Starting phenix.real_space_refine on Tue Aug 26 14:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.map" model { file = "/net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v0d_20994/08_2025/6v0d_20994.cif" } resolution = 3.49 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= 0.000 sd= 0.010 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 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 8.10, per 1000 atoms: 0.21 Number of scatterers: 37920 At special positions: 0 Unit cell: (113.97, 111.35, 238.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 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: 2.61 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 108 helices and 60 sheets defined 13.9% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL A 247 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.773A 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: 4.205A pdb=" N LEU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU A 386 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN A 565 " --> pdb=" O PRO A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA A 598 " --> pdb=" O PRO A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN A 615 " --> pdb=" O ALA A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG A 743 " --> pdb=" O ILE A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL A 802 " --> pdb=" O GLN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE A 834 " --> pdb=" O PHE A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP A 868 " --> pdb=" O PRO A 865 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 869 " --> pdb=" O LYS A 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.500A pdb=" N GLY B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.774A 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: 4.205A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 479 Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA B 598 " --> pdb=" O PRO B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN B 615 " --> pdb=" O ALA B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 744 removed outlier: 4.321A pdb=" N ARG B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL B 802 " --> pdb=" O GLN B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 835 removed outlier: 4.163A pdb=" N ILE B 834 " --> pdb=" O PHE B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP B 868 " --> pdb=" O PRO B 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 869 " --> pdb=" O LYS B 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.687A 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 274 through 278 removed outlier: 3.773A pdb=" N GLN C 278 " --> pdb=" O ALA C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.205A pdb=" N LEU C 358 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 4.105A pdb=" N LEU C 386 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 560 through 567 removed outlier: 3.514A pdb=" N ASN C 565 " --> pdb=" O PRO C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 617 removed outlier: 3.977A 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 716 removed outlier: 4.063A pdb=" N LEU C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG C 743 " --> pdb=" O ILE C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL C 802 " --> pdb=" O GLN C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE C 834 " --> pdb=" O PHE C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP C 868 " --> pdb=" O PRO C 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG C 869 " --> pdb=" O LYS C 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL D 247 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.773A 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: 4.205A pdb=" N LEU D 358 " --> pdb=" O ASN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 Processing helix chain 'D' and resid 500 through 506 Processing helix chain 'D' and resid 560 through 567 removed outlier: 3.512A pdb=" N ASN D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN D 615 " --> pdb=" O ALA D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 631 Processing helix chain 'D' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG D 743 " --> pdb=" O ILE D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL D 802 " --> pdb=" O GLN D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 830 through 835 removed outlier: 4.161A pdb=" N ILE D 834 " --> pdb=" O PHE D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 870 removed outlier: 3.562A pdb=" N TRP D 868 " --> pdb=" O PRO D 865 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 869 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.500A pdb=" N GLY E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 removed outlier: 4.192A pdb=" N VAL E 247 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.774A 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: 4.205A pdb=" N LEU E 358 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU E 386 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 479 Processing helix chain 'E' and resid 500 through 506 Processing helix chain 'E' and resid 560 through 567 removed outlier: 3.514A pdb=" N ASN E 565 " --> pdb=" O PRO E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 600 removed outlier: 3.651A pdb=" N ALA E 598 " --> pdb=" O PRO E 594 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN E 615 " --> pdb=" O ALA E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 631 Processing helix chain 'E' and resid 711 through 716 removed outlier: 4.063A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 744 removed outlier: 4.321A pdb=" N ARG E 743 " --> pdb=" O ILE E 739 " (cutoff:3.500A) Processing helix chain 'E' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL E 802 " --> pdb=" O GLN E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE E 834 " --> pdb=" O PHE E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP E 868 " --> pdb=" O PRO E 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 869 " --> pdb=" O LYS E 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 116 through 122 removed outlier: 3.501A pdb=" N GLY F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 removed outlier: 4.191A pdb=" N VAL F 247 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 3.687A 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: 3.774A 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: 4.204A pdb=" N LEU F 358 " --> pdb=" O ASN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 removed outlier: 4.106A pdb=" N LEU F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 479 Processing helix chain 'F' and resid 500 through 506 Processing helix chain 'F' and resid 560 through 567 removed outlier: 3.513A pdb=" N ASN F 565 " --> pdb=" O PRO F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 600 removed outlier: 3.650A pdb=" N ALA F 598 " --> pdb=" O PRO F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 617 removed outlier: 3.978A pdb=" N GLN F 615 " --> pdb=" O ALA F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 631 Processing helix chain 'F' and resid 711 through 716 removed outlier: 4.062A pdb=" N LEU F 715 " --> pdb=" O LEU F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 744 removed outlier: 4.320A pdb=" N ARG F 743 " --> pdb=" O ILE F 739 " (cutoff:3.500A) Processing helix chain 'F' and resid 798 through 802 removed outlier: 3.625A pdb=" N VAL F 802 " --> pdb=" O GLN F 799 " (cutoff:3.500A) Processing helix chain 'F' and resid 830 through 835 removed outlier: 4.162A pdb=" N ILE F 834 " --> pdb=" O PHE F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 865 through 870 removed outlier: 3.563A pdb=" N TRP F 868 " --> pdb=" O PRO F 865 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 869 " --> pdb=" O LYS F 866 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL A 66 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL A 76 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 6.574A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU A 206 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL A 189 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.864A 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: 6.219A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU A 310 " --> pdb=" O THR A 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR A 326 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 281 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 481 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER A 449 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR A 498 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 451 " --> pdb=" O TYR A 498 " (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: 6.417A pdb=" N ASP A 554 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL A 546 " --> pdb=" O ASP A 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 556 " --> pdb=" O ILE A 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 533 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU A 674 