Starting phenix.real_space_refine on Sat Mar 7 04:03:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0c_20993/03_2026/6v0c_20993.map" } resolution = 3.46 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 24042 2.51 5 N 6522 2.21 5 O 7284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37920 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "B" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "C" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "D" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "E" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Chain: "F" Number of atoms: 6320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6320 Classifications: {'peptide': 832} Link IDs: {'PTRANS': 43, 'TRANS': 788} Time building chain proxies: 7.96, per 1000 atoms: 0.21 Number of scatterers: 37920 At special positions: 0 Unit cell: (113.97, 111.35, 235.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 7284 8.00 N 6522 7.00 C 24042 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8964 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 66 sheets defined 13.2% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 248' Processing helix chain 'A' and resid 274 through 278 removed outlier: 3.639A pdb=" N GLN A 278 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU A 389 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL A 445 " --> pdb=" O HIS A 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS A 446 " --> pdb=" O ARG A 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 446' Processing helix chain 'A' and resid 472 through 479 removed outlier: 3.617A pdb=" N ILE A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU A 567 " --> pdb=" O ARG A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 243 through 248' Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN B 278 " --> pdb=" O ALA B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 354 through 361 removed outlier: 4.055A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 389 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL B 445 " --> pdb=" O HIS B 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS B 446 " --> pdb=" O ARG B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 446' Processing helix chain 'B' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE B 477 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 478 " --> pdb=" O SER B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU B 567 " --> pdb=" O ARG B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.676A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.353A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 248' Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.249A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.198A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 389 " --> pdb=" O LEU C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 3.816A pdb=" N VAL C 445 " --> pdb=" O HIS C 441 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS C 446 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 446' Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.583A pdb=" N ALA C 504 " --> pdb=" O ASN C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 removed outlier: 3.639A pdb=" N LEU C 567 " --> pdb=" O ARG C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.627A pdb=" N GLN C 615 " --> pdb=" O ALA C 611 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 631 Processing helix chain 'C' and resid 711 through 715 removed outlier: 3.504A pdb=" N ILE C 714 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.672A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 243 through 248' Processing helix chain 'D' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN D 278 " --> pdb=" O ALA D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 354 through 361 removed outlier: 4.055A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 389 removed outlier: 4.192A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU D 389 " --> pdb=" O LEU D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL D 445 " --> pdb=" O HIS D 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS D 446 " --> pdb=" O ARG D 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 446' Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE D 477 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 478 " --> pdb=" O SER D 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU D 567 " --> pdb=" O ARG D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 243 through 248' Processing helix chain 'E' and resid 274 through 278 removed outlier: 3.641A pdb=" N GLN E 278 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 389 removed outlier: 4.191A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU E 389 " --> pdb=" O LEU E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL E 445 " --> pdb=" O HIS E 441 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LYS E 446 " --> pdb=" O ARG E 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 441 through 446' Processing helix chain 'E' and resid 472 through 479 removed outlier: 3.618A pdb=" N ILE E 477 " --> pdb=" O ALA E 473 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 478 " --> pdb=" O SER E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA E 504 " --> pdb=" O ASN E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU E 567 " --> pdb=" O ARG E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.676A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS E 617 " --> pdb=" O ALA E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 715 Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.343A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN F 248 " --> pdb=" O ALA F 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 243 through 248' Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.640A pdb=" N GLN F 278 " --> pdb=" O ALA F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 354 through 361 removed outlier: 4.056A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.192A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU F 389 " --> pdb=" O LEU F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 removed outlier: 3.863A pdb=" N VAL F 445 " --> pdb=" O HIS F 441 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LYS F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 441 through 446' Processing helix chain 'F' and resid 472 through 479 removed outlier: 3.617A pdb=" N ILE F 477 " --> pdb=" O ALA F 473 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN F 478 " --> pdb=" O SER F 474 " (cutoff:3.500A) Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.665A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 563 through 567 removed outlier: 3.715A pdb=" N LEU F 567 " --> pdb=" O ARG F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.677A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 617 " --> pdb=" O ALA F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.652A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 76 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR A 131 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE A 181 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 187 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 239 Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 281 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE A 483 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE A 412 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 495 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 460 Processing sheet with id=AA9, first strand: chain 'A' and resid 517 through 521 removed outlier: 3.780A pdb=" N VAL A 517 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS A 558 " --> pdb=" O VAL A 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL A 543 " --> pdb=" O HIS A 558 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR A 624 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE A 573 " --> pdb=" O TYR A 624 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR A 718 " --> pdb=" O VAL A 699 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 653 " --> pdb=" O ILE A 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A 678 " --> pdb=" O GLN A 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 666 " --> pdb=" O GLN A 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN A 676 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A 668 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU A 674 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET A 789 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET A 779 " --> pdb=" O MET A 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 791 " --> pdb=" O THR A 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.096A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL B 76 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR B 131 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE B 181 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY B 187 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AB8, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 281 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE B 483 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE B 412 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 