Starting phenix.real_space_refine on Sat Jul 4 18:46:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.map" model { file = "/net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eva_19996/07_2026/9eva_19996.cif" } resolution = 2.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.032 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: 5 Type Number sf(0) Gaussians Ca 10 9.91 5 S 55 5.16 5 C 14797 2.51 5 N 3739 2.21 5 O 4327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22928 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4633 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4624 Classifications: {'peptide': 588} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 560} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 4515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4515 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 545} Chain breaks: 4 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4534 Classifications: {'peptide': 579} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 551} Chain breaks: 3 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4612 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 558} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 5.29, per 1000 atoms: 0.23 Number of scatterers: 22928 At special positions: 0 Unit cell: (142.195, 143.888, 154.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 10 19.99 S 55 16.00 O 4327 8.00 N 3739 7.00 C 14797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 997.9 milliseconds 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5378 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 29 sheets defined 29.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 514 through 536 removed outlier: 3.959A pdb=" N TYR A 518 " --> pdb=" O ASN A 514 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N VAL A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Proline residue: A 525 - end of helix removed outlier: 3.682A pdb=" N ILE A 536 " --> pdb=" O VAL A 532 " (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 564 removed outlier: 3.501A pdb=" N LEU A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 574 through 604 removed outlier: 3.522A pdb=" N VAL A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 636 Proline residue: A 621 - end of helix Processing helix chain 'B' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 removed outlier: 3.709A pdb=" N THR B 111 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 362 through 365 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 514 through 536 removed outlier: 3.834A pdb=" N TYR B 518 " --> pdb=" O ASN B 514 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N VAL B 524 " --> pdb=" O LEU B 520 " (cutoff:3.500A) Proline residue: B 525 - end of helix removed outlier: 3.702A pdb=" N ILE B 536 " --> pdb=" O VAL B 532 " (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 564 through 567 Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.525A pdb=" N VAL B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 637 Proline residue: B 621 - end of helix removed outlier: 3.808A pdb=" N THR B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.748A pdb=" N LEU C 311 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ARG C 312 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 314 " --> pdb=" O LEU C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 365 Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 514 through 536 removed outlier: 3.839A pdb=" N TYR C 518 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL C 524 " --> pdb=" O LEU C 520 " (cutoff:3.500A) Proline residue: C 525 - end of helix removed outlier: 3.689A pdb=" N ILE C 536 " --> pdb=" O VAL C 532 " (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 removed outlier: 3.515A pdb=" N LEU C 554 " --> pdb=" O SER C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 567 Processing helix chain 'C' and resid 574 through 604 removed outlier: 3.579A pdb=" N VAL C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 637 Proline residue: C 621 - end of helix removed outlier: 3.793A pdb=" N THR C 637 " --> pdb=" O LEU C 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 99 removed outlier: 3.815A pdb=" N GLN D 94 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.709A pdb=" N THR D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 196 through 199 Processing helix chain 'D' and resid 362 through 365 Processing helix chain 'D' and resid 367 through 371 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 514 through 536 removed outlier: 3.909A pdb=" N TYR D 518 " --> pdb=" O ASN D 514 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Proline residue: D 525 - end of helix removed outlier: 3.693A pdb=" N ILE D 536 " --> pdb=" O VAL D 532 " (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 564 through 567 Processing helix chain 'D' and resid 574 through 604 removed outlier: 3.510A pdb=" N VAL D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 636 Proline residue: D 621 - end of helix Processing helix chain 'E' and resid 88 through 100 removed outlier: 3.816A pdb=" N GLN E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL E 95 " --> pdb=" O SER E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 118 removed outlier: 3.709A pdb=" N THR E 111 " --> pdb=" O ILE E 107 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG E 116 " --> pdb=" O ALA E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 196 through 199 Processing helix chain 'E' and resid 362 through 365 Processing helix chain 'E' and resid 367 through 371 Processing helix chain 'E' and resid 382 through 391 Processing helix chain 'E' and resid 514 through 536 removed outlier: 3.929A pdb=" N TYR E 518 " --> pdb=" O ASN E 514 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Proline residue: E 525 - end of helix removed outlier: 3.621A pdb=" N ILE E 536 " --> pdb=" O VAL E 532 " (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 564 through 567 Processing helix chain 'E' and resid 574 through 604 removed outlier: 3.520A pdb=" N VAL E 591 " --> pdb=" O THR E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 636 Proline residue: E 621 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER A 167 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY A 120 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 79 " --> pdb=" O ASP A 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY A 141 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 57 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 204 through 212 removed outlier: 4.232A pdb=" N ALA A 298 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 218 through 222 removed outlier: 7.503A pdb=" N LEU A 247 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE A 259 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 249 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 376 through 379 removed outlier: 4.353A pdb=" N GLN A 411 " --> pdb=" O PHE A 424 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 424 " --> pdb=" O GLN A 411 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE A 413 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N SER A 422 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 415 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A 420 " --> pdb=" O VAL A 415 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 341 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 352 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE A 339 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N THR A 354 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ASP A 337 " --> pdb=" O THR A 354 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N LYS A 356 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ALA A 335 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 