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 678 " --> pdb=" O THR A 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 680 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 663 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 655 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE A 696 " --> pdb=" O GLN A 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE A 732 " --> pdb=" O GLN A 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 638 " --> pdb=" O PHE A 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU A 734 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS A 640 " --> pdb=" O LEU A 734 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG A 793 " --> pdb=" O VAL A 776 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 776 " --> pdb=" O ARG A 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 768 " --> pdb=" O GLU A 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA A 841 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 807 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 808 " --> pdb=" O GLN A 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 860 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.196A pdb=" N VAL B 66 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL B 76 " --> pdb=" O SER B 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER B 93 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 107 through 111 Processing sheet with id=AB5, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU B 206 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL B 189 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 228 through 229 Processing sheet with id=AB7, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 310 " --> pdb=" O THR B 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 326 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 281 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 481 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N SER B 449 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N TYR B 498 " --> pdb=" O SER B 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE B 451 " --> pdb=" O TYR B 498 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 458 through 460 Processing sheet with id=AC1, first strand: chain 'B' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP B 554 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL B 546 " --> pdb=" O ASP B 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP B 556 " --> pdb=" O ILE B 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL B 533 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU B 674 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 678 " --> pdb=" O THR B 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL B 680 " --> pdb=" O ILE B 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 663 " --> pdb=" O VAL B 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP B 659 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR B 655 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE B 696 " --> pdb=" O GLN B 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE B 732 " --> pdb=" O GLN B 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR B 638 " --> pdb=" O PHE B 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 734 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS B 640 " --> pdb=" O LEU B 734 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 748 through 754 removed outlier: 6.383A pdb=" N ARG B 793 " --> pdb=" O VAL B 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL B 776 " --> pdb=" O ARG B 793 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE B 768 " --> pdb=" O GLU B 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA B 841 " --> pdb=" O VAL B 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 807 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE B 808 " --> pdb=" O GLN B 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 860 " --> pdb=" O GLU B 753 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL C 66 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL C 76 " --> pdb=" O SER C 93 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 93 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 107 through 111 Processing sheet with id=AC6, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU C 206 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL C 189 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 228 through 229 Processing sheet with id=AC8, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LEU C 310 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR C 326 " --> pdb=" O LEU C 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 281 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 393 through 399 removed outlier: 6.856A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 481 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER C 449 " --> pdb=" O PRO C 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR C 498 " --> pdb=" O SER C 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 451 " --> pdb=" O TYR C 498 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 458 through 460 Processing sheet with id=AD2, first strand: chain 'C' and resid 517 through 521 removed outlier: 6.417A pdb=" N ASP C 554 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL C 546 " --> pdb=" O ASP C 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP C 556 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL C 533 " --> pdb=" O VAL C 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU C 674 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 678 " --> pdb=" O THR C 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL C 680 " --> pdb=" O ILE C 663 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE C 663 " --> pdb=" O VAL C 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP C 659 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR C 655 " --> pdb=" O ASP C 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE C 696 " --> pdb=" O GLN C 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE C 732 " --> pdb=" O GLN C 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR C 638 " --> pdb=" O PHE C 732 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LEU C 734 " --> pdb=" O THR C 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS C 640 " --> pdb=" O LEU C 734 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG C 793 " --> pdb=" O VAL C 776 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL C 776 " --> pdb=" O ARG C 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU C 772 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE C 768 " --> pdb=" O GLU C 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA C 841 " --> pdb=" O VAL C 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL C 807 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE C 808 " --> pdb=" O GLN C 861 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU C 860 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL D 66 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL D 76 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 93 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 107 through 111 Processing sheet with id=AD7, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU D 206 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL D 189 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 228 through 229 Processing sheet with id=AD9, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU D 310 " --> pdb=" O THR D 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR D 326 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 281 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE D 481 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N SER D 449 " --> pdb=" O PRO D 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR D 498 " --> pdb=" O SER D 449 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE D 451 " --> pdb=" O TYR D 498 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 458 through 460 Processing sheet with id=AE3, first strand: chain 'D' and resid 517 through 521 removed outlier: 6.417A pdb=" N ASP D 554 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL D 546 " --> pdb=" O ASP D 554 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASP D 556 " --> pdb=" O ILE D 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL D 533 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 636 through 641 removed outlier: 3.503A pdb=" N GLU D 674 " --> pdb=" O ILE D 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS D 678 " --> pdb=" O THR D 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL D 680 " --> pdb=" O ILE D 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 663 " --> pdb=" O VAL D 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP D 659 " --> pdb=" O TYR D 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR D 655 " --> pdb=" O ASP D 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE D 696 " --> pdb=" O GLN D 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE D 