495 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AC2, first strand: chain 'B' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL B 517 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS B 558 " --> pdb=" O VAL B 543 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N VAL B 543 " --> pdb=" O HIS B 558 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 533 through 535 removed outlier: 9.242A pdb=" N TYR B 624 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE B 573 " --> pdb=" O TYR B 624 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'B' and resid 695 through 699 removed outlier: 4.599A pdb=" N TYR B 718 " --> pdb=" O VAL B 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 653 " --> pdb=" O ILE B 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS B 678 " --> pdb=" O GLN B 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU B 666 " --> pdb=" O GLN B 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN B 676 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU B 668 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU B 674 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 749 through 754 removed outlier: 7.139A pdb=" N MET B 789 " --> pdb=" O MET B 779 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET B 779 " --> pdb=" O MET B 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA B 791 " --> pdb=" O THR B 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.100A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N VAL C 76 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER C 93 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 107 through 111 removed outlier: 3.741A pdb=" N TYR C 131 " --> pdb=" O VAL C 111 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.096A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AD2, first strand: chain 'C' and resid 340 through 344 removed outlier: 4.660A pdb=" N THR C 298 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR C 302 " --> pdb=" O GLU C 306 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 449 through 453 removed outlier: 6.963A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 495 " --> pdb=" O THR C 396 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AD5, first strand: chain 'C' and resid 517 through 521 removed outlier: 3.851A pdb=" N VAL C 517 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) removed outlier: 9.220A pdb=" N TYR C 624 " --> pdb=" O SER C 571 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE C 573 " --> pdb=" O TYR C 624 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 695 through 699 removed outlier: 4.495A pdb=" N TYR C 718 " --> pdb=" O VAL C 699 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 653 " --> pdb=" O ILE C 660 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS C 678 " --> pdb=" O GLN C 664 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU C 666 " --> pdb=" O GLN C 676 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN C 676 " --> pdb=" O LEU C 666 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 668 " --> pdb=" O GLU C 674 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N GLU C 674 " --> pdb=" O LEU C 668 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 749 through 754 removed outlier: 7.041A pdb=" N MET C 789 " --> pdb=" O MET C 779 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET C 779 " --> pdb=" O MET C 789 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 791 " --> pdb=" O THR C 777 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL D 76 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER D 93 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR D 131 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.153A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE D 181 " --> pdb=" O PRO D 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 187 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AE3, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.166A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL D 281 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE D 483 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE D 412 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 495 " --> pdb=" O THR D 396 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AE6, first strand: chain 'D' and resid 517 through 521 removed outlier: 3.779A pdb=" N VAL D 517 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS D 558 " --> pdb=" O VAL D 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL D 543 " --> pdb=" O HIS D 558 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR D 624 " --> pdb=" O SER D 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE D 573 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR D 718 " --> pdb=" O VAL D 699 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE D 653 " --> pdb=" O ILE D 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS D 678 " --> pdb=" O GLN D 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU D 666 " --> pdb=" O GLN D 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN D 676 " --> pdb=" O LEU D 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU D 668 " --> pdb=" O GLU D 674 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU D 674 " --> pdb=" O LEU D 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET D 789 " --> pdb=" O MET D 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET D 779 " --> pdb=" O MET D 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 791 " --> pdb=" O THR D 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.096A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL E 76 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER E 93 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR E 131 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.152A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE E 181 " --> pdb=" O PRO E 185 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY E 187 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AF5, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL E 281 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 449 through 453 removed outlier: 8.359A pdb=" N ILE E 483 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE E 412 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 495 " --> pdb=" O THR E 396 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AF8, first strand: chain 'E' and resid 517 through 521 removed outlier: 3.778A pdb=" N VAL E 517 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N HIS E 558 " --> pdb=" O VAL E 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL E 543 " --> pdb=" O HIS E 558 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR E 624 " --> pdb=" O SER E 571 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N PHE E 573 " --> pdb=" O TYR E 624 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 695 through 699 removed outlier: 4.599A pdb=" N TYR E 718 " --> pdb=" O VAL E 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 653 " --> pdb=" O ILE E 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS E 678 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU E 666 " --> pdb=" O GLN E 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN E 676 " --> pdb=" O LEU E 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU E 668 " --> pdb=" O GLU E 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU E 674 " --> pdb=" O LEU E 668 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 749 through 754 removed outlier: 7.139A pdb=" N MET E 789 " --> pdb=" O MET E 779 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N MET E 779 " --> pdb=" O MET E 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA E 791 " --> pdb=" O THR E 777 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.097A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL F 76 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER F 93 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 107 through 111 removed outlier: 3.708A pdb=" N TYR F 131 " --> pdb=" O VAL F 111 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.153A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE F 181 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY F 187 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.165A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL F 281 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 449 through 453 removed outlier: 8.360A pdb=" N ILE F 483 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE F 412 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR F 495 " --> pdb=" O THR F 396 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 458 through 460 Processing sheet with id=AG9, first strand: chain 'F' and resid 517 through 521 removed outlier: 3.779A pdb=" N VAL F 517 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS F 558 " --> pdb=" O VAL F 543 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N VAL F 543 " --> pdb=" O HIS F 558 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 533 through 535 removed outlier: 9.241A pdb=" N TYR F 624 " --> pdb=" O SER F 571 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE F 573 " --> pdb=" O TYR F 624 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 695 through 699 removed outlier: 4.600A pdb=" N TYR F 718 " --> pdb=" O VAL F 699 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE F 653 " --> pdb=" O ILE F 660 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS F 678 " --> pdb=" O GLN F 664 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU F 666 " --> pdb=" O GLN F 676 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLN F 676 " --> pdb=" O LEU F 666 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU F 668 " --> pdb=" O GLU F 674 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLU F 674 " --> pdb=" O LEU F 668 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 749 through 754 removed outlier: 7.138A pdb=" N MET F 789 " --> pdb=" O MET F 779 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N MET F 779 " --> pdb=" O MET F 789 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA F 791 " --> pdb=" O THR F 777 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) 1082 hydrogen bonds defined for protein. 