Starting phenix.real_space_refine on Sun Sep 29 04:34:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/09_2024/7q3h_13792.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/09_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_13792/09_2024/7q3h_13792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/09_2024/7q3h_13792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/09_2024/7q3h_13792.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/09_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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 9.90, per 1000 atoms: 0.46 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: 5.24 Conformation dependent library (CDL) restraints added in 2.7 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: 3.29 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: 8.65 Time building geometry restraints manager: 6.07 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: 1.010 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: 0.810 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 46.440 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.060 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.910 ------------------------------------------------------------------------------- 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= 0.242 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 fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 2.495 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: 0.3456 time to fit residues: 173.3792 Evaluate side-chains 244 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.194 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 204 HIS A 292 GLN A 307 ASN A 391 ASN A 545 GLN A 597 GLN E 204 HIS E 292 GLN E 391 ASN E 545 GLN E 597 GLN D 204 HIS D 292 GLN D 307 ASN D 391 ASN D 545 GLN D 597 GLN C 204 HIS C 292 GLN C 307 ASN C 391 ASN C 545 GLN C 597 GLN B 204 HIS B 292 GLN B 307 ASN B 391 ASN B 545 GLN B 597 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1373 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= 0.249 Angle : 0.553 6.522 30125 Z= 0.288 Chirality : 0.042 0.153 3450 Planarity : 0.003 0.031 3910 Dihedral : 4.055 16.652 2995 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.83 % Allowed : 10.11 % Favored : 89.06 % 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: -0.73 (0.16), residues: 2745 helix: 0.85 (0.20), residues: 660 sheet: 0.19 (0.19), residues: 740 loop : -1.60 (0.15), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.003 0.001 HIS D 285 PHE 0.015 0.001 PHE E 232 TYR 0.010 0.001 TYR C 627 ARG 0.003 0.000 ARG B 155 *********************** 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 272 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6938 (ttm110) cc_final: 0.6567 (ttp-110) REVERT: A 248 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6922 (ttp-110) REVERT: A 420 ARG cc_start: 0.7044 (mtm110) cc_final: 0.6829 (mtm110) REVERT: E 248 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6937 (ttp-110) REVERT: D 282 LEU cc_start: 0.8283 (mp) cc_final: 0.8051 (mt) REVERT: D 376 LYS cc_start: 0.7992 (tttt) cc_final: 0.7636 (ttmm) REVERT: C 376 LYS cc_start: 0.7926 (tttt) cc_final: 0.7551 (ttmm) REVERT: B 255 LYS cc_start: 0.6445 (ttmt) cc_final: 0.6230 (ttmt) REVERT: B 356 LYS cc_start: 0.8122 (tttp) cc_final: 0.7916 (tttm) outliers start: 19 outliers final: 13 residues processed: 257 average time/residue: 0.3749 time to fit residues: 143.8137 Evaluate side-chains 243 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 477 LEU 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 138 optimal weight: 3.9990 chunk 77 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 170 optimal weight: 20.0000 chunk 68 optimal weight: 7.9990 chunk 250 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 248 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 470 GLN E 360 HIS C 233 HIS C 545 GLN C 597 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22110 Z= 0.251 Angle : 0.538 5.505 30125 Z= 0.281 Chirality : 0.042 0.165 3450 Planarity : 0.003 0.033 3910 Dihedral : 4.024 16.447 2995 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.70 % Allowed : 11.85 % Favored : 86.45 % 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: -0.74 (0.16), residues: 2745 helix: 0.77 (0.20), residues: 670 sheet: 0.25 (0.20), residues: 740 loop : -1.62 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 359 HIS 0.004 0.001 HIS E 204 PHE 0.015 0.001 PHE A 232 TYR 0.011 0.001 TYR C 627 ARG 0.002 0.000 ARG A 301 *********************** 