Starting phenix.real_space_refine on Sun Feb 18 09:39:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/02_2024/7q3h_13792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/02_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_13792/02_2024/7q3h_13792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/02_2024/7q3h_13792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/02_2024/7q3h_13792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q3h_13792/02_2024/7q3h_13792.pdb" } 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 Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21620 Number of models: 1 Model: "" Number of chains: 5 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 Chain: "E" 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 Chain: "D" 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 Chain: "C" 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 Chain: "B" 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 Time building chain proxies: 11.70, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 8.94 Conformation dependent library (CDL) restraints added in 4.2 seconds 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5170 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 28.3% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 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: 6.33 Time building geometry restraints manager: 9.67 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: 100.65 - 107.32: 709 107.32 - 113.99: 12348 113.99 - 120.67: 8784 120.67 - 127.34: 8074 127.34 - 134.01: 210 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 2.440 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.195 2.440 nonbonded pdb=" OG SER A 533 " pdb=" OD1 ASN A 552 " model vdw 2.196 2.440 nonbonded pdb=" OG SER C 533 " pdb=" OD1 ASN C 552 " model vdw 2.196 2.440 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.196 2.440 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 4.670 Check model and map are aligned: 0.300 Set scattering table: 0.180 Process input model: 57.620 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.840 ------------------------------------------------------------------------------- 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 : 2.734 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: 0.3590 time to fit residues: 179.4382 Evaluate side-chains 244 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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: 7.9990 chunk 208 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 71 optimal weight: 0.0070 chunk 140 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 215 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 131 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 249 optimal weight: 9.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 GLN A 307 ASN A 391 ASN E 292 GLN E 391 ASN D 292 GLN D 307 ASN D 391 ASN C 292 GLN C 307 ASN C 391 ASN B 292 GLN B 307 ASN B 391 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22110 Z= 0.169 Angle : 0.512 6.563 30125 Z= 0.265 Chirality : 0.041 0.144 3450 Planarity : 0.003 0.029 3910 Dihedral : 3.866 16.568 2995 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.65 % Allowed : 9.59 % Favored : 89.76 % 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: 0.89 (0.20), residues: 670 sheet: 0.28 (0.20), residues: 740 loop : -1.60 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.003 0.001 HIS A 233 PHE 0.017 0.001 PHE E 232 TYR 0.009 0.001 TYR B 627 ARG 0.003 0.000 ARG E 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 263 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 248 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.6932 (ttm110) cc_final: 0.6580 (ttp-110) REVERT: A 248 ARG cc_start: 0.7118 (mtm-85) cc_final: 0.6895 (ttp-110) REVERT: A 420 ARG cc_start: 0.6957 (mtm110) cc_final: 0.6719 (mtm110) REVERT: E 420 ARG cc_start: 0.7014 (mtm110) cc_final: 0.6685 (mtm110) REVERT: E 638 ASP cc_start: 0.6232 (m-30) cc_final: 0.6024 (m-30) REVERT: D 281 GLU cc_start: 0.6573 (mp0) cc_final: 0.6185 (mp0) REVERT: C 255 LYS cc_start: 0.6387 (ttmt) cc_final: 0.6101 (ttmt) REVERT: C 376 LYS cc_start: 0.7896 (tttt) cc_final: 0.7545 (ttmm) REVERT: B 356 LYS cc_start: 0.8146 (tttp) cc_final: 0.7934 (tttm) REVERT: B 561 PHE cc_start: 0.7894 (p90) cc_final: 0.7137 (t80) outliers start: 15 outliers final: 11 residues processed: 250 average time/residue: 0.3864 time to fit residues: 143.3858 Evaluate side-chains 236 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 225 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 CYS Chi-restraints excluded: chain A residue 477 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 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: 10.0000 chunk 207 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 chunk 68 optimal weight: 20.0000 chunk 250 optimal weight: 1.9990 chunk 270 optimal weight: 0.8980 chunk 222 optimal weight: 20.0000 chunk 248 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22110 Z= 0.326 Angle : 0.562 5.622 30125 Z= 0.293 Chirality : 0.043 0.165 3450 Planarity : 0.004 0.034 3910 Dihedral : 4.155 17.138 2995 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.61 % Allowed : 12.42 % Favored : 85.97 % 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: -0.68 (0.16), residues: 2745 helix: 0.90 (0.20), residues: 660 sheet: 0.28 (0.19), residues: 740 loop : -1.61 (0.15), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 359 HIS 0.003 0.001 HIS D 233 PHE 0.013 0.002 PHE B 232 TYR 0.013 0.002 TYR A 518 ARG 0.003 0.000 ARG A 246 *********************** 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 274 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 237 time to evaluate : 2.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.6364 (OUTLIER) cc_final: 0.5737 (mm) REVERT: A 420 ARG cc_start: 0.7124 (mtm110) cc_final: 0.6819 (mtm110) REVERT: E 45 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5605 (mm) REVERT: D 45 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5394 (mm) REVERT: D 68 MET cc_start: 0.4136 (ptm) cc_final: 0.3772 (ppp) REVERT: C 45 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5654 (mm) REVERT: C 255 LYS cc_start: 0.6256 (ttmt) cc_final: 0.6021 (ttmt) REVERT: C 561 PHE cc_start: 0.7961 (p90) cc_final: 0.7760 (p90) REVERT: B 45 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.5633 (mm) outliers start: 37 outliers final: 21 residues processed: 249 average time/residue: 0.3791 time to fit residues: 141.0292 Evaluate side-chains 249 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 223 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 371 CYS 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 D residue 45 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 492 THR Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 247 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 119 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 131 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22110 Z= 0.240 Angle : 0.518 5.548 30125 Z= 0.270 Chirality : 0.041 0.148 3450 Planarity : 0.003 0.031 3910 Dihedral : 4.009 16.593 2995 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.14 % Allowed : 15.47 % Favored : 82.40 % 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: -0.70 (0.16), residues: 2745 helix: 0.80 (0.20), residues: 670 sheet: 0.31 (0.19), residues: 740 loop : -1.63 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 359 HIS 0.003 0.001 HIS B 285 PHE 0.014 0.001 PHE B 232 TYR 0.010 0.001 TYR C 627 ARG 0.002 0.000 ARG B 420 *********************** 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 285 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 236 time to evaluate : 2.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ILE cc_start: 0.6321 (OUTLIER) cc_final: 0.5682 (mm) REVERT: A 248 ARG cc_start: 0.7095 (ttp-110) cc_final: 0.6852 (ttp-110) REVERT: A 420 ARG cc_start: 0.7143 (mtm110) cc_final: 0.6844 (mtm110) REVERT: E 45 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5479 (mm) REVERT: E 224 ARG cc_start: 0.6977 (ttm110) cc_final: 0.6504 (ttp-110) REVERT: E 248 ARG cc_start: 0.7152 (ttp-110) cc_final: 0.6873 (ttp-110) REVERT: D 45 ILE cc_start: 0.6028 (OUTLIER) cc_final: 0.5382 (mm) REVERT: D 490 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7165 (tt0) REVERT: C 45 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.5633 (mm) REVERT: C 561 PHE cc_start: 0.7978 (p90) cc_final: 0.7758 (p90) REVERT: B 45 ILE cc_start: 0.6242 (OUTLIER) cc_final: 0.5580 (mm) REVERT: B 248 ARG cc_start: 0.7276 (ttp-110) cc_final: 0.7043 (ttp-110) outliers start: 49 outliers final: 36 residues processed: 263 average time/residue: 0.3720 time to fit residues: 146.0250 Evaluate side-chains 266 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 151 ILE 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 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain E residue 354 THR 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 151 ILE Chi-restraints excluded: chain D residue 247 LEU 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 151 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 354 THR 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 C residue 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 354 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 Chi-restraints excluded: chain B residue 532 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: 9.9990 chunk 150 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 183 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 135 optimal weight: 4.9990 chunk 238 optimal weight: 20.0000 chunk 67 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN A 403 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 22110 Z= 0.435 Angle : 0.605 6.184 30125 Z= 0.317 Chirality : 0.045 0.154 3450 Planarity : 0.004 0.036 3910 Dihedral : 4.476 16.808 2995 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.66 % Allowed : 17.95 % Favored : 79.39 % 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: -0.81 (0.16), residues: 2745 helix: 0.74 (0.20), residues: 660 sheet: 0.23 (0.19), residues: 740 loop : -1.69 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 121 HIS 0.003 0.001 HIS D 285 PHE 0.013 0.002 PHE B 232 TYR 0.016 0.002 TYR A 518 ARG 0.003 0.000 ARG D 634 *********************** 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 290 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 229 time to evaluate : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.7231 (mtm110) cc_final: 0.6919 (mtm110) REVERT: E 224 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6514 (ttp-110) REVERT: E 247 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6032 (tt) REVERT: D 224 ARG cc_start: 0.6878 (ttm110) cc_final: 0.6300 (ttp-110) REVERT: D 490 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7122 (tt0) REVERT: C 247 LEU cc_start: 0.6681 (tp) cc_final: 0.6260 (tp) REVERT: B 248 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.7029 (ttp-110) outliers start: 61 outliers final: 45 residues processed: 266 average time/residue: 0.3642 time to fit residues: 145.6298 Evaluate side-chains 267 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 220 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 151 ILE 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 608 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 247 LEU 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 151 ILE Chi-restraints excluded: chain D residue 280 CYS 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 162 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 371 CYS Chi-restraints excluded: chain C residue 483 VAL 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 B residue 45 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 532 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 89 optimal weight: 3.9990 chunk 239 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 266 optimal weight: 3.9990 chunk 220 optimal weight: 40.0000 chunk 123 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 ASN B 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22110 Z= 0.457 Angle : 0.612 6.630 30125 Z= 0.321 Chirality : 0.045 0.155 3450 Planarity : 0.004 0.037 3910 Dihedral : 4.613 17.578 2995 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.92 % Allowed : 19.35 % 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: -0.94 (0.16), residues: 2745 helix: 0.65 (0.20), residues: 660 sheet: 0.12 (0.19), residues: 745 loop : -1.76 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 121 HIS 0.003 0.001 HIS B 285 PHE 0.013 0.002 PHE E 232 TYR 0.016 0.002 TYR A 518 ARG 0.003 0.000 ARG B 217 *********************** 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: 67 poor density : 219 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.7256 (mtm110) cc_final: 0.6936 (mtm110) REVERT: E 224 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6424 (ttp-110) REVERT: D 224 ARG cc_start: 0.6833 (ttm110) cc_final: 0.6232 (ttp-110) REVERT: D 490 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.7136 (tt0) REVERT: C 247 LEU cc_start: 0.6730 (tp) cc_final: 0.6318 (tp) REVERT: C 561 PHE cc_start: 0.8077 (p90) cc_final: 0.7789 (p90) REVERT: B 68 MET cc_start: 0.5407 (ppp) cc_final: 0.4768 (ppp) outliers start: 67 outliers final: 54 residues processed: 262 average time/residue: 0.3679 time to fit residues: 144.5456 Evaluate side-chains 264 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 209 time to evaluate : 2.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 151 ILE 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 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 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 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 E residue 608 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 255 LYS Chi-restraints excluded: chain D residue 280 CYS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 371 CYS Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 162 THR 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 483 VAL 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 626 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 151 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 608 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 256 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 0.0050 chunk 148 optimal weight: 1.9990 chunk 265 optimal weight: 0.9980 chunk 165 optimal weight: 40.0000 chunk 161 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.9398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2363 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= 0.165 Angle : 0.498 5.528 30125 Z= 0.260 Chirality : 0.041 0.148 3450 Planarity : 0.003 0.032 3910 Dihedral : 4.053 18.494 2995 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.57 % Allowed : 20.57 % Favored : 76.86 % 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: -0.87 (0.16), residues: 2745 helix: 0.65 (0.20), residues: 670 sheet: 0.15 (0.19), residues: 745 loop : -1.69 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 359 HIS 0.003 0.001 HIS C 285 PHE 0.018 0.001 PHE B 232 TYR 0.010 0.001 TYR D 620 ARG 0.003 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 281 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 222 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.7177 (mtm110) cc_final: 0.6837 (mtm110) REVERT: E 68 MET cc_start: 0.5340 (ppp) cc_final: 0.5059 (ppp) REVERT: E 224 ARG cc_start: 0.6886 (ttm110) cc_final: 0.6520 (ttp-110) REVERT: E 490 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: D 224 ARG cc_start: 0.6804 (ttm110) cc_final: 0.6236 (ttp-110) REVERT: D 367 SER cc_start: 0.8403 (t) cc_final: 0.8154 (t) REVERT: D 490 GLU cc_start: 0.7314 (OUTLIER) cc_final: 0.7095 (tt0) REVERT: D 561 PHE cc_start: 0.8164 (p90) cc_final: 0.7485 (t80) REVERT: C 68 MET cc_start: 0.5538 (ppp) cc_final: 0.5148 (ppp) REVERT: C 248 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6990 (ttp-110) REVERT: C 420 ARG cc_start: 0.7134 (mtm110) cc_final: 0.6882 (mtm110) REVERT: C 561 PHE cc_start: 0.7895 (p90) cc_final: 0.7682 (p90) REVERT: B 68 MET cc_start: 0.5286 (ppp) cc_final: 0.4565 (ptm) REVERT: B 224 ARG cc_start: 0.6757 (ttm110) cc_final: 0.6346 (ttp-110) REVERT: B 561 PHE cc_start: 0.8104 (p90) cc_final: 0.7387 (t80) outliers start: 59 outliers final: 40 residues processed: 271 average time/residue: 0.3522 time to fit residues: 144.0320 Evaluate side-chains 258 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 2.558 ------------------------------------------------------------------------------- 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 206 GLN 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 162 THR 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 608 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 255 LYS 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 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 371 CYS 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 608 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 204 HIS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 163 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 158 optimal weight: 0.0770 chunk 79 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 168 optimal weight: 0.0020 chunk 180 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 overall best weight: 0.7348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN E 204 HIS E 206 GLN ** E 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 HIS C 204 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2451 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= 0.152 Angle : 0.495 5.384 30125 Z= 0.259 Chirality : 0.041 0.171 3450 Planarity : 0.003 0.032 3910 Dihedral : 3.873 18.170 2995 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.35 % Allowed : 21.18 % Favored : 76.47 % 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 (0.16), residues: 2745 helix: 0.74 (0.20), residues: 670 sheet: 0.26 (0.19), residues: 740 loop : -1.64 (0.15), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.005 0.001 HIS B 204 PHE 0.021 0.001 PHE E 232 TYR 0.009 0.001 TYR D 620 ARG 0.005 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 289 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 68 MET cc_start: 0.5299 (ppp) cc_final: 0.5026 (ppp) REVERT: E 248 ARG cc_start: 0.7074 (ttp-110) cc_final: 0.6837 (ttp-110) REVERT: E 490 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.7027 (tt0) REVERT: D 224 ARG cc_start: 0.6828 (ttm110) cc_final: 0.6317 (ttp-110) REVERT: D 490 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: D 561 PHE cc_start: 0.8189 (p90) cc_final: 0.7458 (t80) REVERT: C 68 MET cc_start: 0.5470 (ppp) cc_final: 0.5042 (ppp) REVERT: C 248 ARG cc_start: 0.7291 (ttp-110) cc_final: 0.6979 (ttp-110) REVERT: B 68 MET cc_start: 0.5186 (ppp) cc_final: 0.4472 (ptm) REVERT: B 356 LYS cc_start: 0.8178 (tttp) cc_final: 0.7950 (tttm) REVERT: B 561 PHE cc_start: 0.8047 (p90) cc_final: 0.7300 (t80) outliers start: 54 outliers final: 39 residues processed: 280 average time/residue: 0.3396 time to fit residues: 144.8719 Evaluate side-chains 259 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 218 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 206 GLN Chi-restraints excluded: chain A residue 330 VAL 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 151 ILE Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 330 VAL 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 151 ILE Chi-restraints excluded: chain D residue 204 HIS 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 C residue 45 ILE Chi-restraints excluded: chain C residue 204 HIS Chi-restraints excluded: chain C residue 330 VAL 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 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 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 Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 241 optimal weight: 20.0000 chunk 253 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 246 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 223 optimal weight: 0.0270 chunk 233 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 overall best weight: 2.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 GLN E 206 GLN D 360 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2495 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= 0.308 Angle : 0.561 7.469 30125 Z= 0.295 Chirality : 0.043 0.168 3450 Planarity : 0.004 0.038 3910 Dihedral : 4.149 17.854 2995 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.31 % Allowed : 21.61 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.15), residues: 2745 helix: 0.66 (0.20), residues: 670 sheet: 0.17 (0.19), residues: 745 loop : -1.69 (0.15), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.006 0.001 HIS E 204 PHE 0.017 0.002 PHE B 232 TYR 0.013 0.002 TYR A 518 ARG 0.005 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 273 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 220 