2655 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: 10.39 Time building geometry restraints manager: 4.22 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: 10679 1.33 - 1.45: 5659 1.45 - 1.57: 22134 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 38616 Sorted by residual: bond pdb=" N THR C 829 " pdb=" CA THR C 829 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.14e+00 bond pdb=" N THR D 829 " pdb=" CA THR D 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.30e+00 bond pdb=" N THR F 829 " pdb=" CA THR F 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.26e+00 bond pdb=" N THR A 829 " pdb=" CA THR A 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.21e+00 bond pdb=" N THR B 829 " pdb=" CA THR B 829 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 ... (remaining 38611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 52080 4.26 - 8.53: 309 8.53 - 12.79: 9 12.79 - 17.05: 5 17.05 - 21.31: 1 Bond angle restraints: 52404 Sorted by residual: angle pdb=" CA LEU C 583 " pdb=" CB LEU C 583 " pdb=" CG LEU C 583 " ideal model delta sigma weight residual 116.30 137.61 -21.31 3.50e+00 8.16e-02 3.71e+01 angle pdb=" N VAL C 331 " pdb=" CA VAL C 331 " pdb=" CB VAL C 331 " ideal model delta sigma weight residual 112.07 104.66 7.41 1.52e+00 4.33e-01 2.38e+01 angle pdb=" N VAL B 331 " pdb=" CA VAL B 331 " pdb=" CB VAL B 331 " ideal model delta sigma weight residual 112.07 105.37 6.70 1.52e+00 4.33e-01 1.94e+01 angle pdb=" N VAL D 331 " pdb=" CA VAL D 331 " pdb=" CB VAL D 331 " ideal model delta sigma weight residual 112.07 105.37 6.70 1.52e+00 4.33e-01 1.94e+01 angle pdb=" N VAL E 331 " pdb=" CA VAL E 331 " pdb=" CB VAL E 331 " ideal model delta sigma weight residual 112.07 105.39 6.68 1.52e+00 4.33e-01 1.93e+01 ... (remaining 52399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 22016 15.32 - 30.64: 948 30.64 - 45.96: 238 45.96 - 61.28: 6 61.28 - 76.59: 48 Dihedral angle restraints: 23256 sinusoidal: 9180 harmonic: 14076 Sorted by residual: dihedral pdb=" CA ALA C 471 " pdb=" C ALA C 471 " pdb=" N SER C 472 " pdb=" CA SER C 472 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR C 846 " pdb=" C THR C 846 " pdb=" N PRO C 847 " pdb=" CA PRO C 847 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA F 471 " pdb=" C ALA F 471 " pdb=" N SER F 472 " pdb=" CA SER F 472 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 ... (remaining 23253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3729 0.045 - 0.090: 1559 0.090 - 0.135: 615 0.135 - 0.180: 137 0.180 - 0.225: 20 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CG LEU C 583 " pdb=" CB LEU C 583 " pdb=" CD1 LEU C 583 " pdb=" CD2 LEU C 583 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 622 " pdb=" CA ILE B 622 " pdb=" CG1 ILE B 622 " pdb=" CG2 ILE B 622 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB ILE E 622 " pdb=" CA ILE E 622 " pdb=" CG1 ILE E 622 " pdb=" CG2 ILE E 622 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 6057 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 328 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.75e+00 pdb=" N PRO C 329 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO C 329 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 329 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 328 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.17e+00 pdb=" N PRO E 329 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 329 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 329 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 328 " -0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO A 329 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 329 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 329 " -0.037 5.00e-02 4.00e+02 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 9787 2.80 - 3.33: 30923 3.33 - 3.85: 59320 3.85 - 4.38: 67536 4.38 - 4.90: 120220 Nonbonded interactions: 287786 Sorted by model distance: nonbonded pdb=" NH1 ARG F 536 " pdb=" OD2 ASP F 606 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG E 536 " pdb=" OD2 ASP E 606 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG B 536 " pdb=" OD2 ASP B 606 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG A 536 " pdb=" OD2 ASP A 606 " model vdw 2.280 3.120 nonbonded pdb=" NH1 ARG D 536 " pdb=" OD2 ASP D 606 " model vdw 2.280 3.120 ... (remaining 287781 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.050 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: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 36.780 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.007 0.061 38616 Z= 0.286 Angle : 0.937 21.314 52404 Z= 0.493 Chirality : 0.057 0.225 6060 Planarity : 0.007 0.074 6822 Dihedral : 10.081 76.594 14292 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -3.30 (0.09), residues: 4980 helix: -4.39 (0.09), residues: 468 sheet: -1.44 (0.11), residues: 1632 loop : -2.30 (0.09), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 536 TYR 0.017 0.003 TYR F 814 PHE 0.037 0.004 PHE C 605 TRP 0.011 0.002 TRP C 222 HIS 0.008 0.002 HIS C 558 Details of bonding type rmsd covalent geometry : bond 0.00671 (38616) covalent geometry : angle 0.93685 (52404) hydrogen bonds : bond 0.26370 ( 1082) hydrogen bonds : angle 10.05976 ( 2655) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 912 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.6655 (mtp) cc_final: 0.6411 (mtm) REVERT: A 240 LEU cc_start: 0.7503 (tt) cc_final: 0.7065 (tp) REVERT: A 456 ARG cc_start: 0.7472 (mtm110) cc_final: 0.7148 (mmm160) REVERT: A 704 SER cc_start: 0.9242 (m) cc_final: 0.9017 (t) REVERT: B 456 ARG cc_start: 0.7766 (mtm110) cc_final: 0.7479 (mmm160) REVERT: B 627 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6946 (tm-30) REVERT: B 704 SER cc_start: 0.9306 (m) cc_final: 0.8967 (t) REVERT: B 766 VAL cc_start: 0.8629 (t) cc_final: 0.8334 (t) REVERT: C 240 LEU cc_start: 0.7438 (tt) cc_final: 0.7173 (tp) REVERT: C 537 LYS cc_start: 0.8000 (mttt) cc_final: 0.7791 (mttt) REVERT: C 604 SER cc_start: 0.8062 (t) cc_final: 0.7836 (m) REVERT: C 704 SER cc_start: 0.9096 (m) cc_final: 0.8846 (t) REVERT: C 827 THR cc_start: 0.8003 (p) cc_final: 0.7738 (p) REVERT: D 240 LEU cc_start: 0.7461 (tt) cc_final: 0.7009 (tp) REVERT: D 456 ARG cc_start: 0.7429 (mtm110) cc_final: 0.7126 (mmm160) REVERT: D 704 SER cc_start: 0.9273 (m) cc_final: 0.9062 (t) REVERT: E 456 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7476 (mmm160) REVERT: E 488 LYS cc_start: 0.7596 (tttp) cc_final: 0.7368 (tttm) REVERT: E 597 ARG cc_start: 0.7568 (ttt180) cc_final: 0.7364 (ttt180) REVERT: E 704 SER cc_start: 0.9289 (m) cc_final: 0.8999 (t) REVERT: E 766 VAL cc_start: 0.8644 (t) cc_final: 0.8353 (t) REVERT: F 240 LEU cc_start: 0.7460 (tt) cc_final: 0.7158 (tp) REVERT: F 314 ASP cc_start: 0.8090 (m-30) cc_final: 0.7710 (m-30) REVERT: F 491 MET cc_start: 0.8700 (tpp) cc_final: 0.8499 (tpp) REVERT: F 704 SER cc_start: 0.9121 (m) cc_final: 0.8874 (t) outliers start: 0 outliers final: 0 residues processed: 912 average time/residue: 0.2402 time to fit residues: 345.4693 Evaluate side-chains 503 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 503 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN A 316 ASN A 345 ASN A 409 GLN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN B 158 ASN B 164 HIS B 316 ASN B 345 ASN B 409 GLN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN C 69 GLN C 174 ASN C 345 ASN C 409 GLN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN D 316 ASN D 345 ASN D 409 GLN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 GLN E 158 ASN E 164 HIS E 316 ASN E 345 ASN E 409 GLN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN E 584 ASN F 158 ASN F 345 ASN F 409 GLN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN F 591 GLN F 640 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.171966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.131597 restraints weight = 47917.253| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.61 r_work: 0.3161 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 38616 Z= 0.155 Angle : 0.650 9.609 52404 Z= 0.337 Chirality : 0.048 0.165 6060 Planarity : 0.005 0.056 6822 Dihedral : 5.434 24.845 5358 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 10.42 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.82 (0.10), residues: 4980 helix: -3.49 (0.15), residues: 516 sheet: -1.22 (0.12), residues: 1596 loop : -1.96 (0.10), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 103 TYR 0.022 0.002 TYR E 535 PHE 0.017 0.002 PHE B 364 TRP 0.012 0.001 TRP C 109 HIS 0.003 0.001 HIS B 558 Details of bonding type rmsd covalent geometry : bond 0.00357 (38616) covalent geometry : angle 0.65044 (52404) hydrogen bonds : bond 0.05011 ( 1082) hydrogen bonds : angle 7.84633 ( 2655) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 562 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8514 (p-90) cc_final: 0.8238 (p-90) REVERT: A 213 ASP cc_start: 0.8150 (t0) cc_final: 0.7933 (t0) REVERT: A 243 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6251 (mm) REVERT: A 301 MET cc_start: 0.8922 (mmm) cc_final: 0.8695 (mmm) REVERT: A 312 LYS cc_start: 0.8869 (tttt) cc_final: 0.8663 (ttpt) REVERT: A 456 ARG cc_start: 0.7829 (mtm110) cc_final: 0.7075 (mmm160) REVERT: A 570 ASN cc_start: 0.8946 (m-40) cc_final: 0.8628 (m-40) REVERT: A 606 ASP cc_start: 0.8442 (t0) cc_final: 0.8154 (t0) REVERT: B 257 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7707 (tm-30) REVERT: B 456 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7424 (mmm160) REVERT: B 570 ASN cc_start: 0.8930 (m-40) cc_final: 0.7987 (p0) REVERT: B 756 GLU cc_start: 0.8726 (pm20) cc_final: 0.8026 (pm20) REVERT: C 109 TRP cc_start: 0.8502 (p-90) cc_final: 0.8146 (p-90) REVERT: C 240 LEU cc_start: 0.7361 (tt) cc_final: 0.6995 (tp) REVERT: C 570 ASN cc_start: 0.8674 (m-40) cc_final: 0.7934 (p0) REVERT: C 704 SER cc_start: 0.9199 (m) cc_final: 0.8957 (t) REVERT: D 109 TRP cc_start: 0.8550 (p-90) cc_final: 0.8172 (p-90) REVERT: D 145 PHE cc_start: 0.7411 (m-80) cc_final: 0.6514 (m-80) REVERT: D 213 ASP cc_start: 0.8144 (t0) cc_final: 0.7940 (t0) REVERT: D 243 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6290 (mm) REVERT: D 301 MET cc_start: 0.8947 (mmm) cc_final: 0.8712 (mmm) REVERT: D 312 LYS cc_start: 0.8884 (tttt) cc_final: 0.8675 (ttpt) REVERT: D 456 ARG cc_start: 0.7832 (mtm110) cc_final: 0.7027 (mmm160) REVERT: D 500 ASN cc_start: 0.9158 (p0) cc_final: 0.8770 (p0) REVERT: D 503 LYS cc_start: 0.8630 (mtpp) cc_final: 0.8307 (mtpp) REVERT: D 570 ASN cc_start: 0.8915 (m-40) cc_final: 0.8525 (m-40) REVERT: D 606 ASP cc_start: 0.8408 (t0) cc_final: 0.8126 (t0) REVERT: D 736 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: D 784 LEU cc_start: 0.8856 (pp) cc_final: 0.8499 (pp) REVERT: E 214 LEU cc_start: 0.9052 (mt) cc_final: 0.8817 (mt) REVERT: E 456 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7387 (mmm160) REVERT: E 570 ASN cc_start: 0.8932 (m-40) cc_final: 0.7920 (p0) REVERT: E 627 GLU cc_start: 0.7875 (tp30) cc_final: 0.7294 (tp30) REVERT: E 704 SER cc_start: 0.9376 (m) cc_final: 0.9164 (p) REVERT: E 756 GLU cc_start: 0.8700 (pm20) cc_final: 0.8039 (pm20) REVERT: E 818 PHE cc_start: 0.4928 (t80) cc_final: 0.4716 (t80) REVERT: E 831 ASN cc_start: 0.8069 (t0) cc_final: 0.7647 (t0) REVERT: F 109 TRP cc_start: 0.8551 (p-90) cc_final: 0.8217 (p-90) REVERT: F 153 LYS cc_start: 0.7215 (tptt) cc_final: 0.7012 (mmtt) REVERT: F 243 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6424 (mm) outliers start: 64 outliers final: 33 residues processed: 601 average time/residue: 0.2140 time to fit residues: 209.9489 Evaluate side-chains 471 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 434 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 715 LEU Chi-restraints excluded: chain D residue 736 GLU Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 715 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 599 LEU Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 792 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 225 optimal weight: 5.9990 chunk 449 optimal weight: 0.6980 chunk 193 optimal weight: 1.9990 chunk 283 optimal weight: 0.5980 chunk 488 optimal weight: 6.9990 chunk 440 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 chunk 474 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS A 831 ASN B 158 ASN B 454 ASN B 640 HIS B 804 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN C 640 HIS ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 582 GLN D 640 HIS E 158 ASN E 388 HIS ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 HIS F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN F 584 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.159248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122606 restraints weight = 48742.534| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.07 r_work: 0.3191 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38616 Z= 0.163 Angle : 0.618 10.219 52404 Z= 0.321 Chirality : 0.047 0.204 6060 Planarity : 0.004 0.045 6822 Dihedral : 5.137 22.968 5358 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.68 % Allowed : 11.49 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.57 (0.10), residues: 4980 helix: -2.87 (0.18), residues: 516 sheet: -1.16 (0.12), residues: 1506 loop : -1.81 (0.10), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 536 TYR 0.021 0.002 TYR F 535 PHE 0.016 0.002 PHE B 108 TRP 0.008 0.001 TRP F 222 HIS 0.003 0.001 HIS C 414 Details of bonding type rmsd covalent geometry : bond 0.00384 (38616) covalent geometry : angle 0.61842 (52404) hydrogen bonds : bond 0.04240 ( 1082) hydrogen bonds : angle 7.29774 ( 2655) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 482 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8455 (p-90) cc_final: 0.8220 (p-90) REVERT: A 145 PHE cc_start: 0.7298 (m-80) cc_final: 0.6239 (m-80) REVERT: A 213 ASP cc_start: 0.8338 (t0) cc_final: 0.8091 (t0) REVERT: A 301 MET cc_start: 0.9001 (mmm) cc_final: 0.8754 (mmm) REVERT: A 456 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7280 (mmm160) REVERT: A 477 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6973 (pp) REVERT: A 570 ASN cc_start: 0.8942 (m-40) cc_final: 0.8699 (m-40) REVERT: A 606 ASP cc_start: 0.8499 (t0) cc_final: 0.8292 (t0) REVERT: B 456 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7578 (mmm160) REVERT: B 477 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6771 (pp) REVERT: B 570 ASN cc_start: 0.8848 (m-40) cc_final: 0.8074 (p0) REVERT: B 704 SER cc_start: 0.9375 (m) cc_final: 0.9012 (p) REVERT: B 733 GLU cc_start: 0.7508 (mp0) cc_final: 0.7262 (mp0) REVERT: B 756 GLU cc_start: 0.8660 (pm20) cc_final: 0.7989 (pm20) REVERT: C 109 TRP cc_start: 0.8437 (p-90) cc_final: 0.8099 (p-90) REVERT: C 243 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6427 (mm) REVERT: C 570 ASN cc_start: 0.8684 (m-40) cc_final: 0.8054 (p0) REVERT: C 704 SER cc_start: 0.9142 (m) cc_final: 0.8897 (t) REVERT: D 109 TRP cc_start: 0.8444 (p-90) cc_final: 0.8209 (p-90) REVERT: D 145 PHE cc_start: 0.7303 (m-80) cc_final: 0.6366 (m-80) REVERT: D 213 ASP cc_start: 0.8272 (t0) cc_final: 0.8039 (t0) REVERT: D 301 MET cc_start: 0.9035 (mmm) cc_final: 0.8779 (mmm) REVERT: D 456 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7257 (mmm160) REVERT: D 477 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.6992 (pp) REVERT: D 570 ASN cc_start: 0.8917 (m-40) cc_final: 0.8643 (m-40) REVERT: D 606 ASP cc_start: 0.8438 (t0) cc_final: 0.8223 (t0) REVERT: E 109 TRP cc_start: 0.8364 (p-90) cc_final: 0.8042 (p-90) REVERT: E 162 MET cc_start: 0.8622 (tpp) cc_final: 0.8330 (tpt) REVERT: E 456 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7501 (mmm160) REVERT: E 477 ILE cc_start: 0.7155 (OUTLIER) cc_final: 0.6712 (pp) REVERT: E 570 ASN cc_start: 0.8902 (m-40) cc_final: 0.8025 (p0) REVERT: E 733 GLU cc_start: 0.7514 (mp0) cc_final: 0.7239 (mp0) REVERT: E 756 GLU cc_start: 0.8689 (pm20) cc_final: 0.8098 (pm20) REVERT: E 831 ASN cc_start: 0.8319 (t0) cc_final: 0.7912 (t0) REVERT: F 109 TRP cc_start: 0.8614 (p-90) cc_final: 0.8331 (p-90) REVERT: F 416 VAL cc_start: 0.9022 (p) cc_final: 0.8807 (p) REVERT: F 477 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7164 (pp) REVERT: F 756 GLU cc_start: 0.8612 (pm20) cc_final: 0.8305 (pm20) outliers start: 110 outliers final: 64 residues processed: 561 average time/residue: 0.2043 time to fit residues: 191.1899 Evaluate side-chains 500 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 430 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 589 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain E residue 444 LEU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 665 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 243 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 257 optimal weight: 20.0000 chunk 7 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 chunk 359 optimal weight: 1.9990 chunk 466 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 500 ASN A 582 GLN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 831 ASN B 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 591 GLN ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN E 158 ASN E 164 HIS E 388 HIS ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 551 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.169933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128573 restraints weight = 47724.246| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.59 r_work: 0.3168 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 38616 Z= 0.144 Angle : 0.581 8.786 52404 Z= 0.300 Chirality : 0.046 0.174 6060 Planarity : 0.004 0.052 6822 Dihedral : 4.952 23.177 5358 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.90 % Allowed : 12.40 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.42 (0.11), residues: 4980 helix: -2.48 (0.19), residues: 522 sheet: -1.25 (0.12), residues: 1566 loop : -1.63 (0.10), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 536 TYR 0.015 0.001 TYR F 535 PHE 0.015 0.002 PHE D 253 TRP 0.012 0.001 TRP B 109 HIS 0.003 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00340 (38616) covalent geometry : angle 0.58121 (52404) hydrogen bonds : bond 0.03809 ( 1082) hydrogen bonds : angle 6.94612 ( 2655) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 474 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8466 (p-90) cc_final: 0.8132 (p-90) REVERT: A 145 PHE cc_start: 0.7256 (m-80) cc_final: 0.6048 (m-80) REVERT: A 213 ASP cc_start: 0.8430 (t0) cc_final: 0.8223 (t0) REVERT: A 243 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6172 (mm) REVERT: A 301 MET cc_start: 0.9045 (mmm) cc_final: 0.8822 (mmm) REVERT: A 456 ARG cc_start: 0.8141 (mtm110) cc_final: 0.6891 (tpt170) REVERT: A 477 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.6953 (pp) REVERT: A 570 ASN cc_start: 0.9052 (m-40) cc_final: 0.8762 (m-40) REVERT: A 606 ASP cc_start: 0.8650 (t0) cc_final: 0.8433 (t0) REVERT: B 109 TRP cc_start: 0.8395 (p-90) cc_final: 0.7956 (p-90) REVERT: B 257 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7751 (pp20) REVERT: B 456 ARG cc_start: 0.8390 (mtm110) cc_final: 0.7504 (mmm160) REVERT: B 477 ILE cc_start: 0.7183 (OUTLIER) cc_final: 0.6804 (pp) REVERT: B 570 ASN cc_start: 0.8988 (m-40) cc_final: 0.8085 (p0) REVERT: B 704 SER cc_start: 0.9359 (m) cc_final: 0.9002 (p) REVERT: B 733 GLU cc_start: 0.7713 (mp0) cc_final: 0.7441 (mp0) REVERT: B 756 GLU cc_start: 0.8834 (pm20) cc_final: 0.8105 (pm20) REVERT: C 109 TRP cc_start: 0.8609 (p-90) cc_final: 0.8216 (p-90) REVERT: C 243 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6301 (mm) REVERT: C 325 MET cc_start: 0.8343 (ttm) cc_final: 0.8143 (ttm) REVERT: C 570 ASN cc_start: 0.8756 (m-40) cc_final: 0.8070 (p0) REVERT: C 704 SER cc_start: 0.9117 (m) cc_final: 0.8850 (t) REVERT: D 109 TRP cc_start: 0.8454 (p-90) cc_final: 0.8157 (p-90) REVERT: D 145 PHE cc_start: 0.7210 (m-80) cc_final: 0.6113 (m-80) REVERT: D 243 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6218 (mm) REVERT: D 301 MET cc_start: 0.9099 (mmm) cc_final: 0.8867 (mmm) REVERT: D 334 LEU cc_start: 0.9449 (mt) cc_final: 0.9243 (mp) REVERT: D 342 GLU cc_start: 0.8881 (pm20) cc_final: 0.8596 (pt0) REVERT: D 456 ARG cc_start: 0.8176 (mtm110) cc_final: 0.6909 (tpt170) REVERT: D 477 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7004 (pp) REVERT: D 570 ASN cc_start: 0.9025 (m-40) cc_final: 0.8701 (m-40) REVERT: D 589 THR cc_start: 0.7848 (OUTLIER) cc_final: 0.7642 (t) REVERT: D 606 ASP cc_start: 0.8568 (t0) cc_final: 0.8360 (t0) REVERT: E 109 TRP cc_start: 0.8350 (p-90) cc_final: 0.7992 (p-90) REVERT: E 456 ARG cc_start: 0.8317 (mtm110) cc_final: 0.6990 (tpt90) REVERT: E 477 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6665 (pp) REVERT: E 570 ASN cc_start: 0.9022 (m-40) cc_final: 0.8062 (p0) REVERT: E 733 GLU cc_start: 0.7738 (mp0) cc_final: 0.7367 (mp0) REVERT: E 756 GLU cc_start: 0.8859 (pm20) cc_final: 0.8189 (pm20) REVERT: E 831 ASN cc_start: 0.8259 (t0) cc_final: 0.7831 (t0) REVERT: F 109 TRP cc_start: 0.8689 (p-90) cc_final: 0.8338 (p-90) REVERT: F 243 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.6335 (mm) REVERT: F 416 VAL cc_start: 0.9019 (p) cc_final: 0.8806 (p) REVERT: F 477 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7198 (pp) REVERT: F 756 GLU cc_start: 0.8655 (pm20) cc_final: 0.8294 (pm20) outliers start: 119 outliers final: 59 residues processed: 556 average time/residue: 0.1984 time to fit residues: 186.1879 Evaluate side-chains 491 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 422 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 797 ARG Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 247 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 482 optimal weight: 0.1980 chunk 350 optimal weight: 20.0000 chunk 342 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 chunk 169 optimal weight: 30.0000 chunk 373 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 164 HIS B 720 ASN C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN E 158 ASN ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.129566 restraints weight = 47568.208| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.39 r_work: 0.3145 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 38616 Z= 0.239 Angle : 0.658 12.089 52404 Z= 0.338 Chirality : 0.049 0.178 6060 Planarity : 0.004 0.047 6822 Dihedral : 5.151 26.531 5358 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.27 % Allowed : 13.06 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.11), residues: 4980 helix: -2.18 (0.21), residues: 522 sheet: -1.34 (0.12), residues: 1614 loop : -1.59 (0.11), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 536 TYR 0.018 0.002 TYR D 131 PHE 0.018 0.002 PHE A 451 TRP 0.009 0.001 TRP C 222 HIS 0.012 0.001 HIS D 441 Details of bonding type rmsd covalent geometry : bond 0.00579 (38616) covalent geometry : angle 0.65791 (52404) hydrogen bonds : bond 0.04169 ( 1082) hydrogen bonds : angle 6.99942 ( 2655) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 447 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8392 (p-90) cc_final: 0.8088 (p-90) REVERT: A 456 ARG cc_start: 0.7949 (mtm110) cc_final: 0.6864 (tpt90) REVERT: A 477 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.6995 (pp) REVERT: A 570 ASN cc_start: 0.8890 (m-40) cc_final: 0.8643 (m-40) REVERT: A 779 MET cc_start: 0.8115 (mtm) cc_final: 0.7820 (mtm) REVERT: B 109 TRP cc_start: 0.8465 (p-90) cc_final: 0.7974 (p-90) REVERT: B 456 ARG cc_start: 0.8097 (mtm110) cc_final: 0.7548 (mmm160) REVERT: B 477 ILE cc_start: 0.7015 (OUTLIER) cc_final: 0.6688 (pp) REVERT: B 505 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8419 (mt) REVERT: B 570 ASN cc_start: 0.8801 (m-40) cc_final: 0.8021 (p0) REVERT: B 704 SER cc_start: 0.9372 (m) cc_final: 0.8996 (p) REVERT: B 733 GLU cc_start: 0.7752 (mp0) cc_final: 0.7540 (mp0) REVERT: C 109 TRP cc_start: 0.8575 (p-90) cc_final: 0.8211 (p-90) REVERT: C 243 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6223 (mm) REVERT: C 476 TRP cc_start: 0.7027 (t60) cc_final: 0.6809 (t60) REVERT: C 570 ASN cc_start: 0.8789 (m-40) cc_final: 0.8056 (p0) REVERT: C 704 SER cc_start: 0.9126 (m) cc_final: 0.8870 (t) REVERT: C 733 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: C 756 GLU cc_start: 0.8585 (pm20) cc_final: 0.8275 (pm20) REVERT: C 867 GLU cc_start: 0.8210 (mp0) cc_final: 0.7949 (pm20) REVERT: D 109 TRP cc_start: 0.8493 (p-90) cc_final: 0.8175 (p-90) REVERT: D 145 PHE cc_start: 0.7145 (m-80) cc_final: 0.6136 (m-80) REVERT: D 309 GLN cc_start: 0.8525 (tp-100) cc_final: 0.8312 (tp40) REVERT: D 456 ARG cc_start: 0.7944 (mtm110) cc_final: 0.7065 (tpt170) REVERT: D 477 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.6981 (pp) REVERT: D 570 ASN cc_start: 0.8861 (m-40) cc_final: 0.8578 (m-40) REVERT: E 109 TRP cc_start: 0.8430 (p-90) cc_final: 0.8062 (p-90) REVERT: E 237 LYS cc_start: 0.6978 (mtmt) cc_final: 0.6696 (mmtp) REVERT: E 456 ARG cc_start: 0.8059 (mtm110) cc_final: 0.7468 (mmm160) REVERT: E 477 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6670 (pp) REVERT: E 503 LYS cc_start: 0.8594 (mttt) cc_final: 0.8374 (mtpp) REVERT: E 505 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8472 (mt) REVERT: E 570 ASN cc_start: 0.8827 (m-40) cc_final: 0.7979 (p0) REVERT: E 733 GLU cc_start: 0.7711 (mp0) cc_final: 0.7501 (mp0) REVERT: F 109 TRP cc_start: 0.8585 (p-90) cc_final: 0.8233 (p-90) REVERT: F 477 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7184 (pp) REVERT: F 672 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7051 (mtp85) REVERT: F 733 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: F 756 GLU cc_start: 0.8557 (pm20) cc_final: 0.8181 (pm20) outliers start: 134 outliers final: 78 residues processed: 546 average time/residue: 0.1959 time to fit residues: 181.0070 Evaluate side-chains 489 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 400 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 715 LEU Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 715 LEU Chi-restraints excluded: chain C residue 733 GLU Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 715 LEU Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 672 ARG Chi-restraints excluded: chain F residue 715 LEU Chi-restraints excluded: chain F residue 733 GLU Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 208 optimal weight: 4.9990 chunk 447 optimal weight: 1.9990 chunk 326 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 431 optimal weight: 0.0970 chunk 253 optimal weight: 9.9990 chunk 355 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN E 158 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.170175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.129472 restraints weight = 