358 " --> pdb=" O GLY A 333 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N GLY A 333 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N HIS A 360 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 9.339A pdb=" N THR A 331 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP A 328 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN A 464 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL A 330 " --> pdb=" O ASN A 464 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 466 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL A 332 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 399 removed outlier: 5.066A pdb=" N SER A 503 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 502 " --> pdb=" O GLU A 493 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N GLU A 493 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG A 504 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE A 491 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR A 506 " --> pdb=" O GLN A 489 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLN A 489 " --> pdb=" O THR A 506 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A 508 " --> pdb=" O TYR A 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR A 487 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 510 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER B 167 " --> pdb=" O THR B 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY B 120 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 79 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY B 141 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 57 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 204 through 212 removed outlier: 4.315A pdb=" N ALA B 298 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 218 through 222 removed outlier: 7.330A pdb=" N LEU B 247 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N PHE B 259 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 249 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 376 through 379 removed outlier: 4.362A pdb=" N GLN B 411 " --> pdb=" O PHE B 424 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N PHE B 424 " --> pdb=" O GLN B 411 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 413 " --> pdb=" O SER B 422 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N SER B 422 " --> pdb=" O ILE B 413 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 415 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 420 " --> pdb=" O VAL B 415 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 341 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL B 352 " --> pdb=" O ILE B 339 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE B 339 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N THR B 354 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASP B 337 " --> pdb=" O THR B 354 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LYS B 356 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA B 335 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N SER B 358 " --> pdb=" O GLY B 333 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLY B 333 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N HIS B 360 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 9.401A pdb=" N THR B 331 " --> pdb=" O HIS B 360 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP B 328 " --> pdb=" O ILE B 462 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASN B 464 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B 330 " --> pdb=" O ASN B 464 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE B 466 " --> pdb=" O VAL B 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL B 332 " --> pdb=" O ILE B 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 397 through 399 removed outlier: 4.981A pdb=" N SER B 503 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 502 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLU B 493 " --> pdb=" O ASN B 502 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 504 " --> pdb=" O ILE B 491 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILE B 491 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR B 506 " --> pdb=" O GLN B 489 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN B 489 " --> pdb=" O THR B 506 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 508 " --> pdb=" O TYR B 487 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR B 487 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU B 510 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 38 through 45 removed outlier: 5.995A pdb=" N SER C 167 " --> pdb=" O THR C 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY C 120 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 79 " --> pdb=" O ASP C 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY C 141 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 57 " --> pdb=" O GLY C 141 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 204 through 208 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 204 through 208 current: chain 'C' and resid 256 through 259 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 256 through 259 current: chain 'C' and resid 269 through 274 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 376 through 379 removed outlier: 4.328A pdb=" N GLN C 411 " --> pdb=" O PHE C 424 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N PHE C 424 " --> pdb=" O GLN C 411 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE C 413 " --> pdb=" O SER C 422 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER C 422 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 415 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG C 420 " --> pdb=" O VAL C 415 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ASN C 348 " --> pdb=" O GLY C 341 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLY C 341 " --> pdb=" O ASN C 348 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER C 350 " --> pdb=" O ILE C 339 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE C 339 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 352 " --> pdb=" O ASP C 337 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N HIS C 360 " --> pdb=" O LEU C 329 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N LEU C 329 " --> pdb=" O HIS C 360 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ASP C 328 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 464 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL C 330 " --> pdb=" O ASN C 464 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE C 466 " --> pdb=" O VAL C 330 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N VAL C 332 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 397 through 399 removed outlier: 5.001A pdb=" N SER C 503 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN C 502 " --> pdb=" O GLU C 493 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLU C 493 " --> pdb=" O ASN C 502 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG C 504 " --> pdb=" O ILE C 491 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ILE C 491 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 506 " --> pdb=" O GLN C 489 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN C 489 " --> pdb=" O THR C 506 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C 508 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR C 487 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU C 510 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER D 167 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.685A pdb=" N GLY D 120 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 79 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY D 141 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP D 57 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 204 through 212 