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 68 MET cc_start: 0.5472 (ppp) cc_final: 0.5100 (ppp) REVERT: E 248 ARG cc_start: 0.7094 (ttp-110) cc_final: 0.6847 (ttp-110) REVERT: E 490 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: D 68 MET cc_start: 0.5320 (ppp) cc_final: 0.4870 (ppp) REVERT: D 224 ARG cc_start: 0.6827 (ttm110) cc_final: 0.6305 (ttp-110) REVERT: D 490 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: B 68 MET cc_start: 0.5280 (ppp) cc_final: 0.4775 (ppp) outliers start: 53 outliers final: 43 residues processed: 261 average time/residue: 0.3629 time to fit residues: 143.0945 Evaluate side-chains 262 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 151 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 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 151 ILE Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 354 THR 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 608 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 261 optimal weight: 5.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 20.0000 chunk 181 optimal weight: 8.9990 chunk 273 optimal weight: 6.9990 chunk 252 optimal weight: 0.0170 chunk 218 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 168 optimal weight: 0.0970 chunk 133 optimal weight: 30.0000 chunk 173 optimal weight: 0.9990 overall best weight: 1.8222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN E 206 GLN D 204 HIS ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2538 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= 0.237 Angle : 0.534 7.511 30125 Z= 0.281 Chirality : 0.042 0.155 3450 Planarity : 0.003 0.043 3910 Dihedral : 4.081 18.090 2995 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.14 % Allowed : 21.79 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.15), residues: 2745 helix: 0.66 (0.20), residues: 670 sheet: 0.16 (0.19), residues: 745 loop : -1.65 (0.16), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.004 0.001 HIS B 285 PHE 0.020 0.001 PHE E 232 TYR 0.011 0.001 TYR C 627 ARG 0.008 0.000 ARG E 224 ********************** 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 270 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 221 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 68 MET cc_start: 0.5456 (ppp) cc_final: 0.5096 (ppp) REVERT: E 248 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6827 (ttp-110) REVERT: E 490 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7034 (tt0) REVERT: D 68 MET cc_start: 0.5308 (ppp) cc_final: 0.4848 (ppp) REVERT: D 224 ARG cc_start: 0.6852 (ttm110) cc_final: 0.6343 (ttp-110) REVERT: D 490 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7084 (tt0) REVERT: D 561 PHE cc_start: 0.8309 (p90) cc_final: 0.7532 (t80) REVERT: C 248 ARG cc_start: 0.7294 (ttp-110) cc_final: 0.7002 (ttp-110) REVERT: C 420 ARG cc_start: 0.7201 (mtm110) cc_final: 0.6906 (mtm-85) REVERT: B 68 MET cc_start: 0.5285 (ppp) cc_final: 0.4818 (ppp) REVERT: B 420 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6891 (mtm-85) REVERT: B 561 PHE cc_start: 0.8210 (p90) cc_final: 0.7443 (t80) outliers start: 49 outliers final: 44 residues processed: 259 average time/residue: 0.3520 time to fit residues: 139.6029 Evaluate side-chains 265 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 219 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 94 GLN Chi-restraints excluded: chain E residue 151 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 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 151 ILE Chi-restraints excluded: chain D residue 204 HIS Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 477 LEU Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 354 THR 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 608 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 151 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 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 637 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 275 random chunks: chunk 232 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 201 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 218 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 224 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 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 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN E 206 GLN D 204 HIS ** C 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.183640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110576 restraints weight = 25132.403| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.15 r_work: 0.2976 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22110 Z= 0.176 Angle : 0.516 7.560 30125 Z= 0.271 Chirality : 0.041 0.154 3450 Planarity : 0.003 0.038 3910 Dihedral : 4.002 18.046 2995 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.14 % Allowed : 21.83 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.80 (0.16), residues: 2745 helix: 0.69 (0.20), residues: 670 sheet: 0.14 (0.19), residues: 735 loop : -1.59 (0.16), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.004 0.001 HIS D 204 PHE 0.022 0.001 PHE E 232 TYR 0.010 0.001 TYR C 627 ARG 0.008 0.000 ARG E 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5002.60 seconds wall clock time: 91 minutes 2.32 seconds (5462.32 seconds total)