732 " --> pdb=" O GLN D 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR D 638 " --> pdb=" O PHE D 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU D 734 " --> pdb=" O THR D 638 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N HIS D 640 " --> pdb=" O LEU D 734 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG D 793 " --> pdb=" O VAL D 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL D 776 " --> pdb=" O ARG D 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU D 772 " --> pdb=" O PHE D 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE D 768 " --> pdb=" O GLU D 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA D 841 " --> pdb=" O VAL D 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 807 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE D 808 " --> pdb=" O GLN D 861 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 860 " --> pdb=" O GLU D 753 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.197A pdb=" N VAL E 66 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL E 76 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER E 93 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 107 through 111 Processing sheet with id=AE8, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.163A pdb=" N LEU E 206 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL E 189 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 228 through 229 Processing sheet with id=AF1, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU E 310 " --> pdb=" O THR E 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR E 326 " --> pdb=" O LEU E 310 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL E 281 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 393 through 399 removed outlier: 6.856A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 481 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N SER E 449 " --> pdb=" O PRO E 496 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N TYR E 498 " --> pdb=" O SER E 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE E 451 " --> pdb=" O TYR E 498 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 458 through 460 Processing sheet with id=AF4, first strand: chain 'E' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP E 554 " --> pdb=" O VAL E 546 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL E 546 " --> pdb=" O ASP E 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP E 556 " --> pdb=" O ILE E 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL E 533 " --> pdb=" O VAL E 540 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU E 674 " --> pdb=" O ILE E 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 678 " --> pdb=" O THR E 665 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL E 680 " --> pdb=" O ILE E 663 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE E 663 " --> pdb=" O VAL E 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP E 659 " --> pdb=" O TYR E 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR E 655 " --> pdb=" O ASP E 659 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N PHE E 696 " --> pdb=" O GLN E 735 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N PHE E 732 " --> pdb=" O GLN E 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR E 638 " --> pdb=" O PHE E 732 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU E 734 " --> pdb=" O THR E 638 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS E 640 " --> pdb=" O LEU E 734 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG E 793 " --> pdb=" O VAL E 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL E 776 " --> pdb=" O ARG E 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU E 772 " --> pdb=" O PHE E 768 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N PHE E 768 " --> pdb=" O GLU E 772 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ALA E 841 " --> pdb=" O VAL E 807 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL E 807 " --> pdb=" O ALA E 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE E 808 " --> pdb=" O GLN E 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 860 " --> pdb=" O GLU E 753 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.198A pdb=" N VAL F 66 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N VAL F 76 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER F 93 " --> pdb=" O VAL F 76 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 107 through 111 Processing sheet with id=AF9, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.162A pdb=" N LEU F 206 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL F 189 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.219A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU F 310 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR F 326 " --> pdb=" O LEU F 310 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 281 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 393 through 399 removed outlier: 6.855A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE F 481 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N SER F 449 " --> pdb=" O PRO F 496 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N TYR F 498 " --> pdb=" O SER F 449 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE F 451 " --> pdb=" O TYR F 498 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 458 through 460 Processing sheet with id=AG4, first strand: chain 'F' and resid 517 through 521 removed outlier: 6.418A pdb=" N ASP F 554 " --> pdb=" O VAL F 546 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL F 546 " --> pdb=" O ASP F 554 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP F 556 " --> pdb=" O ILE F 544 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL F 533 " --> pdb=" O VAL F 540 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 636 through 641 removed outlier: 3.504A pdb=" N GLU F 674 " --> pdb=" O ILE F 669 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS F 678 " --> pdb=" O THR F 665 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL F 680 " --> pdb=" O ILE F 663 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE F 663 " --> pdb=" O VAL F 680 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP F 659 " --> pdb=" O TYR F 655 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR F 655 " --> pdb=" O ASP F 659 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE F 696 " --> pdb=" O GLN F 735 " (cutoff:3.500A) removed outlier: 9.264A pdb=" N PHE F 732 " --> pdb=" O GLN F 636 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR F 638 " --> pdb=" O PHE F 732 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU F 734 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N HIS F 640 " --> pdb=" O LEU F 734 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 748 through 754 removed outlier: 6.382A pdb=" N ARG F 793 " --> pdb=" O VAL F 776 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N VAL F 776 " --> pdb=" O ARG F 793 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N GLU F 772 " --> pdb=" O PHE F 768 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE F 768 " --> pdb=" O GLU F 772 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA F 841 " --> pdb=" O VAL F 807 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL F 807 " --> pdb=" O ALA F 841 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE F 808 " --> pdb=" O GLN F 861 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 860 " --> pdb=" O GLU F 753 " (cutoff:3.500A) 1158 hydrogen bonds defined for protein. 2898 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: 9.61 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12305 1.34 - 1.46: 5348 1.46 - 1.57: 20813 1.57 - 1.69: 6 1.69 - 1.81: 144 Bond restraints: 38616 Sorted by residual: bond pdb=" CB TRP C 868 " pdb=" CG TRP C 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.54e+00 bond pdb=" CB TRP D 868 " pdb=" CG TRP D 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP A 868 " pdb=" CG TRP A 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP F 868 " pdb=" CG TRP F 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 bond pdb=" CB TRP E 868 " pdb=" CG TRP E 868 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.51e+00 ... (remaining 38611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 51150 2.39 - 4.79: 1088 4.79 - 7.18: 124 7.18 - 9.57: 30 9.57 - 11.96: 12 Bond angle restraints: 52404 Sorted by residual: angle pdb=" C PRO C 876 " pdb=" N LYS C 877 " pdb=" CA LYS C 877 " ideal model delta sigma weight residual 121.70 128.30 -6.60 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C PRO F 876 " pdb=" N LYS F 877 " pdb=" CA LYS F 877 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO D 876 " pdb=" N LYS D 877 " pdb=" CA LYS D 877 " ideal model delta sigma weight residual 121.70 128.27 -6.57 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO E 876 " pdb=" N LYS E 877 " pdb=" CA LYS E 877 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.33e+01 angle pdb=" C PRO B 876 " pdb=" N LYS B 877 " pdb=" CA LYS B 877 " ideal model delta sigma weight residual 121.70 128.25 -6.55 1.80e+00 3.09e-01 1.33e+01 ... (remaining 52399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 22125 15.20 - 30.41: 837 30.41 - 45.61: 240 45.61 - 60.82: 6 60.82 - 76.02: 48 Dihedral angle restraints: 23256 sinusoidal: 9180 harmonic: 14076 Sorted by residual: dihedral pdb=" CA ALA E 471 " pdb=" C ALA E 471 " pdb=" N SER E 472 " pdb=" CA SER E 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.34e+01 dihedral pdb=" CA ALA A 471 " pdb=" C ALA A 471 " pdb=" N SER A 472 " pdb=" CA SER A 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.33e+01 dihedral pdb=" CA ALA D 471 " pdb=" C ALA D 471 " pdb=" N SER D 472 " pdb=" CA SER D 472 " ideal model delta harmonic sigma weight residual 180.00 147.08 32.92 0 5.00e+00 4.00e-02 4.33e+01 ... (remaining 23253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3414 0.035 - 0.071: 1610 0.071 - 0.106: 625 0.106 - 0.142: 331 0.142 - 0.177: 80 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CB ILE C 622 " pdb=" CA ILE C 622 " pdb=" CG1 ILE C 622 " pdb=" CG2 ILE C 622 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.85e-01 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 2.47 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CB ILE F 622 " pdb=" CA ILE F 622 " pdb=" CG1 ILE F 622 " pdb=" CG2 ILE F 622 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 ... (remaining 6057 not shown) Planarity restraints: 6822 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 846 " 0.042 5.00e-02 4.00e+02 6.36e-02 6.47e+00 pdb=" N PRO E 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO E 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 847 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 846 " -0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 847 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 847 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 847 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 846 " 0.042 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO D 847 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 847 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 847 " 0.036 5.00e-02 4.00e+02 ... (remaining 6819 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 11073 2.83 - 3.35: 30658 3.35 - 3.86: 58722 3.86 - 4.38: 64967 4.38 - 4.90: 115733 Nonbonded interactions: 281153 Sorted by model distance: nonbonded pdb=" OG1 THR A 740 " pdb=" O VAL A 776 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR E 740 " pdb=" O VAL E 776 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR F 740 " pdb=" O VAL F 776 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR C 740 " pdb=" O VAL C 776 " model vdw 2.311 3.040 nonbonded pdb=" OG1 THR B 740 " pdb=" O VAL B 776 " model vdw 2.311 3.040 ... (remaining 281148 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: 0.09 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: 1.430 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 34.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.070 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.005 0.049 38616 Z= 0.215 Angle : 0.868 11.965 52404 Z= 0.465 Chirality : 0.054 0.177 6060 Planarity : 0.007 0.064 6822 Dihedral : 9.835 76.021 14292 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 aren not related in a simple way. whole: -3.27 (0.10), residues: 4980 helix: -3.89 (0.12), residues: 528 sheet: -1.63 (0.11), residues: 1728 loop : -2.17 (0.10), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 482 TYR 0.025 0.002 TYR F 814 PHE 0.029 0.003 PHE F 605 TRP 0.018 0.002 TRP E 574 HIS 0.005 0.001 HIS F 441 Details of bonding type rmsd covalent geometry : bond 0.00474 (38616) covalent geometry : angle 0.86846 (52404) hydrogen bonds : bond 0.26394 ( 1158) hydrogen bonds : angle 9.95188 ( 2898) *********************** 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 881 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 881 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8106 (m-80) cc_final: 0.7618 (m-80) REVERT: A 239 LYS cc_start: 0.5960 (ttmt) cc_final: 0.5547 (tttp) REVERT: A 240 LEU cc_start: 0.7887 (tt) cc_final: 0.7586 (tp) REVERT: A 716 GLN cc_start: 0.8641 (tt0) cc_final: 0.8207 (pt0) REVERT: A 795 SER cc_start: 0.8535 (m) cc_final: 0.8315 (t) REVERT: B 51 ILE cc_start: 0.8426 (mt) cc_final: 0.8118 (mt) REVERT: B 145 PHE cc_start: 0.8133 (m-80) cc_final: 0.7664 (m-80) REVERT: B 158 ASN cc_start: 0.8017 (t0) cc_final: 0.7526 (t0) REVERT: B 174 ASN cc_start: 0.7842 (m-40) cc_final: 0.7640 (m-40) REVERT: B 240 LEU cc_start: 0.7928 (tt) cc_final: 0.7572 (tp) REVERT: B 518 SER cc_start: 0.9019 (m) cc_final: 0.8678 (t) REVERT: C 158 ASN cc_start: 0.8207 (t0) cc_final: 0.7877 (t0) REVERT: C 239 LYS cc_start: 0.6575 (ttmt) cc_final: 0.5914 (tttm) REVERT: C 240 LEU cc_start: 0.8169 (tt) cc_final: 0.7793 (tp) REVERT: C 383 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7090 (mm-30) REVERT: C 503 LYS cc_start: 0.8912 (mttt) cc_final: 0.8704 (mtpp) REVERT: C 518 SER cc_start: 0.8966 (m) cc_final: 0.8694 (t) REVERT: C 716 GLN cc_start: 0.8333 (tt0) cc_final: 0.8132 (pt0) REVERT: C 795 SER cc_start: 0.8350 (m) cc_final: 0.7960 (t) REVERT: D 145 PHE cc_start: 0.8065 (m-80) cc_final: 0.7857 (m-80) REVERT: D 158 ASN cc_start: 0.8007 (t0) cc_final: 0.7167 (t0) REVERT: D 239 LYS cc_start: 0.6108 (ttmt) cc_final: 0.5692 (tttp) REVERT: D 240 LEU cc_start: 0.7978 (tt) cc_final: 0.7662 (tp) REVERT: D 354 ASN cc_start: 0.6782 (p0) cc_final: 0.6513 (p0) REVERT: D 701 PRO cc_start: 0.7757 (Cg_exo) cc_final: 0.7441 (Cg_endo) REVERT: D 716 GLN cc_start: 0.8682 (tt0) cc_final: 0.8244 (pt0) REVERT: D 795 SER cc_start: 0.8608 (m) cc_final: 0.8396 (t) REVERT: E 51 ILE cc_start: 0.8424 (mt) cc_final: 0.8135 (mt) REVERT: E 145 PHE cc_start: 0.8139 (m-80) cc_final: 0.7651 (m-80) REVERT: E 158 ASN cc_start: 0.7991 (t0) cc_final: 0.7488 (t0) REVERT: E 240 LEU cc_start: 0.7960 (tt) cc_final: 0.7538 (tp) REVERT: E 383 GLU cc_start: 0.7226 (mm-30) cc_final: 0.7019 (mm-30) REVERT: E 503 LYS cc_start: 0.8914 (mttt) cc_final: 0.8710 (mtpp) REVERT: E 518 SER cc_start: 0.9005 (m) cc_final: 0.8657 (t) REVERT: E 795 SER cc_start: 0.8482 (m) cc_final: 0.8247 (t) REVERT: F 158 ASN cc_start: 0.8170 (t0) cc_final: 0.7868 (t0) REVERT: F 239 LYS cc_start: 0.6968 (ttmt) cc_final: 0.6192 (tttp) REVERT: F 240 LEU cc_start: 0.8164 (tt) cc_final: 0.7817 (tp) REVERT: F 383 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7089 (mm-30) REVERT: F 503 LYS cc_start: 0.8861 (mttt) cc_final: 0.8602 (mtpp) REVERT: F 518 SER cc_start: 0.9020 (m) cc_final: 0.8752 (t) REVERT: F 795 SER cc_start: 0.8402 (m) cc_final: 0.8073 (t) outliers start: 0 outliers final: 0 residues processed: 881 average time/residue: 0.2403 time to fit residues: 335.6968 Evaluate side-chains 521 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 521 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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: 0.9980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 3.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 494 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 164 HIS A 345 ASN A 409 GLN A 441 HIS ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 662 GLN A 832 GLN B 130 ASN B 164 HIS B 316 ASN B 345 ASN B 409 GLN B 441 HIS ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 640 HIS B 662 GLN B 832 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 316 ASN C 345 ASN C 409 GLN C 441 HIS ** C 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 640 HIS C 662 GLN C 832 GLN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 345 ASN D 409 GLN D 441 HIS ** D 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 GLN D 662 GLN D 832 GLN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS E 316 ASN E 345 ASN E 409 GLN E 441 HIS ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 HIS E 662 GLN E 804 ASN E 832 GLN F 130 ASN F 164 HIS F 316 ASN F 345 ASN F 409 GLN F 441 HIS ** F 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 GLN F 640 HIS F 662 GLN F 832 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.184942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124947 restraints weight = 48664.253| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.06 r_work: 0.3149 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 38616 Z= 0.160 Angle : 0.658 9.800 52404 Z= 0.345 Chirality : 0.047 0.176 6060 Planarity : 0.006 0.052 6822 Dihedral : 5.421 28.959 5358 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.15 % Allowed : 9.54 % Favored : 89.31 % 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 aren not related in a simple way. whole: -2.76 (0.10), residues: 4980 helix: -3.20 (0.16), residues: 558 sheet: -1.36 (0.11), residues: 1800 loop : -1.81 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 691 TYR 0.013 0.002 TYR B 744 PHE 0.027 0.002 PHE A 364 TRP 0.014 0.002 TRP B 574 HIS 0.007 0.001 HIS C 441 Details of bonding type rmsd covalent geometry : bond 0.00378 (38616) covalent geometry : angle 0.65784 (52404) hydrogen