Starting phenix.real_space_refine on Wed Nov 20 13:14:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_13792.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_13792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_13792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_13792.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/11_2024/7q3h_13792.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 52 Restraints were copied for chains: C, B, E, D Time building chain proxies: 7.50, per 1000 atoms: 0.35 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: 3.77 Conformation dependent library (CDL) restraints added in 2.0 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: 1.61 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: 4.65 Time building geometry restraints manager: 4.45 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 31.980 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.490 ------------------------------------------------------------------------------- Set refin------------------------------------------------------------------------------- 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= 0.242 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (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 TRP 0.006 0.001 TRP B 121 HIS 0.004 0.001 HIS A 285 PHE 0.020 0.002 PHE C 561 TYR 0.020 0.002 TYR E 487 ARG 0.005 0.000 ARG E 155 *********************** 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 : 1.969 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: 0.6374 (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: 0.6430 (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: 0.2744 time to fit residues: 137.1095 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 : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 30.0000 chunk 208 optimal weight: 3.9990 chunk 115 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 140 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 chunk 215 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 0.6980 chunk 249 optimal weight: 10.0000 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: