REVERT: D 420 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7167 (mtm110) REVERT: D 490 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: D 569 ARG cc_start: 0.7312 (mmt90) cc_final: 0.6984 (tpp-160) REVERT: C 68 MET cc_start: 0.4621 (ppp) cc_final: 0.4387 (ppp) REVERT: C 232 PHE cc_start: 0.7479 (t80) cc_final: 0.7215 (t80) REVERT: C 248 ARG cc_start: 0.6713 (mtm-85) cc_final: 0.6380 (ttp-110) REVERT: C 326 GLU cc_start: 0.7716 (tp30) cc_final: 0.7027 (mt-10) REVERT: C 376 LYS cc_start: 0.7547 (tttt) cc_final: 0.6948 (ttmm) REVERT: C 569 ARG cc_start: 0.7281 (mmt90) cc_final: 0.7055 (mmt180) REVERT: B 420 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6909 (mtm110) REVERT: B 569 ARG cc_start: 0.7430 (mmt90) cc_final: 0.6996 (tpp-160) outliers start: 69 outliers final: 54 residues processed: 286 average time/residue: 0.1499 time to fit residues: 65.2349 Evaluate side-chains 281 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 225 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 204 HIS Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 480 GLU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 259 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 225 ASN A 360 HIS C 206 GLN B 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.177809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.101977 restraints weight = 25288.378| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.22 r_work: 0.2898 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22110 Z= 0.227 Angle : 0.578 6.242 30125 Z= 0.304 Chirality : 0.044 0.178 3450 Planarity : 0.004 0.043 3910 Dihedral : 4.235 18.257 2995 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.09 % Allowed : 20.52 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.15), residues: 2745 helix: 0.64 (0.20), residues: 670 sheet: 0.04 (0.19), residues: 745 loop : -1.68 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 420 TYR 0.015 0.002 TYR A 518 PHE 0.015 0.002 PHE E 232 TRP 0.007 0.001 TRP D 359 HIS 0.011 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00548 (22110) covalent geometry : angle 0.57765 (30125) hydrogen bonds : bond 0.04067 ( 924) hydrogen bonds : angle 4.85645 ( 2640) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 236 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLU cc_start: 0.7910 (tp30) cc_final: 0.7245 (mt-10) REVERT: A 420 ARG cc_start: 0.7649 (mtm110) cc_final: 0.7287 (mtm110) REVERT: A 569 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7101 (tpp-160) REVERT: E 247 LEU cc_start: 0.6484 (tt) cc_final: 0.5981 (tt) REVERT: E 248 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6399 (ttp-110) REVERT: E 326 GLU cc_start: 0.7778 (tp30) cc_final: 0.7165 (mt-10) REVERT: E 490 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7867 (tt0) REVERT: E 569 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7077 (tpp-160) REVERT: D 159 PHE cc_start: 0.7933 (t80) cc_final: 0.7667 (t80) REVERT: D 248 ARG cc_start: 0.6825 (mtm-85) cc_final: 0.6512 (ttp-110) REVERT: D 326 GLU cc_start: 0.7796 (tp30) cc_final: 0.7175 (mt-10) REVERT: D 370 GLN cc_start: 0.8194 (pt0) cc_final: 0.7815 (pp30) REVERT: D 420 ARG cc_start: 0.7554 (mtm110) cc_final: 0.7266 (mtm110) REVERT: D 490 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: D 569 ARG cc_start: 0.7374 (mmt90) cc_final: 0.7023 (tpp-160) REVERT: C 247 LEU cc_start: 0.6665 (tp) cc_final: 0.6323 (tp) REVERT: C 326 GLU cc_start: 0.7765 (tp30) cc_final: 0.7066 (mt-10) REVERT: C 376 LYS cc_start: 0.7603 (tttt) cc_final: 0.7009 (ttmm) REVERT: C 569 ARG cc_start: 0.7362 (mmt90) cc_final: 0.7128 (mmt180) REVERT: C 606 GLN cc_start: 0.7352 (mm-40) cc_final: 0.6968 (mp10) REVERT: B 370 GLN cc_start: 0.8283 (pt0) cc_final: 0.7986 (pp30) REVERT: B 420 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7035 (mtm110) REVERT: B 569 ARG cc_start: 0.7480 (mmt90) cc_final: 0.7041 (tpp-160) REVERT: B 606 GLN cc_start: 0.7386 (mm-40) cc_final: 0.7022 (mp10) outliers start: 71 outliers final: 56 residues processed: 292 average time/residue: 0.1440 time to fit residues: 64.7950 Evaluate side-chains 294 