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 277 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 238 time to evaluate : 2.347 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 45 ILE cc_start: 0.6346 (OUTLIER) cc_final: 0.5686 (mm) REVERT: A 206 GLN cc_start: 0.6077 (pt0) cc_final: 0.5266 (pt0) REVERT: A 248 ARG cc_start: 0.7106 (mtm-85) cc_final: 0.6903 (ttp-110) REVERT: A 281 GLU cc_start: 0.6459 (mp0) cc_final: 0.6247 (mp0) REVERT: A 420 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6832 (mtm110) REVERT: E 45 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5508 (mm) REVERT: E 420 ARG cc_start: 0.7106 (mtm110) cc_final: 0.6848 (mtm110) REVERT: E 613 ASP cc_start: 0.8327 (m-30) cc_final: 0.7802 (m-30) REVERT: D 45 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5352 (mm) REVERT: D 255 LYS cc_start: 0.6432 (ttpt) cc_final: 0.6117 (ttpt) REVERT: D 281 GLU cc_start: 0.6569 (mp0) cc_final: 0.6103 (mp0) REVERT: C 376 LYS cc_start: 0.7916 (tttt) cc_final: 0.7536 (ttmm) REVERT: C 561 PHE cc_start: 0.7964 (p90) cc_final: 0.7710 (p90) REVERT: B 45 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5568 (mm) REVERT: B 356 LYS cc_start: 0.8162 (tttp) cc_final: 0.7950 (tttm) outliers start: 39 outliers final: 31 residues processed: 259 average time/residue: 0.3689 time to fit residues: 142.4851 Evaluate side-chains 262 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 2.390 ------------------------------------------------------------------------------- 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 477 LEU Chi-restraints excluded: chain A residue 532 VAL 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 330 VAL Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL 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 371 CYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 532 VAL 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 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 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 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 0.8980 chunk 188 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 251 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 131 optimal weight: 20.0000 chunk 237 optimal weight: 0.8980 chunk 71 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 HIS C 597 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22110 Z= 0.147 Angle : 0.491 5.362 30125 Z= 0.256 Chirality : 0.040 0.138 3450 Planarity : 0.003 0.029 3910 Dihedral : 3.747 16.598 2995 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.00 % Allowed : 14.90 % Favored : 84.10 % 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: 0.75 (0.20), residues: 675 sheet: 0.34 (0.20), residues: 740 loop : -1.58 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 359 HIS 0.004 0.001 HIS D 204 PHE 0.017 0.001 PHE E 232 TYR 0.009 0.001 TYR D 620 ARG 0.002 0.000 ARG C 155 *********************** 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 273 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 250 time to evaluate : 2.444 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 420 ARG cc_start: 0.7026 (mtm110) cc_final: 0.6785 (mtm110) REVERT: E 248 ARG cc_start: 0.7021 (ttp-110) cc_final: 0.6799 (ttp-110) REVERT: E 420 ARG cc_start: 0.6972 (mtm110) cc_final: 0.6692 (mtm110) REVERT: D 68 MET cc_start: 0.4563 (ppp) cc_final: 0.4331 (ptt) REVERT: D 281 GLU cc_start: 0.6556 (mp0) cc_final: 0.6153 (mp0) REVERT: D 376 LYS cc_start: 0.7989 (tttt) cc_final: 0.7657 (ttmm) REVERT: D 490 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: D 561 PHE cc_start: 0.8098 (p90) cc_final: 0.7279 (t80) REVERT: C 376 LYS cc_start: 0.7903 (tttt) cc_final: 0.7529 (ttmm) REVERT: C 613 ASP cc_start: 0.8485 (m-30) cc_final: 0.8200 (m-30) REVERT: B 248 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.7078 (ttp-110) REVERT: B 356 LYS cc_start: 0.8164 (tttp) cc_final: 0.7913 (tttm) REVERT: B 376 LYS cc_start: 0.8000 (tttt) cc_final: 0.7726 (ttmm) REVERT: B 561 PHE cc_start: 0.7808 (p90) cc_final: 0.7126 (t80) outliers start: 23 outliers final: 20 residues processed: 257 average time/residue: 0.3648 time to fit residues: 140.3687 Evaluate side-chains 252 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 231 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 477 LEU Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 608 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 221 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 226 optimal weight: 0.0570 chunk 183 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 135 optimal weight: 6.9990 chunk 238 optimal weight: 20.0000 chunk 67 optimal weight: 7.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 545 GLN A 597 GLN E 545 GLN E 597 GLN D 360 HIS D 545 GLN D 597 GLN C 597 GLN B 545 GLN B 597 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 22110 Z= 0.502 Angle : 0.648 6.574 30125 Z= 0.341 Chirality : 0.046 0.163 3450 Planarity : 0.004 0.040 3910 Dihedral : 4.479 17.647 2995 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.44 % Allowed : 17.95 % Favored : 79.61 % 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: -0.82 (0.15), residues: 2745 helix: 0.66 (0.20), residues: 660 sheet: 0.23 (0.19), residues: 735 loop : -1.65 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 121 HIS 0.005 0.001 HIS E 204 PHE 0.014 0.002 PHE C 523 TYR 0.018 0.002 TYR A 518 ARG 0.004 0.001 ARG B 246 *********************** 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 293 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.7125 (ttp-110) cc_final: 0.6893 (ttp-110) REVERT: E 68 MET cc_start: 0.5204 (ppp) cc_final: 0.4992 (ppp) REVERT: E 224 ARG cc_start: 0.7042 (ttm110) cc_final: 0.6366 (ttp-110) REVERT: E 420 ARG cc_start: 0.7213 (mtm110) cc_final: 0.6992 (mtm110) REVERT: D 490 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7142 (tt0) REVERT: C 420 ARG cc_start: 0.7297 (mtm110) cc_final: 0.7085 (mtm110) REVERT: B 248 ARG cc_start: 0.7315 (ttp-110) cc_final: 0.7053 (ttp-110) outliers start: 56 outliers final: 39 residues processed: 274 average time/residue: 0.3642 time to fit residues: 150.5261 Evaluate side-chains 265 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.488 ------------------------------------------------------------------------------- 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 447 LYS Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 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 483 VAL Chi-restraints excluded: chain E residue 492 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR 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 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 356 LYS 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 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 354 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 567 LEU 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 89 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 220 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 225 ASN A 360 HIS E 545 GLN E 597 GLN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 597 GLN B 225 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22110 Z= 0.348 Angle : 0.575 6.228 30125 Z= 0.301 Chirality : 0.043 0.159 3450 Planarity : 0.004 0.036 3910 Dihedral : 4.308 18.331 2995 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.96 % Allowed : 18.87 % Favored : 78.17 % 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: -0.89 (0.15), residues: 2745 helix: 0.63 (0.20), residues: 670 sheet: 0.11 (0.19), residues: 740 loop : -1.66 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.005 0.001 HIS E 204 PHE 0.014 0.001 PHE B 232 TYR 0.014 0.002 TYR A 518 ARG 0.004 0.000 ARG B 420 *********************** 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 286 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 218 time to evaluate : 2.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6887 (ttp-110) REVERT: A 281 GLU cc_start: 0.6484 (mp0) cc_final: 0.6271 (mp0) REVERT: A 420 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6942 (mtm110) REVERT: A 613 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8404 (m-30) REVERT: E 247 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5882 (tt) REVERT: E 490 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: D 224 ARG cc_start: 0.6874 (ttm110) cc_final: 0.6271 (ttp-110) REVERT: D 490 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7110 (tt0) REVERT: C 232 PHE cc_start: 0.8124 (t80) cc_final: 0.7903 (t80) REVERT: C 420 ARG cc_start: 0.7237 (mtm110) cc_final: 0.7033 (mtm110) REVERT: B 224 ARG cc_start: 0.6838 (ttm110) cc_final: 0.6554 (ttp-110) REVERT: B 248 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.7009 (ttp-110) outliers start: 68 outliers final: 53 residues processed: 268 average time/residue: 0.3790 time to fit residues: 154.4713 Evaluate side-chains 273 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 216 time to evaluate : 2.639 ------------------------------------------------------------------------------- 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 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 477 LEU 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 613 ASP Chi-restraints excluded: chain A residue 622 LEU 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 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 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 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 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 354 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 471 GLN 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 C residue 626 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 330 VAL 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 Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 626 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 148 optimal weight: 0.9980 chunk 265 optimal weight: 0.9980 chunk 165 optimal weight: 40.0000 chunk 161 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN E 307 ASN B 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22110 Z= 0.177 Angle : 0.511 5.575 30125 Z= 0.267 Chirality : 0.041 0.148 3450 Planarity : 0.003 0.033 3910 Dihedral : 3.943 18.242 2995 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.48 % Allowed : 19.78 % Favored : 77.73 % 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: -0.76 (0.15), residues: 2745 helix: 0.73 (0.20), residues: 670 sheet: 0.18 (0.19), residues: 740 loop : -1.58 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.006 0.001 HIS C 204 PHE 0.018 0.001 PHE E 232 TYR 0.009 0.001 TYR C 627 ARG 0.004 0.000 ARG B 420 *********************** 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 282 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 225 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5569 (ppp) cc_final: 0.5321 (ptm) REVERT: A 248 ARG cc_start: 0.7045 (ttp-110) cc_final: 0.6806 (ttp-110) REVERT: A 460 MET cc_start: 0.8048 (ttm) cc_final: 0.7825 (mtp) REVERT: E 248 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6778 (ttp-110) REVERT: E 420 ARG cc_start: 0.7110 (mtm110) cc_final: 0.6883 (mtm110) REVERT: E 490 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7028 (tt0) REVERT: D 224 ARG cc_start: 0.6873 (ttm110) cc_final: 0.6309 (ttp-110) REVERT: D 281 GLU cc_start: 0.6480 (mp0) cc_final: 0.6220 (mp0) REVERT: D 490 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: D 561 PHE cc_start: 0.8096 (p90) cc_final: 0.7364 (t80) REVERT: C 68 MET cc_start: 0.5297 (ppp) cc_final: 0.4760 (ppp) REVERT: C 420 ARG cc_start: 0.7168 (mtm110) cc_final: 0.6926 (mtm110) REVERT: C 597 GLN cc_start: 0.8920 (mt0) cc_final: 0.8717 (mt0) REVERT: B 68 MET cc_start: 0.5145 (ppp) cc_final: 0.4400 (ppp) REVERT: B 224 ARG cc_start: 0.6894 (ttm110) cc_final: 0.6574 (ttp-110) REVERT: B 248 ARG cc_start: 0.7242 (ttp-110) cc_final: 0.7013 (ttp-110) outliers start: 57 outliers final: 40 residues processed: 273 average time/residue: 0.3614 time to fit residues: 149.6753 Evaluate side-chains 260 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 218 time to evaluate : 2.348 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 477 LEU 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 354 THR 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 330 VAL 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 D residue 626 LEU 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 354 THR Chi-restraints excluded: chain C residue 471 GLN 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 247 LEU Chi-restraints excluded: chain B residue 330 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 158 optimal weight: 0.0170 chunk 79 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 168 optimal weight: 0.0030 chunk 180 optimal weight: 10.0000 chunk 131 optimal weight: 0.3980 chunk 24 optimal weight: 10.0000 chunk 208 optimal weight: 1.9990 overall best weight: 0.6430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN B 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22110 Z= 0.149 Angle : 0.509 6.598 30125 Z= 0.267 Chirality : 0.041 0.159 3450 Planarity : 0.003 0.031 3910 Dihedral : 3.769 17.856 2995 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.22 % Allowed : 20.22 % Favored : 77.56 % 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: 0.76 (0.20), residues: 675 sheet: 0.24 (0.19), residues: 740 loop : -1.52 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.005 0.001 HIS D 204 PHE 0.025 0.001 PHE C 232 TYR 0.009 0.001 TYR E 163 ARG 0.004 0.000 ARG B 420 *********************** 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 287 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 236 time to evaluate : 2.