bonds : bond 0.04485 ( 1158) hydrogen bonds : angle 7.93542 ( 2898) *********************** 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 579 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 532 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 PHE cc_start: 0.8192 (m-80) cc_final: 0.7973 (m-80) REVERT: A 239 LYS cc_start: 0.5988 (ttmt) cc_final: 0.5397 (tttp) REVERT: A 240 LEU cc_start: 0.7687 (tt) cc_final: 0.7337 (tp) REVERT: A 716 GLN cc_start: 0.8734 (tt0) cc_final: 0.8231 (pt0) REVERT: A 858 PHE cc_start: 0.7643 (m-10) cc_final: 0.7415 (m-10) REVERT: B 51 ILE cc_start: 0.8290 (mt) cc_final: 0.7920 (mt) REVERT: B 114 LYS cc_start: 0.8084 (ttpp) cc_final: 0.7281 (tttm) REVERT: B 120 VAL cc_start: 0.8364 (p) cc_final: 0.8104 (m) REVERT: B 145 PHE cc_start: 0.8139 (m-80) cc_final: 0.7457 (m-80) REVERT: B 224 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8493 (m) REVERT: B 240 LEU cc_start: 0.7759 (tt) cc_final: 0.7365 (tp) REVERT: B 518 SER cc_start: 0.9111 (m) cc_final: 0.8868 (t) REVERT: B 556 ASP cc_start: 0.8783 (m-30) cc_final: 0.8392 (m-30) REVERT: B 678 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8542 (ttmm) REVERT: C 135 MET cc_start: 0.6962 (ttp) cc_final: 0.6598 (ptp) REVERT: C 145 PHE cc_start: 0.8064 (m-80) cc_final: 0.7723 (m-80) REVERT: C 158 ASN cc_start: 0.8808 (t0) cc_final: 0.8598 (t0) REVERT: C 239 LYS cc_start: 0.6516 (ttmt) cc_final: 0.5722 (tttm) REVERT: C 240 LEU cc_start: 0.7942 (tt) cc_final: 0.7596 (tp) REVERT: C 322 THR cc_start: 0.9037 (p) cc_final: 0.8682 (t) REVERT: C 383 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8168 (mm-30) REVERT: C 503 LYS cc_start: 0.9225 (mttt) cc_final: 0.8809 (mtpp) REVERT: C 518 SER cc_start: 0.9124 (m) cc_final: 0.8834 (t) REVERT: C 564 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6825 (ttp-170) REVERT: C 716 GLN cc_start: 0.8473 (tt0) cc_final: 0.8185 (pt0) REVERT: C 795 SER cc_start: 0.8339 (m) cc_final: 0.8034 (t) REVERT: D 145 PHE cc_start: 0.8172 (m-80) cc_final: 0.7793 (m-80) REVERT: D 239 LYS cc_start: 0.6155 (ttmt) cc_final: 0.5520 (tttp) REVERT: D 240 LEU cc_start: 0.7819 (tt) cc_final: 0.7415 (tp) REVERT: D 547 ARG cc_start: 0.7328 (ttp-110) cc_final: 0.7112 (ttp-110) REVERT: D 716 GLN cc_start: 0.8810 (tt0) cc_final: 0.8263 (pt0) REVERT: D 766 VAL cc_start: 0.7268 (t) cc_final: 0.7043 (p) REVERT: E 114 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7441 (tttm) REVERT: E 145 PHE cc_start: 0.8145 (m-80) cc_final: 0.7123 (m-80) REVERT: E 240 LEU cc_start: 0.7664 (tt) cc_final: 0.7204 (tp) REVERT: E 279 ARG cc_start: 0.8688 (mpt-90) cc_final: 0.8465 (mtt90) REVERT: E 503 LYS cc_start: 0.9122 (mttt) cc_final: 0.8699 (mtpp) REVERT: E 518 SER cc_start: 0.9114 (m) cc_final: 0.8875 (p) REVERT: E 556 ASP cc_start: 0.8772 (m-30) cc_final: 0.8488 (m-30) REVERT: E 672 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8290 (ptt180) REVERT: E 678 LYS cc_start: 0.8812 (ttpp) cc_final: 0.8553 (ttmm) REVERT: E 804 ASN cc_start: 0.7214 (m110) cc_final: 0.6760 (m110) REVERT: F 239 LYS cc_start: 0.6701 (ttmt) cc_final: 0.5788 (tttm) REVERT: F 240 LEU cc_start: 0.8005 (tt) cc_final: 0.7675 (tp) REVERT: F 383 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8160 (mm-30) REVERT: F 491 MET cc_start: 0.8227 (tpp) cc_final: 0.7961 (mmt) REVERT: F 503 LYS cc_start: 0.9172 (mttt) cc_final: 0.8716 (mtpp) REVERT: F 518 SER cc_start: 0.9138 (m) cc_final: 0.8799 (t) REVERT: F 678 LYS cc_start: 0.8755 (ttpp) cc_final: 0.8553 (ttmm) REVERT: F 795 SER cc_start: 0.8323 (m) cc_final: 0.8068 (t) outliers start: 47 outliers final: 21 residues processed: 557 average time/residue: 0.2573 time to fit residues: 227.6676 Evaluate side-chains 487 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 464 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 564 ARG Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 792 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER 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: 8.9990 chunk 449 optimal weight: 2.9990 chunk 193 optimal weight: 0.8980 chunk 283 optimal weight: 2.9990 chunk 488 optimal weight: 9.9990 chunk 440 optimal weight: 2.9990 chunk 265 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 321 optimal weight: 9.9990 chunk 474 optimal weight: 10.0000 chunk 22 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN A 640 HIS ** B 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 800 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 640 HIS ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN E 800 HIS F 158 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN F 804 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.182976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.126836 restraints weight = 49460.860| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.27 r_work: 0.3176 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 38616 Z= 0.179 Angle : 0.623 9.922 52404 Z= 0.325 Chirality : 0.046 0.178 6060 Planarity : 0.005 0.044 6822 Dihedral : 5.203 26.127 5358 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.78 % Allowed : 9.71 % Favored : 87.51 % 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 aren not related in a simple way. whole: -2.27 (0.11), residues: 4980 helix: -2.53 (0.20), residues: 522 sheet: -1.15 (0.11), residues: 1704 loop : -1.48 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 691 TYR 0.016 0.002 TYR E 154 PHE 0.022 0.002 PHE F 364 TRP 0.012 0.001 TRP D 574 HIS 0.008 0.001 HIS B 800 Details of bonding type rmsd covalent geometry : bond 0.00431 (38616) covalent geometry : angle 0.62273 (52404) hydrogen bonds : bond 0.04311 ( 1158) hydrogen bonds : angle 7.41750 ( 2898) *********************** 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 635 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 521 time to evaluate : 1.341 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 239 LYS cc_start: 0.5808 (ttmt) cc_final: 0.5510 (tttp) REVERT: A 240 LEU cc_start: 0.7739 (tt) cc_final: 0.7346 (tp) REVERT: A 241 GLU cc_start: 0.5952 (mt-10) cc_final: 0.5751 (mt-10) REVERT: A 716 GLN cc_start: 0.8810 (tt0) cc_final: 0.8284 (pt0) REVERT: A 731 ASP cc_start: 0.8617 (t0) cc_final: 0.7981 (p0) REVERT: A 749 SER cc_start: 0.7762 (t) cc_final: 0.7533 (p) REVERT: A 797 ARG cc_start: 0.8803 (ptt-90) cc_final: 0.8601 (ttp-170) REVERT: B 51 ILE cc_start: 0.8384 (mt) cc_final: 0.8004 (mt) REVERT: B 120 VAL cc_start: 0.8507 (p) cc_final: 0.8298 (m) REVERT: B 145 PHE cc_start: 0.8205 (m-80) cc_final: 0.7155 (m-80) REVERT: B 240 LEU cc_start: 0.7820 (tt) cc_final: 0.7493 (tp) REVERT: B 243 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5824 (mm) REVERT: B 518 SER cc_start: 0.9247 (m) cc_final: 0.8834 (p) REVERT: B 556 ASP cc_start: 0.8825 (m-30) cc_final: 0.8390 (m-30) REVERT: B 687 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8302 (tm-30) REVERT: B 801 LEU cc_start: 0.9002 (mp) cc_final: 0.8785 (mp) REVERT: C 98 MET cc_start: 0.8203 (mmt) cc_final: 0.7961 (mmp) REVERT: C 135 MET cc_start: 0.7006 (ttp) cc_final: 0.6675 (ttp) REVERT: C 239 LYS cc_start: 0.6479 (ttmt) cc_final: 0.5775 (tttp) REVERT: C 240 LEU cc_start: 0.7916 (tt) cc_final: 0.7591 (tp) REVERT: C 347 LYS cc_start: 0.5720 (tptp) cc_final: 0.5462 (ptpp) REVERT: C 383 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8022 (mm-30) REVERT: C 491 MET cc_start: 0.8645 (mmt) cc_final: 0.8300 (mmt) REVERT: C 503 LYS cc_start: 0.9155 (mttt) cc_final: 0.8796 (mtpp) REVERT: C 518 SER cc_start: 0.9070 (m) cc_final: 0.8795 (t) REVERT: C 716 GLN cc_start: 0.8434 (tt0) cc_final: 0.8181 (pt0) REVERT: C 795 SER cc_start: 0.8521 (m) cc_final: 0.8148 (t) REVERT: C 804 ASN cc_start: 0.7069 (m110) cc_final: 0.6544 (m110) REVERT: C 830 PHE cc_start: 0.6888 (p90) cc_final: 0.6370 (p90) REVERT: C 832 GLN cc_start: 0.8566 (mp10) cc_final: 0.8082 (mp10) REVERT: D 145 PHE cc_start: 0.8155 (m-80) cc_final: 0.7799 (m-80) REVERT: D 239 LYS cc_start: 0.6042 (ttmt) cc_final: 0.5650 (tttp) REVERT: D 240 LEU cc_start: 0.7932 (tt) cc_final: 0.7482 (tp) REVERT: D 354 ASN cc_start: 0.7113 (p0) cc_final: 0.6723 (p0) REVERT: D 363 THR cc_start: 0.8736 (m) cc_final: 0.8501 (p) REVERT: D 716 GLN cc_start: 0.8874 (tt0) cc_final: 0.8481 (pt0) REVERT: D 731 ASP cc_start: 0.8681 (t0) cc_final: 0.7936 (p0) REVERT: E 114 LYS cc_start: 0.8275 (ttpp) cc_final: 0.7384 (tmtt) REVERT: E 145 PHE cc_start: 0.8226 (m-80) cc_final: 0.7262 (m-80) REVERT: E 224 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8650 (m) REVERT: E 240 LEU cc_start: 0.7807 (tt) cc_final: 0.7453 (tp) REVERT: E 243 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5814 (mm) REVERT: E 503 LYS cc_start: 0.9016 (mttt) cc_final: 0.8633 (mtpp) REVERT: E 518 SER cc_start: 0.9292 (m) cc_final: 0.8912 (p) REVERT: E 556 ASP cc_start: 0.8784 (m-30) cc_final: 0.8405 (m-30) REVERT: E 672 ARG cc_start: 0.8559 (mtm-85) cc_final: 0.8224 (ptt180) REVERT: E 678 LYS cc_start: 0.8833 (ttpp) cc_final: 0.8601 (ttmm) REVERT: E 801 LEU cc_start: 0.8968 (mp) cc_final: 0.8753 (mp) REVERT: E 804 