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 236 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 222 optimal weight: 5.9990 chunk 237 optimal weight: 0.5980 chunk 230 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 51 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 206 GLN C 597 GLN B 94 GLN B 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.183965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110740 restraints weight = 25160.208| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.14 r_work: 0.2974 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22110 Z= 0.118 Angle : 0.517 7.430 30125 Z= 0.272 Chirality : 0.041 0.162 3450 Planarity : 0.003 0.044 3910 Dihedral : 3.944 18.371 2995 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.44 % Allowed : 21.05 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.15), residues: 2745 helix: 0.67 (0.20), residues: 670 sheet: 0.03 (0.20), residues: 710 loop : -1.59 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.010 0.001 TYR C 627 PHE 0.022 0.001 PHE A 232 TRP 0.008 0.001 TRP E 359 HIS 0.006 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00270 (22110) covalent geometry : angle 0.51685 (30125) hydrogen bonds : bond 0.03488 ( 924) hydrogen bonds : angle 4.56144 ( 2640) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6433 (ttp-110) cc_final: 0.6193 (ttp-110) REVERT: A 326 GLU cc_start: 0.7912 (tp30) cc_final: 0.7219 (mt-10) REVERT: A 569 ARG cc_start: 0.7379 (mmt90) cc_final: 0.7031 (tpp-160) REVERT: E 247 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.5796 (tt) REVERT: E 248 ARG cc_start: 0.6698 (mtm-85) cc_final: 0.6402 (ttp-110) REVERT: E 326 GLU cc_start: 0.7745 (tp30) cc_final: 0.7169 (mt-10) REVERT: E 370 GLN cc_start: 0.8425 (pt0) cc_final: 0.8055 (pp30) REVERT: E 418 ASP cc_start: 0.8521 (m-30) cc_final: 0.8314 (m-30) REVERT: E 420 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7399 (mtm110) REVERT: E 432 GLN cc_start: 0.8550 (tp40) cc_final: 0.8158 (tp40) REVERT: E 490 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: E 569 ARG cc_start: 0.7355 (mmt90) cc_final: 0.6996 (tpp-160) REVERT: D 248 ARG cc_start: 0.6682 (mtm-85) cc_final: 0.6412 (ttp-110) REVERT: D 326 GLU cc_start: 0.7773 (tp30) cc_final: 0.7167 (mt-10) REVERT: D 370 GLN cc_start: 0.8225 (pt0) cc_final: 0.7909 (pp30) REVERT: D 420 ARG cc_start: 0.7459 (mtm110) cc_final: 0.7176 (mtm110) REVERT: D 490 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7905 (tt0) REVERT: D 561 PHE cc_start: 0.8181 (p90) cc_final: 0.7121 (t80) REVERT: D 569 ARG cc_start: 0.7281 (mmt90) cc_final: 0.6960 (tpp-160) REVERT: C 247 LEU cc_start: 0.6623 (tp) cc_final: 0.5946 (mt) REVERT: C 326 GLU cc_start: 0.7709 (tp30) cc_final: 0.7004 (mt-10) REVERT: C 370 GLN cc_start: 0.8396 (pt0) cc_final: 0.7954 (pp30) REVERT: C 376 LYS cc_start: 0.7533 (tttt) cc_final: 0.6926 (ttmm) REVERT: C 420 ARG cc_start: 0.7614 (mtm110) cc_final: 0.7290 (mtm-85) REVERT: C 569 ARG cc_start: 0.7267 (mmt90) cc_final: 0.7045 (mmt180) REVERT: B 370 GLN cc_start: 0.8191 (pt0) cc_final: 0.7989 (pp30) REVERT: B 420 ARG cc_start: 0.7446 (mtm110) cc_final: 0.6931 (mtm110) REVERT: B 561 PHE cc_start: 0.8216 (p90) cc_final: 0.7098 (t80) REVERT: B 569 ARG cc_start: 0.7383 (mmt90) cc_final: 0.6967 (tpp-160) outliers start: 56 outliers final: 45 residues processed: 282 average time/residue: 0.1453 time to fit residues: 62.5918 Evaluate side-chains 282 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 214 optimal weight: 0.7980 chunk 170 optimal weight: 0.0870 chunk 146 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN D 225 ASN C 206 GLN B 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.182450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108836 restraints weight = 25129.180| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.14 r_work: 0.2947 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22110 Z= 0.161 Angle : 0.540 6.168 30125 Z= 0.284 Chirality : 0.042 0.154 3450 Planarity : 0.003 0.044 3910 Dihedral : 4.016 18.122 2995 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.48 % Allowed : 21.22 