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.5565 (ppp) cc_final: 0.5282 (ptm) REVERT: A 248 ARG cc_start: 0.7002 (ttp-110) cc_final: 0.6779 (ttp-110) REVERT: A 420 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6910 (mtm110) REVERT: A 460 MET cc_start: 0.8048 (ttm) cc_final: 0.7839 (mtp) REVERT: A 613 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8327 (m-30) REVERT: E 248 ARG cc_start: 0.7041 (ttp-110) cc_final: 0.6818 (ttp-110) REVERT: E 490 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: D 251 ASP cc_start: 0.7313 (p0) cc_final: 0.6887 (p0) REVERT: D 281 GLU cc_start: 0.6379 (mp0) cc_final: 0.6109 (mp0) REVERT: D 376 LYS cc_start: 0.7956 (tttt) cc_final: 0.7568 (ttmm) REVERT: D 490 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: D 561 PHE cc_start: 0.8049 (p90) cc_final: 0.7339 (t80) REVERT: C 68 MET cc_start: 0.5162 (ppp) cc_final: 0.4693 (ppp) REVERT: C 376 LYS cc_start: 0.7916 (tttt) cc_final: 0.7541 (ttmm) REVERT: B 224 ARG cc_start: 0.6901 (ttm110) cc_final: 0.6591 (ttp-110) REVERT: B 248 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6991 (ttp-110) REVERT: B 356 LYS cc_start: 0.8165 (tttp) cc_final: 0.7934 (tttm) REVERT: B 376 LYS cc_start: 0.8003 (tttt) cc_final: 0.7677 (ttmm) outliers start: 51 outliers final: 40 residues processed: 275 average time/residue: 0.3399 time to fit residues: 140.4350 Evaluate side-chains 268 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 225 time to evaluate : 2.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE 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 477 LEU Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 330 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 D residue 45 ILE Chi-restraints excluded: chain D residue 330 VAL 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 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 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 471 GLN 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 204 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 330 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 231 optimal weight: 30.0000 chunk 246 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 193 optimal weight: 0.0870 chunk 75 optimal weight: 9.9990 chunk 223 optimal weight: 0.0030 chunk 233 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.4568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN E 514 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 GLN C 597 GLN B 206 GLN B 597 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 22110 Z= 0.136 Angle : 0.499 5.493 30125 Z= 0.261 Chirality : 0.041 0.154 3450 Planarity : 0.003 0.034 3910 Dihedral : 3.602 17.304 2995 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.14 % Allowed : 20.65 % Favored : 77.21 % 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: -0.58 (0.16), residues: 2745 helix: 0.81 (0.20), residues: 675 sheet: 0.39 (0.20), residues: 720 loop : -1.48 (0.15), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 359 HIS 0.006 0.001 HIS D 204 PHE 0.025 0.001 PHE B 232 TYR 0.009 0.001 TYR C 163 ARG 0.003 0.000 ARG C 420 *********************** 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 298 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 249 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 612 ILE cc_start: 0.9072 (mt) cc_final: 0.8743 (mp) REVERT: A 613 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8330 (m-30) REVERT: E 248 ARG cc_start: 0.6920 (ttp-110) cc_final: 0.6716 (ttp-110) REVERT: E 490 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: D 248 ARG cc_start: 0.7225 (ttp-110) cc_final: 0.6976 (ttp-110) REVERT: D 251 ASP cc_start: 0.7214 (p0) cc_final: 0.6773 (p0) REVERT: D 376 LYS cc_start: 0.7925 (tttt) cc_final: 0.7549 (ttmm) REVERT: D 561 PHE cc_start: 0.8028 (p90) cc_final: 0.7251 (t80) REVERT: C 68 MET cc_start: 0.5028 (ppp) cc_final: 0.4543 (ppp) REVERT: C 248 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6979 (ttp-110) REVERT: C 376 LYS cc_start: 0.7958 (tttt) cc_final: 0.7604 (ttmm) REVERT: C 420 ARG cc_start: 0.6945 (mtm110) cc_final: 0.6694 (mtm-85) REVERT: B 248 ARG cc_start: 0.7150 (ttp-110) cc_final: 0.6924 (ttp-110) REVERT: B 356 LYS cc_start: 0.8167 (tttp) cc_final: 0.7925 (tttm) REVERT: B 376 LYS cc_start: 0.7979 (tttt) cc_final: 0.7674 (ttmm) REVERT: B 420 ARG cc_start: 0.7040 (mtm110) cc_final: 0.6647 (mtm-85) outliers start: 49 outliers final: 40 residues processed: 284 average time/residue: 0.3523 time to fit residues: 150.8584 Evaluate side-chains 274 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 232 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE 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 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 613 ASP Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 330 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 D residue 45 ILE Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU 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 330 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 330 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 4.9990 chunk 159 optimal weight: 0.6980 chunk 123 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 273 optimal weight: 0.9990 chunk 252 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 22 optimal weight: 0.0040 chunk 168 optimal weight: 30.0000 chunk 133 optimal weight: 0.6980 chunk 173 optimal weight: 10.0000 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 GLN E 545 GLN E 597 GLN C 206 GLN B 206 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22110 Z= 0.145 Angle : 0.508 5.710 30125 Z= 0.264 Chirality : 0.041 0.146 3450 Planarity : 0.003 0.033 3910 Dihedral : 3.578 16.959 2995 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.09 % Allowed : 21.00 % Favored : 76.91 % 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: -0.53 (0.16), residues: 2745 helix: 0.82 (0.20), residues: 675 sheet: 0.35 (0.20), residues: 730 loop : -1.40 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 359 HIS 0.005 0.001 HIS C 204 PHE 0.024 0.001 PHE E 232 TYR 0.009 0.001 TYR C 627 ARG 0.004 0.000 ARG A 420 ********************** 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 286 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6845 (mtp85) cc_final: 0.6291 (ttm110) REVERT: A 612 ILE cc_start: 0.9075 (mt) cc_final: 0.8744 (mp) REVERT: E 420 ARG cc_start: 0.6872 (mtm110) cc_final: 0.6643 (mtm-85) REVERT: E 490 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: D 248 ARG cc_start: 0.7210 (ttp-110) cc_final: 0.7005 (ttp-110) REVERT: D 251 ASP cc_start: 0.7313 (p0) cc_final: 0.6861 (p0) REVERT: D 376 LYS cc_start: 0.7936 (tttt) cc_final: 0.7565 (ttmm) REVERT: D 561 PHE cc_start: 0.8073 (p90) cc_final: 0.7232 (t80) REVERT: C 376 LYS cc_start: 0.7941 (tttt) cc_final: 0.7589 (ttmm) REVERT: B 356 LYS cc_start: 0.8160 (tttp) cc_final: 0.7931 (tttm) REVERT: B 376 LYS cc_start: 0.7990 (tttt) cc_final: 0.7684 (ttmm) REVERT: B 420 ARG cc_start: 0.7042 (mtm110) cc_final: 0.6642 (mtm-85) outliers start: 48 outliers final: 42 residues processed: 273 average time/residue: 0.3550 time to fit residues: 146.0712 Evaluate side-chains 277 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE 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 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 94 GLN Chi-restraints excluded: chain E residue 330 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 D residue 45 ILE Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU 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 247 LEU Chi-restraints excluded: chain C residue 330 VAL 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 C residue 608 VAL Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 330 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 201 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 191 optimal weight: 6.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 391 ASN E 514 ASN ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN B 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.184553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111406 restraints weight = 25032.122| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.16 r_work: 0.2993 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22110 Z= 0.219 Angle : 0.531 5.679 30125 Z= 0.277 Chirality : 0.041 0.147 3450 Planarity : 0.003 0.032 3910 Dihedral : 3.762 17.069 2995 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.05 % Allowed : 21.22 % Favored : 76.73 % 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: -0.57 (0.16), residues: 2745 helix: 0.79 (0.20), residues: 675 sheet: 0.31 (0.19), residues: 730 loop : -1.40 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 359 HIS 0.006 0.001 HIS E 204 PHE 0.021 0.001 PHE E 232 TYR 0.010 0.001 TYR C 627 ARG 0.006 0.000 ARG C 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4976.05 seconds wall clock time: 91 minutes 43.43 seconds (5503.43 seconds total)