48443.200| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.72 r_work: 0.3126 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 38616 Z= 0.151 Angle : 0.592 9.844 52404 Z= 0.304 Chirality : 0.046 0.160 6060 Planarity : 0.004 0.052 6822 Dihedral : 4.961 22.538 5358 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.88 % Allowed : 14.18 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.34 (0.11), residues: 4980 helix: -2.00 (0.21), residues: 558 sheet: -1.31 (0.12), residues: 1596 loop : -1.57 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 536 TYR 0.012 0.001 TYR D 718 PHE 0.016 0.002 PHE D 253 TRP 0.009 0.001 TRP F 222 HIS 0.006 0.001 HIS E 441 Details of bonding type rmsd covalent geometry : bond 0.00360 (38616) covalent geometry : angle 0.59187 (52404) hydrogen bonds : bond 0.03734 ( 1082) hydrogen bonds : angle 6.71677 ( 2655) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 431 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8487 (p-90) cc_final: 0.8195 (p-90) REVERT: A 145 PHE cc_start: 0.7230 (m-80) cc_final: 0.6168 (m-80) REVERT: A 243 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6112 (mm) REVERT: A 456 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7100 (tpt170) REVERT: A 477 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6889 (pp) REVERT: A 570 ASN cc_start: 0.8986 (m-40) cc_final: 0.8638 (m-40) REVERT: A 606 ASP cc_start: 0.8591 (t0) cc_final: 0.8338 (t0) REVERT: A 779 MET cc_start: 0.8274 (mtm) cc_final: 0.8004 (mtm) REVERT: A 789 MET cc_start: 0.8685 (mtm) cc_final: 0.8223 (mmm) REVERT: A 867 GLU cc_start: 0.8275 (mp0) cc_final: 0.8055 (pm20) REVERT: B 109 TRP cc_start: 0.8422 (p-90) cc_final: 0.7945 (p-90) REVERT: B 456 ARG cc_start: 0.8072 (mtm110) cc_final: 0.7449 (mmm160) REVERT: B 477 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6455 (pp) REVERT: B 505 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 570 ASN cc_start: 0.8875 (m-40) cc_final: 0.7994 (p0) REVERT: B 704 SER cc_start: 0.9346 (m) cc_final: 0.8950 (p) REVERT: B 756 GLU cc_start: 0.8887 (pm20) cc_final: 0.8069 (pm20) REVERT: C 109 TRP cc_start: 0.8577 (p-90) cc_final: 0.8246 (p-90) REVERT: C 135 MET cc_start: 0.7058 (mtt) cc_final: 0.6800 (mtt) REVERT: C 243 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6205 (mm) REVERT: C 570 ASN cc_start: 0.8796 (m-40) cc_final: 0.7913 (p0) REVERT: C 704 SER cc_start: 0.9053 (m) cc_final: 0.8753 (t) REVERT: C 756 GLU cc_start: 0.8596 (pm20) cc_final: 0.8208 (pm20) REVERT: C 867 GLU cc_start: 0.8364 (mp0) cc_final: 0.8130 (pm20) REVERT: D 109 TRP cc_start: 0.8586 (p-90) cc_final: 0.8252 (p-90) REVERT: D 145 PHE cc_start: 0.7201 (m-80) cc_final: 0.6266 (m-80) REVERT: D 243 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6193 (mm) REVERT: D 456 ARG cc_start: 0.7950 (mtm110) cc_final: 0.7030 (tpt170) REVERT: D 477 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6843 (pp) REVERT: D 570 ASN cc_start: 0.8930 (m-40) cc_final: 0.8556 (m-40) REVERT: D 606 ASP cc_start: 0.8561 (t0) cc_final: 0.8333 (t0) REVERT: E 109 TRP cc_start: 0.8448 (p-90) cc_final: 0.8188 (p-90) REVERT: E 237 LYS cc_start: 0.6933 (mtmt) cc_final: 0.6627 (mmtp) REVERT: E 456 ARG cc_start: 0.8017 (mtm110) cc_final: 0.7398 (mmm160) REVERT: E 477 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6554 (pp) REVERT: E 503 LYS cc_start: 0.8547 (mttt) cc_final: 0.8325 (mtpp) REVERT: E 505 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8483 (mt) REVERT: E 535 TYR cc_start: 0.7225 (t80) cc_final: 0.6487 (t80) REVERT: E 570 ASN cc_start: 0.8932 (m-40) cc_final: 0.7943 (p0) REVERT: E 659 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8414 (m-30) REVERT: E 756 GLU cc_start: 0.8867 (pm20) cc_final: 0.8001 (pm20) REVERT: F 109 TRP cc_start: 0.8558 (p-90) cc_final: 0.8219 (p-90) REVERT: F 135 MET cc_start: 0.7059 (mtt) cc_final: 0.6798 (mtt) REVERT: F 243 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6164 (mm) REVERT: F 477 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7131 (pp) REVERT: F 756 GLU cc_start: 0.8642 (pm20) cc_final: 0.8248 (pm20) outliers start: 118 outliers final: 76 residues processed: 512 average time/residue: 0.1966 time to fit residues: 171.6268 Evaluate side-chains 490 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 402 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 651 MET Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 752 VAL Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 54 MET Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 660 ILE Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 63 optimal weight: 2.9990 chunk 276 optimal weight: 0.5980 chunk 454 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 295 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 337 optimal weight: 30.0000 chunk 242 optimal weight: 4.9990 chunk 300 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 327 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 551 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.170723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131144 restraints weight = 47401.191| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.70 r_work: 0.3155 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 38616 Z= 0.119 Angle : 0.568 9.237 52404 Z= 0.291 Chirality : 0.046 0.173 6060 Planarity : 0.004 0.046 6822 Dihedral : 4.766 23.080 5358 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.61 % Allowed : 14.93 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.14 (0.11), residues: 4980 helix: -1.91 (0.21), residues: 558 sheet: -1.07 (0.13), residues: 1500 loop : -1.51 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 103 TYR 0.021 0.001 TYR D 131 PHE 0.015 0.001 PHE D 253 TRP 0.007 0.001 TRP F 222 HIS 0.008 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00280 (38616) covalent geometry : angle 0.56812 (52404) hydrogen bonds : bond 0.03470 ( 1082) hydrogen bonds : angle 6.50245 ( 2655) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 451 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8461 (p-90) cc_final: 0.8157 (p-90) REVERT: A 145 PHE cc_start: 0.7199 (m-80) cc_final: 0.6198 (m-80) REVERT: A 243 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6102 (mm) REVERT: A 456 ARG cc_start: 0.7971 (mtm110) cc_final: 0.7128 (tpt90) REVERT: A 475 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6466 (mt-10) REVERT: A 477 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.6838 (pp) REVERT: A 570 ASN cc_start: 0.8968 (m-40) cc_final: 0.8622 (m-40) REVERT: A 606 ASP cc_start: 0.8498 (t0) cc_final: 0.8197 (t0) REVERT: A 779 MET cc_start: 0.8242 (mtm) cc_final: 0.7981 (mtm) REVERT: A 789 MET cc_start: 0.8707 (mtm) cc_final: 0.8253 (mmm) REVERT: B 109 TRP cc_start: 0.8498 (p-90) cc_final: 0.8063 (p-90) REVERT: B 239 LYS cc_start: 0.6514 (mttt) cc_final: 0.6130 (mtpt) REVERT: B 296 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8659 (t0) REVERT: B 456 ARG cc_start: 0.8034 (mtm110) cc_final: 0.7493 (mmm160) REVERT: B 477 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6300 (pp) REVERT: B 505 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 535 TYR cc_start: 0.7188 (t80) cc_final: 0.6388 (t80) REVERT: B 570 ASN cc_start: 0.8831 (m-40) cc_final: 0.7965 (p0) REVERT: B 704 SER cc_start: 0.9354 (m) cc_final: 0.9003 (p) REVERT: B 733 GLU cc_start: 0.7842 (mp0) cc_final: 0.7473 (mp0) REVERT: B 756 GLU cc_start: 0.8919 (pm20) cc_final: 0.8101 (pm20) REVERT: C 109 TRP cc_start: 0.8550 (p-90) cc_final: 0.8181 (p-90) REVERT: C 243 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6244 (mm) REVERT: C 336 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8401 (mtp85) REVERT: C 570 ASN cc_start: 0.8796 (m-40) cc_final: 0.7936 (p0) REVERT: C 756 GLU cc_start: 0.8618 (pm20) cc_final: 0.8181 (pm20) REVERT: D 109 TRP cc_start: 0.8553 (p-90) cc_final: 0.8241 (p-90) REVERT: D 145 PHE cc_start: 0.7309 (m-80) cc_final: 0.6400 (m-80) REVERT: D 243 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6183 (mm) REVERT: D 456 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7041 (tpt170) REVERT: D 477 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6823 (pp) REVERT: D 570 ASN cc_start: 0.8924 (m-40) cc_final: 0.8572 (m-40) REVERT: D 606 ASP cc_start: 0.8527 (t0) cc_final: 0.8309 (t0) REVERT: E 109 TRP cc_start: 0.8375 (p-90) cc_final: 0.8155 (p-90) REVERT: E 162 MET cc_start: 0.8317 (tpt) cc_final: 0.7985 (tpt) REVERT: E 237 LYS cc_start: 0.7062 (mtmt) cc_final: 0.6743 (mmtp) REVERT: E 240 LEU cc_start: 0.7502 (tt) cc_final: 0.7202 (tp) REVERT: E 296 ASP cc_start: 0.8864 (OUTLIER) cc_final: 0.8608 (t0) REVERT: E 456 ARG cc_start: 0.7994 (mtm110) cc_final: 0.7429 (mmm160) REVERT: E 477 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6415 (pp) REVERT: E 505 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8408 (mt) REVERT: E 535 TYR cc_start: 0.7283 (t80) cc_final: 0.6728 (t80) REVERT: E 570 ASN cc_start: 0.8871 (m-40) cc_final: 0.7946 (p0) REVERT: E 733 GLU cc_start: 0.7851 (mp0) cc_final: 0.7442 (mp0) REVERT: F 109 TRP cc_start: 0.8522 (p-90) cc_final: 0.8163 (p-90) REVERT: F 243 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6159 (mm) REVERT: F 477 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7147 (pp) REVERT: F 756 GLU cc_start: 0.8631 (pm20) cc_final: 0.8264 (pm20) outliers start: 107 outliers final: 69 residues processed: 525 average time/residue: 0.1953 time to fit residues: 175.9115 Evaluate side-chains 508 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 425 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain C residue 807 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 376 GLU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 807 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 249 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 375 optimal weight: 2.9990 chunk 283 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 466 optimal weight: 2.9990 chunk 486 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 309 GLN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 551 ASN ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN E 309 GLN ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 ASN F 804 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.166907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.126103 restraints weight = 48636.924| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.81 r_work: 0.3076 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 38616 Z= 0.265 Angle : 0.685 11.946 52404 Z= 0.349 Chirality : 0.049 0.214 6060 Planarity : 0.004 0.045 6822 Dihedral : 5.116 27.484 5358 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.88 % Allowed : 15.35 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.12 (0.11), residues: 4980 helix: -1.78 (0.23), residues: 486 sheet: -1.31 (0.12), residues: 1596 loop : -1.36 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 456 TYR 0.020 0.002 TYR C 535 PHE 0.021 0.002 PHE C 451 TRP 0.010 0.002 TRP C 222 HIS 0.008 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00649 (38616) covalent geometry : angle 0.68459 (52404) hydrogen bonds : bond 0.04162 ( 1082) hydrogen bonds : angle 6.81968 ( 2655) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 413 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8468 (p-90) cc_final: 0.8168 (p-90) REVERT: A 206 LEU cc_start: 0.9015 (tp) cc_final: 0.8746 (mp) REVERT: A 243 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6122 (mm) REVERT: A 456 ARG cc_start: 0.8014 (mtm110) cc_final: 0.7020 (tpt90) REVERT: A 475 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6519 (mt-10) REVERT: A 477 ILE cc_start: 0.7430 (OUTLIER) cc_final: 0.6915 (pp) REVERT: A 570 ASN cc_start: 0.8998 (m-40) cc_final: 0.8649 (m-40) REVERT: A 606 ASP cc_start: 0.8570 (t0) cc_final: 0.8231 (t0) REVERT: B 109 TRP cc_start: 0.8370 (p-90) cc_final: 0.8035 (p-90) REVERT: B 240 LEU cc_start: 0.7416 (tt) cc_final: 0.7135 (tp) REVERT: B 296 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8780 (t70) REVERT: B 456 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7471 (mmm160) REVERT: B 477 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6695 (pp) REVERT: B 505 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8428 (mt) REVERT: B 535 TYR cc_start: 0.7240 (t80) cc_final: 0.6437 (t80) REVERT: B 570 ASN cc_start: 0.8873 (m-40) cc_final: 0.7994 (p0) REVERT: B 704 SER cc_start: 0.9444 (m) cc_final: 0.9008 (p) REVERT: C 109 TRP cc_start: 0.8636 (p-90) cc_final: 0.8239 (p-90) REVERT: C 243 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6220 (mm) REVERT: C 456 ARG cc_start: 0.6541 (mmm160) cc_final: 0.6066 (tpt170) REVERT: C 570 ASN cc_start: 0.8805 (m-40) cc_final: 0.7966 (p0) REVERT: C 756 GLU cc_start: 0.8542 (pm20) cc_final: 0.8127 (pm20) REVERT: D 109 TRP cc_start: 0.8570 (p-90) cc_final: 0.8253 (p-90) REVERT: D 145 PHE cc_start: 0.7312 (m-80) cc_final: 0.6498 (m-80) REVERT: D 206 LEU cc_start: 0.9066 (tp) cc_final: 0.8851 (mt) REVERT: D 456 ARG cc_start: 0.8011 (mtm110) cc_final: 0.6992 (tpt170) REVERT: D 477 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.6920 (pp) REVERT: D 570 ASN cc_start: 0.8982 (m-40) cc_final: 0.8625 (m-40) REVERT: D 606 ASP cc_start: 0.8568 (t0) cc_final: 0.8249 (t0) REVERT: E 109 TRP cc_start: 0.8425 (p-90) cc_final: 0.8205 (p-90) REVERT: E 162 MET cc_start: 0.8526 (tpt) cc_final: 0.8222 (tpt) REVERT: E 296 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8767 (t0) REVERT: E 456 ARG cc_start: 0.8027 (mtm110) cc_final: 0.7433 (mmm160) REVERT: E 477 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6622 (pp) REVERT: E 535 TYR cc_start: 0.7372 (t80) cc_final: 0.6731 (t80) REVERT: E 570 ASN cc_start: 0.8927 (m-40) cc_final: 0.7954 (p0) REVERT: F 109 TRP cc_start: 0.8631 (p-90) cc_final: 0.8266 (p-90) REVERT: F 243 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6168 (mm) REVERT: F 477 ILE cc_start: 0.7503 (OUTLIER) cc_final: 0.7178 (pp) REVERT: F 551 ASN cc_start: 0.7055 (m-40) cc_final: 0.5846 (p0) REVERT: F 756 GLU cc_start: 0.8674 (pm20) cc_final: 0.8297 (pm20) outliers start: 118 outliers final: 73 residues processed: 496 average time/residue: 0.1954 time to fit residues: 164.5932 Evaluate side-chains 473 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 389 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 742 SER Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 742 SER Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 810 LEU Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 742 SER Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 665 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 792 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 247 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 429 optimal weight: 0.0770 chunk 228 optimal weight: 2.9990 chunk 445 optimal weight: 0.9980 chunk 411 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.171145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.130967 restraints weight = 48241.087| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.80 r_work: 0.3160 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38616 Z= 0.122 Angle : 0.598 10.220 52404 Z= 0.303 Chirality : 0.046 0.172 6060 Planarity : 0.004 0.054 6822 Dihedral : 4.823 23.007 5358 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.29 % Allowed : 16.35 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.11), residues: 4980 helix: -1.83 (0.22), residues: 534 sheet: -1.11 (0.13), residues: 1494 loop : -1.36 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 103 TYR 0.021 0.001 TYR D 131 PHE 0.016 0.001 PHE D 253 TRP 0.009 0.001 TRP A 809 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00285 (38616) covalent geometry : angle 0.59791 (52404) hydrogen bonds : bond 0.03490 ( 1082) hydrogen bonds : angle 6.50697 ( 2655) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 428 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8419 (p-90) cc_final: 0.8101 (p-90) REVERT: A 145 PHE cc_start: 0.7161 (m-80) cc_final: 0.6166 (m-80) REVERT: A 162 MET cc_start: 0.8665 (tpt) cc_final: 0.8230 (tpp) REVERT: A 206 LEU cc_start: 0.8933 (tp) cc_final: 0.8666 (mp) REVERT: A 243 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6086 (mm) REVERT: A 456 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7097 (tpt170) REVERT: A 475 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6512 (mt-10) REVERT: A 477 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.6811 (pp) REVERT: A 570 ASN cc_start: 0.8896 (m-40) cc_final: 0.8570 (m-40) REVERT: A 606 ASP cc_start: 0.8464 (t0) cc_final: 0.8198 (t0) REVERT: A 789 MET cc_start: 0.8715 (mtm) cc_final: 0.8232 (mmm) REVERT: B 109 TRP cc_start: 0.8337 (p-90) cc_final: 0.8014 (p-90) REVERT: B 456 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7472 (mmm160) REVERT: B 477 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6312 (pp) REVERT: B 505 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8414 (mt) REVERT: B 535 TYR cc_start: 0.7293 (t80) cc_final: 0.6498 (t80) REVERT: B 570 ASN cc_start: 0.8817 (m-40) cc_final: 0.7945 (p0) REVERT: B 659 ASP cc_start: 0.8549 (t0) cc_final: 0.8331 (m-30) REVERT: B 704 SER cc_start: 0.9433 (m) cc_final: 0.9030 (p) REVERT: C 109 TRP cc_start: 0.8590 (p-90) cc_final: 0.8175 (p-90) REVERT: C 243 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6162 (mm) REVERT: C 570 ASN cc_start: 0.8779 (m-40) cc_final: 0.7908 (p0) REVERT: C 756 GLU cc_start: 0.8610 (pm20) cc_final: 0.8177 (pm20) REVERT: C 779 MET cc_start: 0.8172 (mtt) cc_final: 0.7735 (mtt) REVERT: D 109 TRP cc_start: 0.8536 (p-90) cc_final: 0.8214 (p-90) REVERT: D 145 PHE cc_start: 0.7299 (m-80) cc_final: 0.6476 (m-80) REVERT: D 243 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6113 (mm) REVERT: D 456 ARG cc_start: 0.7949 (mtm110) cc_final: 0.7005 (tpt170) REVERT: D 477 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6756 (pp) REVERT: D 570 ASN cc_start: 0.8921 (m-40) cc_final: 0.8569 (m-40) REVERT: D 606 ASP cc_start: 0.8506 (t0) cc_final: 0.8171 (t0) REVERT: E 109 TRP cc_start: 0.8404 (p-90) cc_final: 0.8181 (p-90) REVERT: E 237 LYS cc_start: 0.7039 (mtmt) cc_final: 0.6826 (mmtp) REVERT: E 456 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7378 (mmm160) REVERT: E 477 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6370 (pp) REVERT: E 505 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8448 (mt) REVERT: E 535 TYR cc_start: 0.7252 (t80) cc_final: 0.6699 (t80) REVERT: E 570 ASN cc_start: 0.8892 (m-40) cc_final: 0.7908 (p0) REVERT: E 659 