ASN cc_start: 0.7084 (m110) cc_final: 0.6683 (m110) REVERT: E 858 PHE cc_start: 0.7774 (m-10) cc_final: 0.7520 (m-10) REVERT: F 239 LYS cc_start: 0.6764 (ttmt) cc_final: 0.6104 (tttp) REVERT: F 240 LEU cc_start: 0.7968 (tt) cc_final: 0.7632 (tp) REVERT: F 383 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8016 (mm-30) REVERT: F 491 MET cc_start: 0.8210 (tpp) cc_final: 0.8001 (mmt) REVERT: F 503 LYS cc_start: 0.9069 (mttt) cc_final: 0.8673 (mtpp) REVERT: F 518 SER cc_start: 0.9118 (m) cc_final: 0.8825 (t) REVERT: F 722 GLU cc_start: 0.7924 (mp0) cc_final: 0.7404 (mp0) REVERT: F 731 ASP cc_start: 0.8937 (t0) cc_final: 0.8085 (p0) REVERT: F 795 SER cc_start: 0.8452 (m) cc_final: 0.8108 (t) REVERT: F 804 ASN cc_start: 0.7191 (m110) cc_final: 0.6546 (m110) outliers start: 114 outliers final: 58 residues processed: 591 average time/residue: 0.2085 time to fit residues: 200.1006 Evaluate side-chains 527 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 466 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 658 ILE Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 658 ILE Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 501 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 243 optimal weight: 40.0000 chunk 35 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 354 optimal weight: 3.9990 chunk 359 optimal weight: 0.9990 chunk 466 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 196 optimal weight: 9.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 673 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 673 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN F 158 ASN F 673 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.183162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.127700 restraints weight = 49439.952| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.33 r_work: 0.3171 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 38616 Z= 0.150 Angle : 0.592 9.206 52404 Z= 0.305 Chirality : 0.045 0.162 6060 Planarity : 0.004 0.043 6822 Dihedral : 4.967 24.646 5358 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.32 % Allowed : 11.40 % Favored : 86.29 % 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 aren not related in a simple way. whole: -2.22 (0.11), residues: 4980 helix: -2.39 (0.20), residues: 558 sheet: -1.10 (0.11), residues: 1716 loop : -1.47 (0.11), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 797 TYR 0.014 0.001 TYR D 154 PHE 0.017 0.001 PHE B 858 TRP 0.011 0.001 TRP B 574 HIS 0.003 0.001 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00356 (38616) covalent geometry : angle 0.59187 (52404) hydrogen bonds : bond 0.03811 ( 1158) hydrogen bonds : angle 7.17421 ( 2898) *********************** 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 598 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 503 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8888 (m-80) cc_final: 0.8505 (m-10) REVERT: A 239 LYS cc_start: 0.5756 (ttmt) cc_final: 0.5388 (tttp) REVERT: A 240 LEU cc_start: 0.7657 (tt) cc_final: 0.7269 (tp) REVERT: A 241 GLU cc_start: 0.5887 (mt-10) cc_final: 0.5657 (mt-10) REVERT: A 312 LYS cc_start: 0.8797 (tttt) cc_final: 0.8567 (ttpt) REVERT: A 397 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8986 (pp) REVERT: A 716 GLN cc_start: 0.8821 (tt0) cc_final: 0.8451 (pt0) REVERT: A 731 ASP cc_start: 0.8598 (t0) cc_final: 0.7887 (p0) REVERT: A 797 ARG cc_start: 0.8819 (ptt-90) cc_final: 0.8578 (ttp-170) REVERT: B 51 ILE cc_start: 0.8371 (mt) cc_final: 0.7983 (mt) REVERT: B 120 VAL cc_start: 0.8475 (p) cc_final: 0.8223 (m) REVERT: B 145 PHE cc_start: 0.8180 (m-80) cc_final: 0.7112 (m-80) REVERT: B 224 VAL cc_start: 0.8683 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 240 LEU cc_start: 0.7795 (tt) cc_final: 0.7480 (tp) REVERT: B 243 LEU cc_start: 0.6189 (OUTLIER) cc_final: 0.5811 (mm) REVERT: B 312 LYS cc_start: 0.8725 (tttt) cc_final: 0.8467 (ttpt) REVERT: B 518 SER cc_start: 0.9241 (m) cc_final: 0.8838 (p) REVERT: B 556 ASP cc_start: 0.8772 (m-30) cc_final: 0.8393 (m-30) REVERT: B 687 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8248 (tm-30) REVERT: B 722 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8443 (mm-30) REVERT: C 98 MET cc_start: 0.8384 (mmt) cc_final: 0.8117 (mmp) REVERT: C 135 MET cc_start: 0.7067 (ttp) cc_final: 0.6714 (ttp) REVERT: C 239 LYS cc_start: 0.6616 (ttmt) cc_final: 0.5793 (tttp) REVERT: C 240 LEU cc_start: 0.8065 (tt) cc_final: 0.7676 (tp) REVERT: C 347 LYS cc_start: 0.5736 (tptp) cc_final: 0.5479 (ptpp) REVERT: C 383 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8042 (mm-30) REVERT: C 491 MET cc_start: 0.8506 (mmt) cc_final: 0.8201 (mmt) REVERT: C 503 LYS cc_start: 0.9144 (mttt) cc_final: 0.8793 (mtpp) REVERT: C 518 SER cc_start: 0.9046 (m) cc_final: 0.8707 (p) REVERT: C 716 GLN cc_start: 0.8518 (tt0) cc_final: 0.8258 (pt0) REVERT: C 731 ASP cc_start: 0.8785 (t0) cc_final: 0.7832 (p0) REVERT: C 795 SER cc_start: 0.8412 (m) cc_final: 0.8051 (t) REVERT: C 804 ASN cc_start: 0.6920 (m110) cc_final: 0.6375 (m110) REVERT: C 858 PHE cc_start: 0.7757 (m-10) cc_final: 0.7392 (m-10) REVERT: D 108 PHE cc_start: 0.8857 (m-80) cc_final: 0.8434 (m-10) REVERT: D 239 LYS cc_start: 0.5998 (ttmt) cc_final: 0.5621 (tttp) REVERT: D 240 LEU cc_start: 0.7864 (tt) cc_final: 0.7445 (tp) REVERT: D 312 LYS cc_start: 0.8789 (tttt) cc_final: 0.8555 (ttpt) REVERT: D 397 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9012 (pp) REVERT: D 716 GLN cc_start: 0.8822 (tt0) cc_final: 0.8388 (pt0) REVERT: D 731 ASP cc_start: 0.8611 (t0) cc_final: 0.7799 (p0) REVERT: D 798 TYR cc_start: 0.9129 (m-10) cc_final: 0.8670 (m-10) REVERT: D 804 ASN cc_start: 0.7347 (m-40) cc_final: 0.6724 (m110) REVERT: E 145 PHE cc_start: 0.8210 (m-80) cc_final: 0.7193 (m-80) REVERT: E 224 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8645 (m) REVERT: E 240 LEU cc_start: 0.7806 (tt) cc_final: 0.7401 (tp) REVERT: E 243 LEU cc_start: 0.6261 (OUTLIER) cc_final: 0.5868 (mm) REVERT: E 503 LYS cc_start: 0.9001 (mttt) cc_final: 0.8605 (mtpp) REVERT: E 518 SER cc_start: 0.9278 (m) cc_final: 0.8877 (p) REVERT: E 556 ASP cc_start: 0.8758 (m-30) cc_final: 0.8409 (m-30) REVERT: E 672 ARG cc_start: 0.8557 (mtm-85) cc_final: 0.8209 (ptt180) REVERT: E 678 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8531 (ttmm) REVERT: E 804 ASN cc_start: 0.7043 (m110) cc_final: 0.6663 (m110) REVERT: F 239 LYS cc_start: 0.6926 (ttmt) cc_final: 0.6244 (tttp) REVERT: F 240 LEU cc_start: 0.8083 (tt) cc_final: 0.7710 (tp) REVERT: F 312 LYS cc_start: 0.8792 (tttt) cc_final: 0.8421 (ttpt) REVERT: F 383 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8096 (mm-30) REVERT: F 491 MET cc_start: 0.8280 (tpp) cc_final: 0.8049 (mmt) REVERT: F 503 LYS cc_start: 0.9026 (mttt) cc_final: 0.8625 (mtpp) REVERT: F 518 SER cc_start: 0.9149 (m) cc_final: 0.8823 (p) REVERT: F 731 ASP cc_start: 0.8957 (t0) cc_final: 0.8067 (p0) REVERT: F 795 SER cc_start: 0.8372 (m) cc_final: 0.8032 (t) REVERT: F 804 ASN cc_start: 0.7071 (m110) cc_final: 0.6451 (m110) outliers start: 95 outliers final: 59 residues processed: 561 average time/residue: 0.2149 time to fit residues: 193.5366 Evaluate side-chains 532 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 467 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 637 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 792 MET Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 247 optimal weight: 9.9990 chunk 222 optimal weight: 2.9990 chunk 312 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 163 optimal weight: 30.0000 chunk 482 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 342 optimal weight: 0.2980 chunk 299 optimal weight: 0.9980 chunk 169 optimal weight: 0.0980 chunk 373 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 ASN B 636 GLN B 804 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 673 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 673 ASN F 158 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.187213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.125147 restraints weight = 48838.294| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.91 r_work: 0.3131 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 38616 Z= 0.131 Angle : 0.583 10.272 52404 Z= 0.298 Chirality : 0.046 0.202 6060 Planarity : 0.004 0.045 6822 Dihedral : 4.782 20.997 5358 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.66 % Allowed : 12.20 % Favored : 85.14 % 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 aren not related in a simple way. whole: -2.02 (0.11), residues: 4980 helix: -2.29 (0.21), residues: 510 sheet: -1.02 (0.12), residues: 1716 loop : -1.31 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 547 TYR 0.014 0.001 TYR E 154 PHE 0.017 0.001 PHE E 858 TRP 0.010 0.001 TRP C 574 HIS 0.003 0.001 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00307 (38616) covalent geometry : angle 0.58313 (52404) hydrogen bonds : bond 0.03621 ( 1158) hydrogen bonds : angle 6.97720 ( 2898) *********************** 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 