removed outlier: 4.252A pdb=" N ALA D 298 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA D 234 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 218 through 222 removed outlier: 7.340A pdb=" N LEU D 247 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D 259 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU D 249 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 376 through 379 removed outlier: 4.330A pdb=" N GLN D 411 " --> pdb=" O PHE D 424 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 424 " --> pdb=" O GLN D 411 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE D 413 " --> pdb=" O SER D 422 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER D 422 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL D 415 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG D 420 " --> pdb=" O VAL D 415 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY D 341 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL D 352 " --> pdb=" O ILE D 339 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ILE D 339 " --> pdb=" O VAL D 352 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N THR D 354 " --> pdb=" O ASP D 337 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ASP D 337 " --> pdb=" O THR D 354 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N LYS D 356 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ALA D 335 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER D 358 " --> pdb=" O GLY D 333 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N GLY D 333 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N HIS D 360 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N THR D 331 " --> pdb=" O HIS D 360 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP D 328 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN D 464 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 330 " --> pdb=" O ASN D 464 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 466 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL D 332 " --> pdb=" O ILE D 466 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.062A pdb=" N SER D 503 " --> pdb=" O LEU D 454 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN D 502 " --> pdb=" O GLU D 493 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLU D 493 " --> pdb=" O ASN D 502 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ARG D 504 " --> pdb=" O ILE D 491 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 491 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR D 506 " --> pdb=" O GLN D 489 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLN D 489 " --> pdb=" O THR D 506 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR D 508 " --> pdb=" O TYR D 487 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TYR D 487 " --> pdb=" O THR D 508 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU D 510 " --> pdb=" O THR D 485 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 38 through 45 removed outlier: 5.996A pdb=" N SER E 167 " --> pdb=" O THR E 71 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.686A pdb=" N GLY E 120 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 79 " --> pdb=" O ASP E 122 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N GLY E 141 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP E 57 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 204 through 212 removed outlier: 4.124A pdb=" N ALA E 298 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 218 through 222 removed outlier: 7.412A pdb=" N LEU E 247 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N PHE E 259 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU E 249 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 376 through 379 removed outlier: 4.293A pdb=" N GLN E 411 " --> pdb=" O PHE E 424 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N PHE E 424 " --> pdb=" O GLN E 411 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ILE E 413 " --> pdb=" O SER E 422 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N SER E 422 " --> pdb=" O ILE E 413 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL E 415 " --> pdb=" O ARG E 420 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ARG E 420 " --> pdb=" O VAL E 415 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY E 341 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL E 352 " --> pdb=" O ILE E 339 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ILE E 339 " --> pdb=" O VAL E 352 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N THR E 354 " --> pdb=" O ASP E 337 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP E 337 " --> pdb=" O THR E 354 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS E 356 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ALA E 335 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N SER E 358 " --> pdb=" O GLY E 333 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N GLY E 333 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N HIS E 360 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N THR E 331 " --> pdb=" O HIS E 360 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ASP E 328 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ASN E 464 " --> pdb=" O ASP E 328 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL E 330 " --> pdb=" O ASN E 464 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE E 466 " --> pdb=" O VAL E 330 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL E 332 " --> pdb=" O ILE E 466 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 397 through 399 removed outlier: 5.043A pdb=" N SER E 503 " --> pdb=" O LEU E 454 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASN E 502 " --> pdb=" O GLU E 493 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU E 493 " --> pdb=" O ASN E 502 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ARG E 504 " --> pdb=" O ILE E 491 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE E 491 " --> pdb=" O ARG E 504 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR E 506 " --> pdb=" O GLN E 489 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN E 489 " --> pdb=" O THR E 506 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 508 " --> pdb=" O TYR E 487 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR E 487 " --> pdb=" O THR E 508 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU E 510 " --> pdb=" O THR E 485 " (cutoff:3.500A) 1059 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4918 1.33 - 1.45: 5432 1.45 - 1.57: 13008 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 23438 Sorted by residual: bond pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.63e+01 bond pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 1.524 1.472 0.052 1.29e-02 6.01e+03 1.60e+01 bond pdb=" CA ALA E 99 " pdb=" C ALA E 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.58e+01 bond pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 1.526 1.489 0.037 9.20e-03 1.18e+04 1.58e+01 bond pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.29e-02 6.01e+03 1.57e+01 ... (remaining 23433 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 31409 1.97 - 3.94: 422 3.94 - 5.91: 47 5.91 - 7.89: 12 7.89 - 9.86: 6 Bond angle restraints: 31896 Sorted by residual: angle pdb=" N ILE C 199 " pdb=" CA ILE C 199 " pdb=" C ILE C 199 " ideal model delta sigma weight residual 109.34 119.20 -9.86 2.08e+00 2.31e-01 2.25e+01 angle pdb=" C LYS C 200 " pdb=" N PRO C 201 " pdb=" CA PRO C 201 " ideal model delta sigma weight residual 119.84 125.53 -5.69 1.25e+00 6.40e-01 2.08e+01 angle pdb=" N GLU E 103 " pdb=" CA GLU E 103 " pdb=" C GLU E 103 " ideal model delta sigma weight residual 110.56 101.82 8.74 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N GLU A 103 " pdb=" CA GLU A 103 " pdb=" C GLU A 103 " ideal model delta sigma weight residual 110.56 101.83 8.73 