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: E 744 TYR cc_start: 0.8850 (m-10) cc_final: 0.8465 (m-10) REVERT: F 109 TRP cc_start: 0.8550 (p-90) cc_final: 0.8184 (p-90) REVERT: F 243 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6115 (mm) REVERT: F 477 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7093 (pp) REVERT: F 551 ASN cc_start: 0.7051 (m-40) cc_final: 0.5848 (p0) REVERT: F 756 GLU cc_start: 0.8559 (pm20) cc_final: 0.8027 (pm20) REVERT: F 860 LEU cc_start: 0.8934 (mt) cc_final: 0.8672 (mt) outliers start: 94 outliers final: 68 residues processed: 491 average time/residue: 0.1952 time to fit residues: 163.6391 Evaluate side-chains 489 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 409 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 441 HIS Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 659 ASP Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 158 ASN Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 783 THR Chi-restraints excluded: chain F residue 792 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 37 optimal weight: 0.5980 chunk 457 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 254 optimal weight: 10.0000 chunk 402 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 399 optimal weight: 0.7980 chunk 148 optimal weight: 1.9990 chunk 180 optimal weight: 0.0570 chunk 274 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 584 ASN ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.121454 restraints weight = 48472.797| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.47 r_work: 0.3147 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 38616 Z= 0.131 Angle : 0.603 10.815 52404 Z= 0.304 Chirality : 0.046 0.174 6060 Planarity : 0.004 0.046 6822 Dihedral : 4.750 23.894 5358 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.10 % Allowed : 16.59 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.97 (0.11), residues: 4980 helix: -1.77 (0.22), residues: 534 sheet: -1.06 (0.13), residues: 1494 loop : -1.33 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 456 TYR 0.017 0.001 TYR E 744 PHE 0.015 0.002 PHE D 253 TRP 0.009 0.001 TRP B 109 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00312 (38616) covalent geometry : angle 0.60269 (52404) hydrogen bonds : bond 0.03497 ( 1082) hydrogen bonds : angle 6.43236 ( 2655) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9960 Ramachandran restraints generated. 4980 Oldfield, 0 Emsley, 4980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 416 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 109 TRP cc_start: 0.8399 (p-90) cc_final: 0.8094 (p-90) REVERT: A 145 PHE cc_start: 0.7162 (m-80) cc_final: 0.6149 (m-80) REVERT: A 162 MET cc_start: 0.8674 (tpt) cc_final: 0.8356 (tpt) REVERT: A 206 LEU cc_start: 0.8957 (tp) cc_final: 0.8588 (mp) REVERT: A 243 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 456 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7139 (tpt170) REVERT: A 475 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6424 (mt-10) REVERT: A 477 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6807 (pp) REVERT: A 570 ASN cc_start: 0.8970 (m-40) cc_final: 0.8659 (m-40) REVERT: A 606 ASP cc_start: 0.8442 (t0) cc_final: 0.8181 (t0) REVERT: A 789 MET cc_start: 0.8723 (mtm) cc_final: 0.8274 (mmm) REVERT: B 109 TRP cc_start: 0.8265 (p-90) cc_final: 0.7998 (p-90) REVERT: B 239 LYS cc_start: 0.6327 (mttt) cc_final: 0.5792 (mtpp) REVERT: B 456 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7486 (mmm160) REVERT: B 477 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6355 (pp) REVERT: B 505 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8354 (mt) REVERT: B 535 TYR cc_start: 0.7321 (t80) cc_final: 0.6500 (t80) REVERT: B 570 ASN cc_start: 0.8846 (m-40) cc_final: 0.7989 (p0) REVERT: B 659 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8324 (m-30) REVERT: B 704 SER cc_start: 0.9437 (m) cc_final: 0.9045 (p) REVERT: C 109 TRP cc_start: 0.8551 (p-90) cc_final: 0.8131 (p-90) REVERT: C 243 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6117 (mm) REVERT: C 570 ASN cc_start: 0.8812 (m-40) cc_final: 0.7938 (p0) REVERT: C 756 GLU cc_start: 0.8669 (pm20) cc_final: 0.8204 (pm20) REVERT: D 109 TRP cc_start: 0.8506 (p-90) cc_final: 0.8196 (p-90) REVERT: D 145 PHE cc_start: 0.7311 (m-80) cc_final: 0.6490 (m-80) REVERT: D 243 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6122 (mm) REVERT: D 456 ARG cc_start: 0.7946 (mtm110) cc_final: 0.7031 (tpt170) REVERT: D 477 ILE cc_start: 0.7315 (OUTLIER) cc_final: 0.6769 (pp) REVERT: D 570 ASN cc_start: 0.8947 (m-40) cc_final: 0.8637 (m-40) REVERT: D 606 ASP cc_start: 0.8471 (t0) cc_final: 0.8198 (t0) REVERT: E 109 TRP cc_start: 0.8365 (p-90) cc_final: 0.8150 (p-90) REVERT: E 162 MET cc_start: 0.8473 (tpt) cc_final: 0.8189 (tpt) REVERT: E 237 LYS cc_start: 0.7073 (mtmt) cc_final: 0.6818 (mmtp) REVERT: E 240 LEU cc_start: 0.7466 (tt) cc_final: 0.7175 (tp) REVERT: E 258 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: E 456 ARG cc_start: 0.7987 (mtm110) cc_final: 0.6955 (tpt90) REVERT: E 477 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6427 (pp) REVERT: E 505 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8378 (mt) REVERT: E 535 TYR cc_start: 0.7275 (t80) cc_final: 0.6668 (t80) REVERT: E 570 ASN cc_start: 0.8932 (m-40) cc_final: 0.7928 (p0) REVERT: E 744 TYR cc_start: 0.8880 (m-10) cc_final: 0.8278 (m-10) REVERT: E 818 PHE cc_start: 0.5374 (t80) cc_final: 0.5133 (t80) REVERT: F 109 TRP cc_start: 0.8513 (p-90) cc_final: 0.8155 (p-90) REVERT: F 243 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6077 (mm) REVERT: F 477 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.7124 (pp) REVERT: F 551 ASN cc_start: 0.7029 (m-40) cc_final: 0.5869 (p0) REVERT: F 756 GLU cc_start: 0.8601 (pm20) cc_final: 0.8061 (pm20) outliers start: 86 outliers final: 70 residues processed: 475 average time/residue: 0.1970 time to fit residues: 159.6052 Evaluate side-chains 485 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 402 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 589 THR Chi-restraints excluded: chain A residue 699 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 792 MET Chi-restraints excluded: chain A residue 846 THR Chi-restraints excluded: chain B residue 108 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 659 ASP Chi-restraints excluded: chain B residue 660 ILE Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 792 MET Chi-restraints excluded: chain B residue 807 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 441 HIS Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 501 LEU Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 745 LEU Chi-restraints excluded: chain C residue 783 THR Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 441 HIS Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 540 VAL Chi-restraints excluded: chain D residue 589 THR Chi-restraints excluded: chain D residue 699 VAL Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 MET Chi-restraints excluded: chain D residue 846 THR Chi-restraints excluded: chain E residue 108 PHE Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 428 SER Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 477 ILE Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 660 ILE Chi-restraints excluded: chain E residue 740 THR Chi-restraints excluded: chain E residue 767 LEU Chi-restraints excluded: chain E residue 783 THR Chi-restraints excluded: chain E residue 792 MET Chi-restraints excluded: chain E residue 807 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 296 ASP Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 540 VAL Chi-restraints excluded: chain F residue 590 VAL Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 714 ILE Chi-restraints excluded: chain F residue 792 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 196 optimal weight: 0.6980 chunk 251 optimal weight: 0.9980 chunk 450 optimal weight: 2.9990 chunk 326 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 391 optimal weight: 5.9990 chunk 408 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 406 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.159695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.120039 restraints weight = 49094.708| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.38 r_work: 0.3120 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 38616 Z= 0.213 Angle : 0.653 10.832 52404 Z= 0.331 Chirality : 0.048 0.181 6060 Planarity : 0.004 0.048 6822 Dihedral : 4.946 23.907 5358 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.39 % Allowed : 16.28 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.03 (0.11), residues: 4980 helix: -1.67 (0.23), residues: 522 sheet: -1.20 (0.12), residues: 1668 loop : -1.32 (0.11), residues: 2790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 730 TYR 0.020 0.002 TYR D 131 PHE 0.017 0.002 PHE D 253 TRP 0.009 0.001 TRP B 809 HIS 0.007 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00517 (38616) covalent geometry : angle 0.65307 (52404) hydrogen bonds : bond 0.03869 ( 1082) hydrogen bonds : angle 6.59551 ( 2655) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7706.41 seconds wall clock time: 132 minutes 54.09 seconds (7974.09 seconds total)