608 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 499 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 PHE cc_start: 0.8864 (m-80) cc_final: 0.8449 (m-10) REVERT: A 239 LYS cc_start: 0.5657 (ttmt) cc_final: 0.5155 (tttp) REVERT: A 240 LEU cc_start: 0.7562 (tt) cc_final: 0.7228 (tp) REVERT: A 312 LYS cc_start: 0.8795 (tttt) cc_final: 0.8576 (ttpt) REVERT: A 397 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9031 (pp) REVERT: A 716 GLN cc_start: 0.8666 (tt0) cc_final: 0.8320 (pt0) REVERT: A 731 ASP cc_start: 0.8659 (t0) cc_final: 0.7860 (p0) REVERT: A 797 ARG cc_start: 0.8843 (ptt-90) cc_final: 0.8623 (ttp-170) REVERT: A 804 ASN cc_start: 0.7202 (m110) cc_final: 0.6630 (m110) REVERT: B 51 ILE cc_start: 0.8283 (mt) cc_final: 0.7908 (mt) REVERT: B 120 VAL cc_start: 0.8466 (p) cc_final: 0.8223 (m) REVERT: B 145 PHE cc_start: 0.8150 (m-80) cc_final: 0.7041 (m-80) REVERT: B 224 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8495 (m) REVERT: B 240 LEU cc_start: 0.7729 (tt) cc_final: 0.7366 (tp) REVERT: B 312 LYS cc_start: 0.8743 (tttt) cc_final: 0.8497 (ttpt) REVERT: B 397 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8687 (pp) REVERT: B 518 SER cc_start: 0.9253 (m) cc_final: 0.8826 (p) REVERT: B 556 ASP cc_start: 0.8806 (m-30) cc_final: 0.8457 (m-30) REVERT: B 687 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8334 (tm-30) REVERT: B 722 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8419 (mm-30) REVERT: B 801 LEU cc_start: 0.9071 (mp) cc_final: 0.8851 (mp) REVERT: B 804 ASN cc_start: 0.7065 (m110) cc_final: 0.6663 (m110) REVERT: B 858 PHE cc_start: 0.7712 (m-10) cc_final: 0.7382 (m-80) REVERT: C 98 MET cc_start: 0.8416 (mmt) cc_final: 0.8156 (mmp) REVERT: C 135 MET cc_start: 0.7060 (ttp) cc_final: 0.6661 (ttp) REVERT: C 240 LEU cc_start: 0.7736 (tt) cc_final: 0.7349 (tp) REVERT: C 347 LYS cc_start: 0.5840 (tptp) cc_final: 0.5597 (ptpp) REVERT: C 383 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8147 (mm-30) REVERT: C 491 MET cc_start: 0.8469 (mmt) cc_final: 0.8168 (mmt) REVERT: C 503 LYS cc_start: 0.9098 (mttt) cc_final: 0.8745 (mtpp) REVERT: C 518 SER cc_start: 0.9051 (m) cc_final: 0.8684 (p) REVERT: C 665 THR cc_start: 0.8957 (t) cc_final: 0.8682 (p) REVERT: C 716 GLN cc_start: 0.8533 (tt0) cc_final: 0.8261 (pt0) REVERT: C 731 ASP cc_start: 0.8907 (t0) cc_final: 0.7342 (p0) REVERT: C 795 SER cc_start: 0.8454 (m) cc_final: 0.8107 (t) REVERT: C 804 ASN cc_start: 0.6962 (m110) cc_final: 0.6435 (m110) REVERT: C 858 PHE cc_start: 0.7967 (m-10) cc_final: 0.7648 (m-10) REVERT: D 54 MET cc_start: 0.5666 (ttp) cc_final: 0.5255 (ttt) REVERT: D 108 PHE cc_start: 0.8840 (m-80) cc_final: 0.8414 (m-10) REVERT: D 239 LYS cc_start: 0.5960 (ttmt) cc_final: 0.5564 (tttp) REVERT: D 240 LEU cc_start: 0.7748 (tt) cc_final: 0.7380 (tp) REVERT: D 312 LYS cc_start: 0.8836 (tttt) cc_final: 0.8618 (ttpt) REVERT: D 397 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9040 (pp) REVERT: D 538 PHE cc_start: 0.6713 (t80) cc_final: 0.6477 (t80) REVERT: D 716 GLN cc_start: 0.8851 (tt0) cc_final: 0.8395 (pt0) REVERT: D 731 ASP cc_start: 0.8682 (t0) cc_final: 0.7855 (p0) REVERT: D 798 TYR cc_start: 0.9188 (m-10) cc_final: 0.8749 (m-10) REVERT: E 145 PHE cc_start: 0.8161 (m-80) cc_final: 0.7156 (m-80) REVERT: E 224 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8697 (m) REVERT: E 240 LEU cc_start: 0.7704 (tt) cc_final: 0.7310 (tp) REVERT: E 243 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6083 (mm) REVERT: E 397 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8663 (pp) REVERT: E 503 LYS cc_start: 0.9044 (mttt) cc_final: 0.8602 (mtpp) REVERT: E 518 SER cc_start: 0.9083 (m) cc_final: 0.8698 (p) REVERT: E 556 ASP cc_start: 0.8820 (m-30) cc_final: 0.8474 (m-30) REVERT: E 672 ARG cc_start: 0.8667 (mtm-85) cc_final: 0.8305 (ptt180) REVERT: E 804 ASN cc_start: 0.7041 (m110) cc_final: 0.6624 (m110) REVERT: F 239 LYS cc_start: 0.6918 (ttmt) cc_final: 0.6189 (tttp) REVERT: F 240 LEU cc_start: 0.8034 (tt) cc_final: 0.7648 (tp) REVERT: F 312 LYS cc_start: 0.8868 (tttt) cc_final: 0.8630 (ttpt) REVERT: F 491 MET cc_start: 0.8251 (tpp) cc_final: 0.8038 (mmt) REVERT: F 503 LYS cc_start: 0.9003 (mttt) cc_final: 0.8624 (mtpp) REVERT: F 518 SER cc_start: 0.9173 (m) cc_final: 0.8839 (p) REVERT: F 666 LEU cc_start: 0.8745 (mp) cc_final: 0.8529 (mt) REVERT: F 731 ASP cc_start: 0.9029 (t0) cc_final: 0.8029 (p0) REVERT: F 795 SER cc_start: 0.8582 (m) cc_final: 0.8237 (t) REVERT: F 804 ASN cc_start: 0.6901 (m110) cc_final: 0.6242 (m110) REVERT: F 858 PHE cc_start: 0.7702 (m-10) cc_final: 0.7291 (m-80) outliers start: 109 outliers final: 70 residues processed: 571 average time/residue: 0.2165 time to fit residues: 199.7782 Evaluate side-chains 559 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 482 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 331 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 397 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 208 optimal weight: 7.9990 chunk 447 optimal weight: 0.9990 chunk 326 optimal weight: 50.0000 chunk 213 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 431 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 281 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN B 584 ASN B 636 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 584 ASN ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN E 636 GLN F 158 ASN F 584 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.184781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135421 restraints weight = 49536.675| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.17 r_work: 0.3248 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38616 Z= 0.175 Angle : 0.610 12.376 52404 Z= 0.311 Chirality : 0.046 0.187 6060 Planarity : 0.004 0.046 6822 Dihedral : 4.852 20.379 5358 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.93 % Allowed : 12.84 % Favored : 84.24 % 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 aren not related in a simple way. whole: -1.87 (0.11), residues: 4980 helix: -2.09 (0.22), residues: 474 sheet: -1.03 (0.12), residues: 1638 loop : -1.17 (0.11), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 547 TYR 0.015 0.001 TYR D 154 PHE 0.015 0.002 PHE D 253 TRP 0.011 0.001 TRP D 222 HIS 0.004 0.001 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00420 (38616) covalent geometry : angle 0.60959 (52404) hydrogen bonds : bond 0.03777 ( 1158) hydrogen bonds : angle 6.95121 ( 2898) *********************** 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 629 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 509 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.5786 (ttp) cc_final: 0.5443 (ttt) REVERT: A 108 PHE cc_start: 0.8802 (m-80) cc_final: 0.8425 (m-10) REVERT: A 239 LYS cc_start: 0.5735 (ttmt) cc_final: 0.5319 (tttp) REVERT: A 240 LEU cc_start: 0.7714 (tt) cc_final: 0.7355 (tp) REVERT: A 397 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9038 (pp) REVERT: A 716 GLN cc_start: 0.8670 (tt0) cc_final: 0.8331 (pt0) REVERT: A 804 ASN cc_start: 0.7139 (m110) cc_final: 0.6570 (m-40) REVERT: B 120 VAL cc_start: 0.8558 (p) cc_final: 0.8289 (m) REVERT: B 145 PHE cc_start: 0.8285 (m-80) cc_final: 0.7313 (m-80) REVERT: B 224 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8451 (m) REVERT: B 240 LEU cc_start: 0.7921 (tt) cc_final: 0.7522 (tp) REVERT: B 397 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8748 (pp) REVERT: B 411 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8387 (mt) REVERT: B 518 SER cc_start: 0.9268 (m) cc_final: 0.8875 (p) REVERT: B 556 ASP cc_start: 0.8798 (m-30) cc_final: 0.8496 (m-30) REVERT: B 666 LEU cc_start: 0.9070 (mp) cc_final: 0.8843 (mp) REVERT: B 687 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 722 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8383 (mm-30) REVERT: B 801 LEU cc_start: 0.9132 (mp) cc_final: 0.8930 (mp) REVERT: B 804 ASN cc_start: 0.7081 (m110) cc_final: 0.6701 (m-40) REVERT: C 98 MET cc_start: 0.8162 (mmt) cc_final: 0.7937 (mmp) REVERT: C 135 MET cc_start: 0.7295 (ttp) cc_final: 0.6932 (ttp) REVERT: C 240 LEU cc_start: 0.7931 (tt) cc_final: 0.7513 (tp) REVERT: C 503 LYS cc_start: 0.9140 (mttt) cc_final: 0.8885 (mtpp) REVERT: C 518 SER cc_start: 0.8862 (m) cc_final: 0.8496 (p) REVERT: C 716 GLN cc_start: 0.8598 (tt0) cc_final: 0.8358 (pt0) REVERT: C 795 SER cc_start: 0.8610 (m) cc_final: 0.8269 (t) REVERT: C 804 ASN cc_start: 0.7079 (m110) cc_final: 0.6626 (m110) REVERT: D 54 MET cc_start: 0.5594 (ttp) cc_final: 0.5227 (ttt) REVERT: D 108 PHE cc_start: 0.8751 (m-80) cc_final: 0.8314 (m-10) REVERT: D 239 LYS cc_start: 0.5943 (ttmt) cc_final: 0.5634 (tttp) REVERT: D 240 LEU cc_start: 0.7941 (tt) cc_final: 0.7512 (tp) REVERT: D 383 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8137 (mm-30) REVERT: D 397 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9034 (pp) REVERT: D 477 ILE cc_start: 0.7437 (pp) cc_final: 0.7185 (pt) REVERT: D 716 GLN cc_start: 0.8877 (tt0) cc_final: 0.8466 (pt0) REVERT: E 