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.15), residues: 2745 helix: 0.67 (0.20), residues: 670 sheet: 0.04 (0.19), residues: 745 loop : -1.60 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.011 0.001 TYR C 627 PHE 0.020 0.001 PHE C 232 TRP 0.007 0.001 TRP D 359 HIS 0.006 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00384 (22110) covalent geometry : angle 0.53989 (30125) hydrogen bonds : bond 0.03728 ( 924) hydrogen bonds : angle 4.67272 ( 2640) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 233 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.6509 (ttp-110) cc_final: 0.6309 (ttp-110) REVERT: A 326 GLU cc_start: 0.7909 (tp30) cc_final: 0.7232 (mt-10) REVERT: A 420 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7325 (mtm110) REVERT: A 569 ARG cc_start: 0.7415 (mmt90) cc_final: 0.7044 (tpp-160) REVERT: E 248 ARG cc_start: 0.6672 (mtm-85) cc_final: 0.6364 (ttp-110) REVERT: E 326 GLU cc_start: 0.7729 (tp30) cc_final: 0.7160 (mt-10) REVERT: E 370 GLN cc_start: 0.8429 (pt0) cc_final: 0.8032 (pp30) REVERT: E 418 ASP cc_start: 0.8536 (m-30) cc_final: 0.8233 (m-30) REVERT: E 420 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7408 (mtm110) REVERT: E 432 GLN cc_start: 0.8600 (tp40) cc_final: 0.8124 (tp40) REVERT: E 490 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: E 569 ARG cc_start: 0.7407 (mmt90) cc_final: 0.7070 (tpp-160) REVERT: D 248 ARG cc_start: 0.6690 (mtm-85) cc_final: 0.6412 (ttp-110) REVERT: D 326 GLU cc_start: 0.7754 (tp30) cc_final: 0.7162 (mt-10) REVERT: D 370 GLN cc_start: 0.8346 (pt0) cc_final: 0.8059 (pp30) REVERT: D 420 ARG cc_start: 0.7484 (mtm110) cc_final: 0.7186 (mtm110) REVERT: D 490 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: D 569 ARG cc_start: 0.7308 (mmt90) cc_final: 0.6983 (tpp-160) REVERT: C 326 GLU cc_start: 0.7739 (tp30) cc_final: 0.7017 (mt-10) REVERT: C 370 GLN cc_start: 0.8374 (pt0) cc_final: 0.7969 (pp30) REVERT: C 420 ARG cc_start: 0.7619 (mtm110) cc_final: 0.7337 (mtm-85) REVERT: C 569 ARG cc_start: 0.7290 (mmt90) cc_final: 0.7063 (mmt180) REVERT: B 420 ARG cc_start: 0.7430 (mtm110) cc_final: 0.6895 (mtm110) REVERT: B 569 ARG cc_start: 0.7437 (mmt90) cc_final: 0.7002 (tpp-160) outliers start: 57 outliers final: 49 residues processed: 278 average time/residue: 0.1470 time to fit residues: 63.4865 Evaluate side-chains 281 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 490 GLU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain E residue 547 GLU Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 622 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 377 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 11 optimal weight: 20.0000 chunk 181 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 82 optimal weight: 0.0030 chunk 27 optimal weight: 4.9990 chunk 257 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 117 optimal weight: 0.1980 chunk 123 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 2.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN C 597 GLN B 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.181305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.107234 restraints weight = 25165.474| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.18 r_work: 0.2927 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22110 Z= 0.175 Angle : 0.548 6.279 30125 Z= 0.289 Chirality : 0.042 0.154 3450 Planarity : 0.004 0.043 3910 Dihedral : 4.089 18.436 2995 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.75 % Allowed : 21.22 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2745 helix: 0.67 (0.20), residues: 670 sheet: 0.01 (0.19), residues: 745 loop : -1.61 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 420 TYR 0.011 0.001 TYR E 518 PHE 0.019 0.001 PHE C 232 TRP 0.007 0.001 TRP D 359 HIS 0.006 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00420 (22110) covalent geometry : angle 0.54840 (30125) hydrogen bonds : bond 0.03817 ( 924) hydrogen bonds : angle 4.71848 ( 2640) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6178.38 seconds wall clock time: 105 minutes 59.57 seconds (6359.57 seconds total)