1.94e+00 2.66e-01 2.03e+01 angle pdb=" N TYR E 620 " pdb=" CA TYR E 620 " pdb=" C TYR E 620 " ideal model delta sigma weight residual 113.25 119.06 -5.81 1.30e+00 5.92e-01 2.00e+01 ... (remaining 31891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 13208 16.50 - 32.99: 430 32.99 - 49.49: 90 49.49 - 65.99: 25 65.99 - 82.48: 7 Dihedral angle restraints: 13760 sinusoidal: 5384 harmonic: 8376 Sorted by residual: dihedral pdb=" CA ILE D 522 " pdb=" C ILE D 522 " pdb=" N PHE D 523 " pdb=" CA PHE D 523 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA ILE B 522 " pdb=" C ILE B 522 " pdb=" N PHE B 523 " pdb=" CA PHE B 523 " ideal model delta harmonic sigma weight residual -180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PRO A 265 " pdb=" C PRO A 265 " pdb=" N GLY A 266 " pdb=" CA GLY A 266 " ideal model delta harmonic sigma weight residual -180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 13757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3011 0.054 - 0.108: 513 0.108 - 0.162: 106 0.162 - 0.217: 1 0.217 - 0.271: 8 Chirality restraints: 3639 Sorted by residual: chirality pdb=" CA TYR E 620 " pdb=" N TYR E 620 " pdb=" C TYR E 620 " pdb=" CB TYR E 620 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA ASN E 104 " pdb=" N ASN E 104 " pdb=" C ASN E 104 " pdb=" CB ASN E 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA ASN A 104 " pdb=" N ASN A 104 " pdb=" C ASN A 104 " pdb=" CB ASN A 104 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3636 not shown) Planarity restraints: 4125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU C 198 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C GLU C 198 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU C 198 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE C 199 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 619 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 619 " -0.041 2.00e-02 2.50e+03 pdb=" O ILE E 619 " 0.015 2.00e-02 2.50e+03 pdb=" N TYR E 620 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 200 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.52e+00 pdb=" N PRO C 201 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.028 5.00e-02 4.00e+02 ... (remaining 4122 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4611 2.78 - 3.31: 19923 3.31 - 3.84: 35568 3.84 - 4.37: 41196 4.37 - 4.90: 73905 Nonbonded interactions: 175203 Sorted by model distance: nonbonded pdb=" OG SER B 367 " pdb=" OD1 ASP B 369 " model vdw 2.252 3.040 nonbonded pdb=" OG SER C 367 " pdb=" OD1 ASP C 369 " model vdw 2.252 3.040 nonbonded pdb=" O TYR E 129 " pdb="CA CA E 702 " model vdw 2.273 3.250 nonbonded pdb=" OG SER B 533 " pdb=" OD1 ASN B 552 " model vdw 2.275 3.040 nonbonded pdb=" OG SER E 533 " pdb=" OD1 ASN E 552 " model vdw 2.308 3.040 ... (remaining 175198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 198 or (resid 199 through 200 and (name N or name CA or name C or name O or na \ me CB )) or resid 201 or (resid 202 through 203 and (name N or name CA or name C \ or name O or name CB )) or resid 204 through 209 or resid 217 through 238 or re \ sid 245 through 287 or resid 301 through 310 or resid 322 through 368 or (resid \ 369 through 370 and (name N or name CA or name C or name O or name CB )) or resi \ d 371 through 702)) selection = (chain 'B' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 321 or resid 323 through 368 or (resid 369 through 370 \ and (name N or name CA or name C or name O or name CB )) or resid 371 through 7 \ 02)) selection = (chain 'C' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 138 or (resid \ 139 and (name N or name CA or name C or name O or name CB )) or resid 140 throug \ h 201 or (resid 202 through 203 and (name N or name CA or name C or name O or na \ me CB )) or resid 204 through 245 or (resid 246 and (name N or name CA or name C \ or name O or name CB )) or resid 247 through 310 or resid 314 or resid 323 thro \ ugh 368 or (resid 369 through 370 and (name N or name CA or name C or name O or \ name CB )) or resid 371 through 702)) selection = (chain 'D' and (resid 37 through 198 or (resid 199 through 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 209 or resid 217 th \ rough 238 or resid 245 or (resid 246 and (name N or name CA or name C or name O \ or name CB )) or resid 247 through 287 or resid 301 through 310 or resid 322 thr \ ough 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) \ or resid 371 through 702)) selection = (chain 'E' and (resid 37 through 95 or (resid 96 through 99 and (name N or name \ CA or name C or name O or name CB )) or resid 100 or (resid 107 and (name N or n \ ame CA or name C or name O or name CB )) or resid 108 or (resid 109 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 198 or (resid \ 199 through 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 209 or resid 217 through 238 or resid 245 or (resid 246 and (name \ N or name CA or name C or name O or name CB )) or resid 247 through 287 or resid \ 301 through 310 or resid 322 through 368 or (resid 369 through 370 and (name N \ or name CA or name C or name O or name CB )) or resid 371 through 702)) } 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: 3.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.870 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:8.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 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 : 0.003 0.053 23438 Z= 0.222 Angle : 0.590 9.857 31896 Z= 0.341 Chirality : 0.045 0.271 3639 Planarity : 0.004 0.053 4125 Dihedral : 9.401 82.484 8382 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.54 % Favored : 97.36 % Rotamer: Outliers : 0.68 % Allowed : 3.27 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 2875 helix: 1.66 (0.21), residues: 702 sheet: 1.04 (0.16), residues: 977 loop : -0.34 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 578 TYR 0.014 0.001 TYR C 517 PHE 0.011 0.001 PHE B 561 TRP 0.005 0.001 TRP E 630 HIS 0.003 0.001 HIS A 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.22 (23438) covalent geometry : angle 0.59030 / 0.34 (31896) hydrogen bonds : bond 0.19100 / 12.63 ( 1059) hydrogen bonds : angle 6.35638 / 4.39 ( 2919) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 695 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7475 (mm-30) REVERT: A 425 GLU cc_start: 0.7823 (tt0) cc_final: 0.7462 (tt0) REVERT: A 480 GLU cc_start: 0.7964 (mp0) cc_final: 0.7456 (mp0) REVERT: A 481 GLU cc_start: 0.7762 (tt0) cc_final: 0.7474 (tt0) REVERT: B 58 MET cc_start: 0.6081 (mmp) cc_final: 0.5629 (mmm) REVERT: B 236 VAL cc_start: 0.8639 (p) cc_final: 0.8390 (m) REVERT: B 345 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7666 (mtp85) REVERT: C 270 GLU cc_start: 0.6769 (pt0) cc_final: 0.6541 (pt0) REVERT: C 286 VAL cc_start: 0.4468 (OUTLIER) cc_final: 0.4157 (t) REVERT: C 437 ASP cc_start: 0.8123 (t0) cc_final: 0.7889 (t70) REVERT: D 58 MET cc_start: 0.0630 (mmp) cc_final: 0.0421 (mtt) REVERT: D 347 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 364 LEU cc_start: 0.8401 (mp) cc_final: 0.8149 (mp) REVERT: E 207 GLU cc_start: 0.6817 (tt0) cc_final: 0.6607 (tt0) REVERT: E 425 GLU cc_start: 0.7614 (tt0) cc_final: 0.7287 (tt0) REVERT: E 480 GLU cc_start: 0.7755 (mp0) cc_final: 0.7336 (mp0) outliers start: 17 outliers final: 5 residues processed: 706 average time/residue: 0.6150 time to fit residues: 492.4451 Evaluate side-chains 584 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 578 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 255 LYS Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 620 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN A 338 GLN A 344 GLN A 405 ASN A 409 GLN B 154 GLN B 344 GLN B 360 HIS B 432 GLN B 464 ASN B 476 GLN B 611 GLN C 409 GLN C 432 GLN C 611 GLN D 233 HIS D 338 GLN D 560 ASN D 611 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN E 514 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136480 restraints weight = 30525.874| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.86 r_work: 0.3704 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3563 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23438 Z= 0.262 Angle : 0.683 10.679 31896 Z= 0.370 Chirality : 0.050 0.172 3639 Planarity : 0.005 0.046 4125 Dihedral : 5.516 57.220 3146 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.11 % Allowed : 10.42 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.15), residues: 2875 helix: 1.49 (0.20), residues: 738 sheet: 1.02 (0.17), residues: 899 loop : -0.48 (0.17), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 217 TYR 0.049 0.003 TYR C 53 PHE 0.033 0.003 PHE E 135 TRP 0.013 0.002 TRP C 121 HIS 0.009 0.002 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 (23438) covalent geometry : angle 0.68304 / 0.37 (31896) hydrogen bonds : bond 0.08259 / 5.54 ( 1059) hydrogen bonds : angle 5.02522 / 3.44 ( 2919) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 606 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8561 (tt) cc_final: 0.8343 (tp) REVERT: A 259 PHE cc_start: 0.7841 (t80) cc_final: 0.7627 (t80) REVERT: A 347 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7542 (tt0) REVERT: A 425 GLU cc_start: 0.8187 (tt0) cc_final: 0.7937 (tt0) REVERT: A 480 GLU cc_start: 0.8430 (mp0) cc_final: 0.7811 (mp0) REVERT: A 481 GLU cc_start: 0.8257 (tt0) cc_final: 0.8013 (tt0) REVERT: B 303 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8631 (mp) REVERT: B 345 ARG cc_start: 0.8518 (mtp85) cc_final: 0.8314 (mtp85) REVERT: C 82 MET cc_start: 0.5379 (pmm) cc_final: 0.5072 (pmm) REVERT: C 286 VAL cc_start: 0.5071 (OUTLIER) cc_final: 0.4684 (t) REVERT: C 347 GLU cc_start: 0.8610 (mt-10) cc_final: 0.7790 (mt-10) REVERT: C 425 GLU cc_start: 0.8072 (tt0) cc_final: 0.7772 (tt0) REVERT: C 468 ARG cc_start: 0.7844 (mtt180) cc_final: 0.7588 (mtt180) REVERT: C 480 GLU cc_start: 0.8271 (mp0) cc_final: 0.7848 (mp0) REVERT: C 620 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7218 (t80) REVERT: D 58 MET cc_start: -0.1168 (mmp) cc_final: -0.2325 (mtt) REVERT: D 347 GLU cc_start: 0.8384 (mt-10) cc_final: 0.7921 (mt-10) REVERT: D 370 GLN cc_start: 0.7645 (mp10) cc_final: 0.7339 (mp10) REVERT: E 109 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7520 (mp0) REVERT: E 347 GLU cc_start: 0.8620 (mt-10) cc_final: 0.7723 (tt0) REVERT: E 480 GLU cc_start: 0.8271 (mp0) cc_final: 0.8039 (mp0) REVERT: E 481 GLU cc_start: 0.8323 (tt0) cc_final: 0.8099 (tt0) REVERT: E 515 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8633 (mp) outliers start: 78 outliers final: 39 residues processed: 639 average time/residue: 0.6511 time to fit residues: 468.9307 Evaluate side-chains 635 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 592 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 550 SER Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain D residue 622 LEU Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 269 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 268 optimal weight: 0.9990 chunk 258 optimal weight: 0.7980 chunk 167 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 255 optimal weight: 6.9990 chunk 185 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 233 HIS A 410 ASN A 432 GLN A 560 ASN B 154 GLN B 360 HIS B 432 GLN B 459 ASN B 476 GLN C 160 GLN C 169 GLN C 409 GLN C 432 GLN C 560 ASN D 221 GLN D 432 GLN D 560 ASN E 432 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.160471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.140004 restraints weight = 30700.060| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 1.87 r_work: 0.3750 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23438 Z= 0.130 Angle : 0.541 6.753 31896 Z= 0.290 Chirality : 0.043 0.164 3639 Planarity : 0.004 0.041 4125 Dihedral : 5.006 51.776 3142 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.03 % Allowed : 12.61 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2875 helix: 1.90 (0.20), residues: 734 sheet: 1.14 (0.16), residues: 958 loop : -0.42 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 521 TYR 0.018 0.002 TYR C 53 PHE 0.021 0.001 PHE C 168 TRP 0.009 0.001 TRP E 359 HIS 0.004 0.001 HIS B 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (23438) covalent geometry : angle 0.54112 / 0.29 (31896) hydrogen bonds : bond 0.05857 / 3.92 ( 1059) hydrogen bonds : angle 4.53171 / 3.09 ( 2919) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 596 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8539 (tt) cc_final: 0.8324 (tp) REVERT: A 347 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7678 (tt0) REVERT: A 425 GLU cc_start: 0.8184 (tt0) cc_final: 0.7933 (tt0) REVERT: A 480 GLU cc_start: 0.8315 (mp0) cc_final: 0.7710 (mp0) REVERT: A 481 GLU cc_start: 0.8263 (tt0) cc_final: 0.8042 (tt0) REVERT: B 207 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7275 (tp30) REVERT: B 303 LEU cc_start: 0.8843 (mt) cc_final: 0.8626 (mp) REVERT: B 345 ARG cc_start: 0.8568 (mtp85) cc_final: 0.8362 (mtp85) REVERT: C 255 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5408 (tmtp) REVERT: C 286 VAL cc_start: 0.5000 (OUTLIER) cc_final: 0.4637 (t) REVERT: C 347 GLU cc_start: 0.8593 (mt-10) cc_final: 0.7671 (tt0) REVERT: C 425 GLU cc_start: 0.8022 (tt0) cc_final: 0.7761 (tt0) REVERT: C 480 GLU cc_start: 0.8241 (mp0) cc_final: 0.7732 (mp0) REVERT: C 620 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.7179 (t80) REVERT: D 58 MET cc_start: -0.0917 (mmp) cc_final: -0.2102 (mtm) REVERT: D 269 VAL cc_start: 0.7746 (t) cc_final: 0.7452 (m) REVERT: E 109 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7618 (mp0) REVERT: E 347 GLU cc_start: 0.8492 (mt-10) cc_final: 0.7480 (tt0) REVERT: E 480 GLU cc_start: 0.8268 (mp0) cc_final: 0.7935 (mp0) REVERT: E 515 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8491 (mp) outliers start: 76 outliers final: 39 residues processed: 625 average time/residue: 0.7002 time to fit residues: 493.7689 Evaluate side-chains 635 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 591 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 515 LEU Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 58 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 258 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 409 GLN A 410 ASN B 60 GLN B 360 HIS B 432 GLN B 476 GLN C 144 HIS C 169 GLN C 432 GLN C 560 ASN D 338 GLN D 611 GLN E 70 ASN E 344 GLN E 432 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.156823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136603 restraints weight = 30458.706| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 1.84 r_work: 0.3709 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23438 Z= 0.198 Angle : 0.609 8.410 31896 Z= 0.328 Chirality : 0.046 0.186 3639 Planarity : 0.004 0.060 4125 Dihedral : 5.184 51.290 3142 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.07 % Allowed : 13.49 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2875 helix: 1.75 (0.20), residues: 737 sheet: 1.04 (0.16), residues: 931 loop : -0.57 (0.17), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 521 TYR 0.034 0.002 TYR C 53 PHE 0.032 0.002 PHE E 414 TRP 0.012 0.001 TRP C 121 HIS 0.007 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.20 (23438) covalent geometry : angle 0.60895 / 0.33 (31896) hydrogen bonds : bond 0.07266 / 4.86 ( 1059) hydrogen bonds : angle 4.70172 / 3.21 ( 2919) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 594 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8511 (mt-10) cc_final: 0.7584 (tt0) REVERT: A 425 GLU cc_start: 0.8195 (tt0) cc_final: 0.7938 (tt0) REVERT: A 480 GLU cc_start: 0.8351 (mp0) cc_final: 0.7748 (mp0) REVERT: A 481 GLU cc_start: 0.8328 (tt0) cc_final: 0.8088 (tt0) REVERT: B 303 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8638 (mp) REVERT: C 58 MET cc_start: 0.5374 (OUTLIER) cc_final: 0.4968 (mtt) REVERT: C 82 MET cc_start: 0.5586 (pmm) cc_final: 0.5324 (pmm) REVERT: C 235 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7897 (pt) REVERT: C 255 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5493 (tmtp) REVERT: C 286 VAL cc_start: 0.5154 (OUTLIER) cc_final: 0.4754 (t) REVERT: C 347 GLU cc_start: 0.8628 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 425 GLU cc_start: 0.8060 (tt0) cc_final: 0.7795 (tt0) REVERT: C 480 GLU cc_start: 0.8262 (mp0) cc_final: 0.7930 (mp0) REVERT: C 498 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.5763 (tpp-160) REVERT: C 620 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7288 (t80) REVERT: C 633 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8463 (mp) REVERT: D 58 MET cc_start: -0.0883 (mmp) cc_final: -0.1983 (mtm) REVERT: D 269 VAL cc_start: 0.7796 (t) cc_final: 0.7519 (m) REVERT: E 347 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7415 (tt0) REVERT: E 468 ARG cc_start: 0.8231 (mtt180) cc_final: 0.8021 (mtt180) REVERT: E 566 ASP cc_start: 0.7463 (m-30) cc_final: 0.7214 (m-30) REVERT: E 620 TYR cc_start: 0.7885 (OUTLIER) cc_final: 0.7036 (t80) outliers start: 102 outliers final: 55 residues processed: 641 average time/residue: 0.7267 time to fit residues: 524.5556 Evaluate side-chains 647 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 583 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 633 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 270 GLU Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 603 VAL Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 87 optimal weight: 0.7980 chunk 264 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 410 ASN A 514 ASN B 360 HIS B 410 ASN B 432 GLN B 476 GLN C 169 GLN C 432 GLN D 221 GLN D 432 GLN E 70 ASN E 360 HIS E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.158496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.138451 restraints weight = 30320.526| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.84 r_work: 0.3732 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23438 Z= 0.136 Angle : 0.545 7.028 31896 Z= 0.292 Chirality : 0.044 0.174 3639 Planarity : 0.004 0.044 4125 Dihedral : 4.966 51.223 3142 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.47 % Allowed : 15.56 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 2875 helix: 1.94 (0.20), residues: 736 sheet: 1.08 (0.16), residues: 943 loop : -0.51 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 521 TYR 0.021 0.002 TYR E 300 PHE 0.025 0.002 PHE C 168 TRP 0.009 0.001 TRP E 359 HIS 0.006 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (23438) covalent geometry : angle 0.54518 / 0.29 (31896) hydrogen bonds : bond 0.05834 / 3.90 ( 1059) hydrogen bonds : angle 4.43432 / 3.03 ( 2919) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 584 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7726 (tt0) REVERT: A 425 GLU cc_start: 0.8169 (tt0) cc_final: 0.7918 (tt0) REVERT: A 480 GLU cc_start: 0.8338 (mp0) cc_final: 0.7745 (mp0) REVERT: A 481 GLU cc_start: 0.8321 (tt0) cc_final: 0.8067 (tt0) REVERT: A 521 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7989 (mtp-110) REVERT: B 207 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: B 303 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8542 (mp) REVERT: C 58 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5237 (mtt) REVERT: C 235 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7998 (pt) REVERT: C 255 LYS cc_start: 0.5753 (OUTLIER) cc_final: 0.5482 (tmtp) REVERT: C 286 VAL cc_start: 0.5162 (OUTLIER) cc_final: 0.4794 (t) REVERT: C 347 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 425 GLU cc_start: 0.8006 (tt0) cc_final: 0.7754 (tt0) REVERT: C 480 GLU cc_start: 0.8244 (mp0) cc_final: 0.7881 (mp0) REVERT: C 498 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5691 (tpp-160) REVERT: C 620 TYR cc_start: 0.7590 (OUTLIER) cc_final: 0.7240 (t80) REVERT: D 58 MET cc_start: -0.0841 (mmp) cc_final: -0.1998 (mtm) REVERT: D 269 VAL cc_start: 0.7776 (t) cc_final: 0.7493 (m) REVERT: D 370 GLN cc_start: 0.7819 (mp10) cc_final: 0.7450 (mp10) REVERT: E 347 GLU cc_start: 0.8499 (mt-10) cc_final: 0.7512 (tt0) REVERT: E 468 ARG cc_start: 0.8269 (mtt180) cc_final: 0.8057 (mtt180) REVERT: E 480 GLU cc_start: 0.8213 (mp0) cc_final: 0.7972 (mp0) REVERT: E 620 TYR cc_start: 0.7801 (OUTLIER) cc_final: 0.6905 (t80) REVERT: E 635 PHE cc_start: 0.8205 (m-80) cc_final: 0.7998 (m-80) outliers start: 87 outliers final: 47 residues processed: 624 average time/residue: 0.6642 time to fit residues: 467.9049 Evaluate side-chains 638 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 582 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 60 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 344 GLN A 410 ASN A 514 ASN B 360 HIS B 432 GLN B 476 GLN C 60 GLN C 169 GLN C 432 GLN D 338 GLN D 560 ASN D 611 GLN E 70 ASN E 360 HIS E 432 GLN E 560 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.153915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.134678 restraints weight = 30450.790| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.79 r_work: 0.3681 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 23438 Z= 0.257 Angle : 0.667 8.486 31896 Z= 0.361 Chirality : 0.049 0.219 3639 Planarity : 0.005 0.049 4125 Dihedral : 5.386 51.470 3142 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.11 % Allowed : 14.72 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.16), residues: 2875 helix: 1.60 (0.20), residues: 738 sheet: 0.88 (0.17), residues: 900 loop : -0.71 (0.17), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 521 TYR 0.040 0.003 TYR C 53 PHE 0.030 0.002 PHE B 561 TRP 0.024 0.002 TRP D 121 HIS 0.009 0.002 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (23438) covalent geometry : angle 0.66715 / 0.36 (31896) hydrogen bonds : bond 0.08203 / 5.49 ( 1059) hydrogen bonds : angle 4.88051 / 3.32 ( 2919) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 590 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8550 (tt) cc_final: 0.8326 (tp) REVERT: A 248 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7806 (ptp-170) REVERT: A 347 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7571 (mt-10) REVERT: A 425 GLU cc_start: 0.8136 (tt0) cc_final: 0.7891 (tt0) REVERT: A 480 GLU cc_start: 0.8356 (mp0) cc_final: 0.7775 (mp0) REVERT: A 481 GLU cc_start: 0.8328 (tt0) cc_final: 0.8089 (tt0) REVERT: A 633 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8478 (mp) REVERT: B 207 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: B 303 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8493 (mp) REVERT: B 578 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8374 (mtt-85) REVERT: C 58 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6031 (mtt) REVERT: C 235 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7979 (pt) REVERT: C 255 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.5438 (tmtp) REVERT: C 286 VAL cc_start: 0.5291 (OUTLIER) cc_final: 0.4922 (t) REVERT: C 347 GLU cc_start: 0.8600 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 425 GLU cc_start: 0.8036 (tt0) cc_final: 0.7808 (tt0) REVERT: C 480 GLU cc_start: 0.8230 (mp0) cc_final: 0.7956 (mp0) REVERT: C 498 ARG cc_start: 0.6009 (OUTLIER) cc_final: 0.5759 (tpp-160) REVERT: C 620 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7314 (t80) REVERT: D 58 MET cc_start: -0.0825 (mmp) cc_final: -0.1868 (mtm) REVERT: D 269 VAL cc_start: 0.7912 (t) cc_final: 0.7665 (m) REVERT: D 370 GLN cc_start: 0.7929 (mp10) cc_final: 0.7543 (mp10) REVERT: E 277 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7898 (mp10) REVERT: E 347 GLU cc_start: 0.8562 (mt-10) cc_final: 0.7893 (mt-10) REVERT: E 468 ARG cc_start: 0.8332 (mtt180) cc_final: 0.8122 (mtt180) REVERT: E 480 GLU cc_start: 0.8241 (mp0) cc_final: 0.8002 (mp0) REVERT: E 620 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.7064 (t80) outliers start: 103 outliers final: 62 residues processed: 632 average time/residue: 0.6664 time to fit residues: 474.9595 Evaluate side-chains 659 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 585 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 248 ARG Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 255 LYS Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 515 LEU Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 564 SER Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 52 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 202 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 222 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 196 optimal weight: 0.9990 chunk 151 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 277 GLN A 344 GLN A 405 ASN A 410 ASN A 514 ASN B 360 HIS B 432 GLN B 476 GLN C 169 GLN C 206 GLN C 432 GLN D 338 GLN D 611 GLN E 70 ASN E 432 GLN E 459 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.157038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.137663 restraints weight = 30422.146| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.81 r_work: 0.3725 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3592 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23438 Z= 0.132 Angle : 0.564 7.902 31896 Z= 0.301 Chirality : 0.044 0.186 3639 Planarity : 0.004 0.045 4125 Dihedral : 5.008 51.362 3140 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 16.56 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 2875 helix: 1.95 (0.20), residues: 729 sheet: 0.87 (0.16), residues: 927 loop : -0.58 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 521 TYR 0.025 0.002 TYR E 300 PHE 0.025 0.001 PHE C 168 TRP 0.033 0.001 TRP B 615 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (23438) covalent geometry : angle 0.56443 / 0.30 (31896) hydrogen bonds : bond 0.05907 / 3.95 ( 1059) hydrogen bonds : angle 4.49949 / 3.08 ( 2919) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 590 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 LEU cc_start: 0.8545 (tt) cc_final: 0.8328 (tp) REVERT: A 347 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7595 (tt0) REVERT: A 425 GLU cc_start: 0.8131 (tt0) cc_final: 0.7899 (tt0) REVERT: A 480 GLU cc_start: 0.8332 (mp0) cc_final: 0.7731 (mp0) REVERT: A 481 GLU cc_start: 0.8348 (tt0) cc_final: 0.8111 (tt0) REVERT: B 207 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7298 (tp30) REVERT: B 303 LEU cc_start: 0.8815 (mt) cc_final: 0.8520 (mp) REVERT: C 58 MET cc_start: 0.6393 (OUTLIER) cc_final: 0.5979 (mtt) REVERT: C 235 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7979 (pt) REVERT: C 286 VAL cc_start: 0.5229 (OUTLIER) cc_final: 0.4885 (t) REVERT: C 347 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7821 (mt-10) REVERT: C 425 GLU cc_start: 0.8004 (tt0) cc_final: 0.7770 (tt0) REVERT: C 480 GLU cc_start: 0.8238 (mp0) cc_final: 0.7952 (mp0) REVERT: C 498 ARG cc_start: 0.5956 (OUTLIER) cc_final: 0.5701 (tpp-160) REVERT: C 620 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.7194 (t80) REVERT: D 58 MET cc_start: -0.0724 (mmp) cc_final: -0.1910 (mtm) REVERT: D 86 ILE cc_start: 0.0545 (OUTLIER) cc_final: 0.0324 (pp) REVERT: D 269 VAL cc_start: 0.7851 (t) cc_final: 0.7587 (m) REVERT: D 370 GLN cc_start: 0.7884 (mp10) cc_final: 0.7509 (mp10) REVERT: E 208 LEU cc_start: 0.7967 (mt) cc_final: 0.7729 (mp) REVERT: E 245 PRO cc_start: 0.8267 (Cg_endo) cc_final: 0.8015 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7867 (mp10) REVERT: E 347 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7321 (tt0) REVERT: E 468 ARG cc_start: 0.8228 (mtt180) cc_final: 0.8005 (mtt180) REVERT: E 620 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.6854 (t80) outliers start: 77 outliers final: 46 residues processed: 623 average time/residue: 0.7178 time to fit residues: 504.6225 Evaluate side-chains 636 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 581 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 370 GLN Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 184 optimal weight: 0.0980 chunk 224 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 280 optimal weight: 1.9990 chunk 137 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN B 360 HIS B 432 GLN B 476 GLN C 169 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.156841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137496 restraints weight = 30428.784| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.81 r_work: 0.3734 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23438 Z= 0.135 Angle : 0.559 8.481 31896 Z= 0.298 Chirality : 0.043 0.181 3639 Planarity : 0.004 0.041 4125 Dihedral : 4.799 50.592 3136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.99 % Allowed : 16.84 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2875 helix: 2.00 (0.20), residues: 731 sheet: 0.97 (0.16), residues: 920 loop : -0.59 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 521 TYR 0.023 0.002 TYR E 300 PHE 0.026 0.001 PHE C 168 TRP 0.017 0.001 TRP B 615 HIS 0.004 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (23438) covalent geometry : angle 0.55857 / 0.30 (31896) hydrogen bonds : bond 0.05753 / 3.84 ( 1059) hydrogen bonds : angle 4.38697 / 3.01 ( 2919) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 586 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.6783 (mmt180) REVERT: A 347 GLU cc_start: 0.8496 (mt-10) cc_final: 0.7602 (tt0) REVERT: A 425 GLU cc_start: 0.8147 (tt0) cc_final: 0.7912 (tt0) REVERT: A 480 GLU cc_start: 0.8349 (mp0) cc_final: 0.7770 (mp0) REVERT: A 481 GLU cc_start: 0.8360 (tt0) cc_final: 0.8131 (tt0) REVERT: C 58 MET cc_start: 0.6454 (OUTLIER) cc_final: 0.6027 (mtt) REVERT: C 235 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7991 (pt) REVERT: C 286 VAL cc_start: 0.5314 (OUTLIER) cc_final: 0.4952 (t) REVERT: C 347 GLU cc_start: 0.8574 (mt-10) cc_final: 0.7864 (mt-10) REVERT: C 425 GLU cc_start: 0.7996 (tt0) cc_final: 0.7769 (tt0) REVERT: C 480 GLU cc_start: 0.8254 (mp0) cc_final: 0.7960 (mp0) REVERT: C 498 ARG cc_start: 0.5957 (OUTLIER) cc_final: 0.5692 (tpp-160) REVERT: C 620 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7183 (t80) REVERT: D 58 MET cc_start: -0.0757 (mmp) cc_final: -0.1904 (mtm) REVERT: D 370 GLN cc_start: 0.7879 (mp10) cc_final: 0.7503 (mp10) REVERT: E 208 LEU cc_start: 0.7911 (mt) cc_final: 0.7692 (mp) REVERT: E 216 THR cc_start: 0.6466 (OUTLIER) cc_final: 0.6254 (p) REVERT: E 277 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7816 (mp10) REVERT: E 347 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7844 (mt-10) REVERT: E 468 ARG cc_start: 0.8248 (mtt180) cc_final: 0.8031 (mtt180) REVERT: E 480 GLU cc_start: 0.8188 (mp0) cc_final: 0.7922 (mp0) REVERT: E 620 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.6825 (t80) outliers start: 75 outliers final: 49 residues processed: 621 average time/residue: 0.6990 time to fit residues: 490.4071 Evaluate side-chains 646 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 588 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 269 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 240 optimal weight: 2.9990 chunk 165 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 265 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN A 409 GLN A 410 ASN A 502 ASN B 360 HIS B 432 GLN B 476 GLN B 502 ASN C 169 GLN D 221 GLN D 432 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.153956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134699 restraints weight = 30454.021| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 1.82 r_work: 0.3697 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23438 Z= 0.214 Angle : 0.641 9.511 31896 Z= 0.345 Chirality : 0.047 0.202 3639 Planarity : 0.005 0.054 4125 Dihedral : 5.123 50.867 3136 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.79 % Allowed : 17.16 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2875 helix: 1.71 (0.20), residues: 738 sheet: 0.85 (0.16), residues: 922 loop : -0.71 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 521 TYR 0.035 0.002 TYR C 53 PHE 0.027 0.002 PHE B 561 TRP 0.021 0.001 TRP D 121 HIS 0.006 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (23438) covalent geometry : angle 0.64058 / 0.34 (31896) hydrogen bonds : bond 0.07419 / 4.96 ( 1059) hydrogen bonds : angle 4.68777 / 3.20 ( 2919) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 581 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8525 (mt-10) cc_final: 0.7658 (tt0) REVERT: A 425 GLU cc_start: 0.8196 (tt0) cc_final: 0.7963 (tt0) REVERT: A 480 GLU cc_start: 0.8366 (mp0) cc_final: 0.7829 (mp0) REVERT: A 481 GLU cc_start: 0.8355 (tt0) cc_final: 0.8148 (tt0) REVERT: C 58 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6350 (mtt) REVERT: C 235 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8037 (pt) REVERT: C 286 VAL cc_start: 0.5413 (OUTLIER) cc_final: 0.5046 (t) REVERT: C 347 GLU cc_start: 0.8590 (mt-10) cc_final: 0.7958 (mt-10) REVERT: C 498 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5820 (tpp-160) REVERT: C 620 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7253 (t80) REVERT: D 58 MET cc_start: -0.0772 (mmp) cc_final: -0.1866 (mtm) REVERT: D 86 ILE cc_start: 0.0363 (OUTLIER) cc_final: 0.0087 (pp) REVERT: D 370 GLN cc_start: 0.7930 (mp10) cc_final: 0.7488 (mp10) REVERT: E 245 PRO cc_start: 0.8282 (Cg_endo) cc_final: 0.8029 (Cg_exo) REVERT: E 277 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: E 347 GLU cc_start: 0.8542 (mt-10) cc_final: 0.7874 (mt-10) REVERT: E 620 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.6927 (t80) outliers start: 70 outliers final: 50 residues processed: 611 average time/residue: 0.6950 time to fit residues: 478.5450 Evaluate side-chains 628 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 570 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 272 ASN Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 270 GLU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 521 ARG Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 337 ASP Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 564 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 103 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 255 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 182 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN A 344 GLN A 405 ASN A 410 ASN A 432 GLN B 360 HIS B 432 GLN B 476 GLN C 169 GLN C 432 GLN D 560 ASN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137275 restraints weight = 30627.416| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.81 r_work: 0.3725 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23438 Z= 0.134 Angle : 0.571 8.953 31896 Z= 0.303 Chirality : 0.044 0.196 3639 Planarity : 0.004 0.042 4125 Dihedral : 4.873 50.941 3136 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.35 % Allowed : 17.92 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.16), residues: 2875 helix: 2.00 (0.20), residues: 730 sheet: 0.86 (0.16), residues: 929 loop : -0.58 (0.18), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 521 TYR 0.023 0.002 TYR E 300 PHE 0.022 0.001 PHE B 561 TRP 0.014 0.001 TRP B 615 HIS 0.004 0.001 HIS B 285 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (23438) covalent geometry : angle 0.57125 / 0.30 (31896) hydrogen bonds : bond 0.05727 / 3.83 ( 1059) hydrogen bonds : angle 4.42900 / 3.04 ( 2919) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5750 Ramachandran restraints generated. 2875 Oldfield, 0 Emsley, 2875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 576 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7662 (tt0) REVERT: A 425 GLU cc_start: 0.8136 (tt0) cc_final: 0.7905 (tt0) REVERT: A 480 GLU cc_start: 0.8355 (mp0) cc_final: 0.7780 (mp0) REVERT: A 481 GLU cc_start: 0.8368 (tt0) cc_final: 0.8142 (tt0) REVERT: C 58 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6321 (mtt) REVERT: C 235 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8006 (pt) REVERT: C 286 VAL cc_start: 0.5285 (OUTLIER) cc_final: 0.4916 (t) REVERT: C 347 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 498 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5690 (tpp-160) REVERT: C 620 TYR cc_start: 0.7598 (OUTLIER) cc_final: 0.7236 (t80) REVERT: D 58 MET cc_start: -0.0725 (mmp) cc_final: -0.1838 (mtm) REVERT: D 86 ILE cc_start: 0.0460 (OUTLIER) cc_final: 0.0163 (pp) REVERT: D 370 GLN cc_start: 0.7876 (mp10) cc_final: 0.7447 (mp10) REVERT: E 277 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: E 347 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7579 (tt0) REVERT: E 620 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6887 (t80) outliers start: 59 outliers final: 38 residues processed: 605 average time/residue: 0.7096 time to fit residues: 483.7574 Evaluate side-chains 619 residues out of total 2527 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 573 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain A residue 391 ASN Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 526 LEU Chi-restraints excluded: chain A residue 619 ILE Chi-restraints excluded: chain A residue 620 TYR Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 620 TYR Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain C residue 58 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 498 ARG Chi-restraints excluded: chain C residue 620 TYR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 620 TYR Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 281 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 337 ASP Chi-restraints excluded: chain E residue 373 CYS Chi-restraints excluded: chain E residue 498 ARG Chi-restraints excluded: chain E residue 500 SER Chi-restraints excluded: chain E residue 562 THR Chi-restraints excluded: chain E residue 606 GLN Chi-restraints excluded: chain E residue 620 TYR Chi-restraints excluded: chain E residue 622 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 36 optimal weight: 0.3980 chunk 199 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 264 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 405 ASN A 410 ASN A 502 ASN B 360 HIS B 476 GLN C 169 GLN D 611 GLN E 70 ASN E 432 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.155574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136406 restraints weight = 30531.391| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.82 r_work: 0.3719 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23438 Z= 0.158 Angle : 0.594 9.286 31896 Z= 0.317 Chirality : 0.045 0.199 3639 Planarity : 0.004 0.065 4125 Dihedral : 4.917 50.580 3136 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.27 % Allowed : 18.52 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.16), residues: 2875 helix: 1.92 (0.20), residues: 729 sheet: 0.91 (0.17), residues: 915 loop : -0.66 (0.18), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 521 TYR 0.026 0.002 TYR E 300 PHE 0.024 0.002 PHE B 561 TRP 0.014 0.001 TRP D 121 HIS 0.005 0.001 HIS B 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (23438) covalent geometry : angle 0.59401 / 0.32 (31896) hydrogen bonds : bond 0.06243 / 4.18 ( 1059) hydrogen bonds : angle 4.47908 / 3.07 ( 2919) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12712.07 seconds wall clock time: 215 minutes 50.49 seconds (12950.49 seconds total)