224 VAL cc_start: 0.8912 (OUTLIER) cc_final: 0.8689 (m) REVERT: E 240 LEU cc_start: 0.7890 (tt) cc_final: 0.7491 (tp) REVERT: E 397 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8742 (pp) REVERT: E 411 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8399 (mt) REVERT: E 503 LYS cc_start: 0.9080 (mttt) cc_final: 0.8743 (mtpp) REVERT: E 518 SER cc_start: 0.9216 (m) cc_final: 0.8849 (p) REVERT: E 556 ASP cc_start: 0.8832 (m-30) cc_final: 0.8575 (m-30) REVERT: E 672 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8082 (ptt180) REVERT: E 801 LEU cc_start: 0.9033 (mp) cc_final: 0.8781 (mp) REVERT: E 804 ASN cc_start: 0.7080 (m110) cc_final: 0.6744 (m-40) REVERT: E 830 PHE cc_start: 0.7056 (p90) cc_final: 0.6532 (p90) REVERT: E 858 PHE cc_start: 0.7292 (m-10) cc_final: 0.7084 (m-10) REVERT: F 107 GLN cc_start: 0.8662 (mp10) cc_final: 0.8252 (mp10) REVERT: F 239 LYS cc_start: 0.7105 (ttmt) cc_final: 0.6268 (tttm) REVERT: F 240 LEU cc_start: 0.8100 (tt) cc_final: 0.7751 (tp) REVERT: F 503 LYS cc_start: 0.9052 (mttt) cc_final: 0.8736 (mtpp) REVERT: F 518 SER cc_start: 0.9061 (m) cc_final: 0.8757 (p) REVERT: F 731 ASP cc_start: 0.8870 (t0) cc_final: 0.7964 (p0) REVERT: F 795 SER cc_start: 0.8522 (m) cc_final: 0.8229 (t) REVERT: F 804 ASN cc_start: 0.6995 (m110) cc_final: 0.6352 (m110) REVERT: F 830 PHE cc_start: 0.6602 (p90) cc_final: 0.6380 (p90) outliers start: 120 outliers final: 79 residues processed: 593 average time/residue: 0.2087 time to fit residues: 200.2936 Evaluate side-chains 566 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 479 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 512 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 512 LEU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 752 VAL Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 63 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 chunk 454 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 337 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 327 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN B 702 GLN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 832 GLN D 130 ASN D 804 ASN E 130 ASN F 158 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.185235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136454 restraints weight = 49492.418| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.10 r_work: 0.3235 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38616 Z= 0.179 Angle : 0.620 14.491 52404 Z= 0.313 Chirality : 0.046 0.181 6060 Planarity : 0.004 0.058 6822 Dihedral : 4.873 19.840 5358 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.81 % Allowed : 13.71 % Favored : 83.48 % 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 aren not related in a simple way. whole: -1.85 (0.11), residues: 4980 helix: -2.04 (0.22), residues: 474 sheet: -1.09 (0.12), residues: 1614 loop : -1.12 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 725 TYR 0.018 0.001 TYR D 798 PHE 0.026 0.002 PHE B 858 TRP 0.012 0.001 TRP D 222 HIS 0.003 0.001 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00430 (38616) covalent geometry : angle 0.62011 (52404) hydrogen bonds : bond 0.03737 ( 1158) hydrogen bonds : angle 6.90428 ( 2898) *********************** 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 618 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 503 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.5485 (ttp) cc_final: 0.5133 (ttt) REVERT: A 108 PHE cc_start: 0.8756 (m-80) cc_final: 0.8429 (m-10) REVERT: A 239 LYS cc_start: 0.5739 (ttmt) cc_final: 0.5328 (tttp) REVERT: A 240 LEU cc_start: 0.7779 (tt) cc_final: 0.7417 (tp) REVERT: A 397 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9054 (pp) REVERT: A 477 ILE cc_start: 0.7534 (OUTLIER) cc_final: 0.7280 (pt) REVERT: A 716 GLN cc_start: 0.8631 (tt0) cc_final: 0.8281 (pt0) REVERT: A 725 ARG cc_start: 0.7060 (mmm160) cc_final: 0.6750 (mmp80) REVERT: A 804 ASN cc_start: 0.7113 (m110) cc_final: 0.6549 (m-40) REVERT: B 120 VAL cc_start: 0.8589 (p) cc_final: 0.8326 (m) REVERT: B 145 PHE cc_start: 0.8304 (m-80) cc_final: 0.7347 (m-80) REVERT: B 224 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8478 (m) REVERT: B 240 LEU cc_start: 0.7909 (tt) cc_final: 0.7480 (tp) REVERT: B 397 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8726 (pp) REVERT: B 411 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8391 (mt) REVERT: B 518 SER cc_start: 0.9120 (m) cc_final: 0.8756 (p) REVERT: B 556 ASP cc_start: 0.8734 (m-30) cc_final: 0.8472 (m-30) REVERT: B 687 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8328 (tm-30) REVERT: B 801 LEU cc_start: 0.9157 (mp) cc_final: 0.8933 (mp) REVERT: B 804 ASN cc_start: 0.7010 (m110) cc_final: 0.6698 (m-40) REVERT: C 135 MET cc_start: 0.7337 (ttp) cc_final: 0.6962 (ttp) REVERT: C 240 LEU cc_start: 0.7938 (tt) cc_final: 0.7498 (tp) REVERT: C 503 LYS cc_start: 0.9137 (mttt) cc_final: 0.8847 (mtpp) REVERT: C 518 SER cc_start: 0.8892 (m) cc_final: 0.8514 (p) REVERT: C 666 LEU cc_start: 0.8717 (mp) cc_final: 0.8501 (mt) REVERT: C 716 GLN cc_start: 0.8678 (tt0) cc_final: 0.8426 (pt0) REVERT: C 795 SER cc_start: 0.8628 (m) cc_final: 0.8295 (t) REVERT: C 804 ASN cc_start: 0.6971 (m110) cc_final: 0.6559 (m110) REVERT: C 858 PHE cc_start: 0.7585 (m-10) cc_final: 0.7236 (m-10) REVERT: D 54 MET cc_start: 0.5628 (ttp) cc_final: 0.5264 (ttt) REVERT: D 108 PHE cc_start: 0.8715 (m-80) cc_final: 0.8325 (m-10) REVERT: D 239 LYS cc_start: 0.5986 (ttmt) cc_final: 0.5569 (tttp) REVERT: D 240 LEU cc_start: 0.7821 (tt) cc_final: 0.7407 (tp) REVERT: D 383 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8083 (mm-30) REVERT: D 397 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9051 (pp) REVERT: D 477 ILE cc_start: 0.7470 (OUTLIER) cc_final: 0.7224 (pt) REVERT: D 716 GLN cc_start: 0.8708 (tt0) cc_final: 0.8248 (pt0) REVERT: D 725 ARG cc_start: 0.6967 (mmm160) cc_final: 0.6676 (mmp80) REVERT: D 804 ASN cc_start: 0.7258 (m110) cc_final: 0.6773 (m-40) REVERT: E 145 PHE cc_start: 0.8291 (m-80) cc_final: 0.7391 (m-80) REVERT: E 224 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8676 (m) REVERT: E 240 LEU cc_start: 0.7872 (tt) cc_final: 0.7431 (tp) REVERT: E 324 GLU cc_start: 0.7890 (pt0) cc_final: 0.7500 (pt0) REVERT: E 397 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8711 (pp) REVERT: E 411 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8387 (mt) REVERT: E 503 LYS cc_start: 0.9057 (mttt) cc_final: 0.8719 (mtpp) REVERT: E 518 SER cc_start: 0.9156 (m) cc_final: 0.8800 (p) REVERT: E 556 ASP cc_start: 0.8761 (m-30) cc_final: 0.8459 (m-30) REVERT: E 672 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8049 (ptt180) REVERT: E 801 LEU cc_start: 0.8993 (mp) cc_final: 0.8725 (mp) REVERT: E 804 ASN cc_start: 0.7120 (m110) cc_final: 0.6778 (m-40) REVERT: E 830 PHE cc_start: 0.7032 (p90) cc_final: 0.6585 (p90) REVERT: F 98 MET cc_start: 0.7994 (mmt) cc_final: 0.7731 (mmp) REVERT: F 107 GLN cc_start: 0.8724 (mp10) cc_final: 0.8243 (mp10) REVERT: F 239 LYS cc_start: 0.7124 (ttmt) cc_final: 0.6283 (tttm) REVERT: F 240 LEU cc_start: 0.8078 (tt) cc_final: 0.7719 (tp) REVERT: F 503 LYS cc_start: 0.9051 (mttt) cc_final: 0.8763 (mtpp) REVERT: F 518 SER cc_start: 0.9047 (m) cc_final: 0.8724 (p) REVERT: F 795 SER cc_start: 0.8542 (m) cc_final: 0.8270 (t) REVERT: F 804 ASN cc_start: 0.6994 (m110) cc_final: 0.6403 (m110) REVERT: F 830 PHE cc_start: 0.6715 (p90) cc_final: 0.6455 (p90) outliers start: 115 outliers final: 84 residues processed: 581 average time/residue: 0.2279 time to fit residues: 213.6650 Evaluate side-chains 566 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 472 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 829 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 752 VAL Chi-restraints excluded: chain E residue 829 THR Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 249 optimal weight: 10.0000 chunk 252 optimal weight: 4.9990 chunk 375 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 466 optimal weight: 0.1980 chunk 486 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 323 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 HIS ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.183795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.133279 restraints weight = 49074.478| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.00 r_work: 0.3248 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38616 Z= 0.176 Angle : 0.628 15.545 52404 Z= 0.315 Chirality : 0.046 0.173 6060 Planarity : 0.004 0.051 6822 Dihedral : 4.868 21.271 5358 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.93 % Allowed : 14.08 % Favored : 82.99 % 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 aren not related in a simple way. whole: -1.90 (0.11), residues: 4980 helix: -2.15 (0.21), residues: 510 sheet: -1.08 (0.12), residues: 1614 loop : -1.14 (0.11), residues: 2856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 725 TYR 0.022 0.001 TYR D 798 PHE 0.028 0.002 PHE E 858 TRP 0.011 0.001 TRP D 222 HIS 0.003 0.001 HIS F 558 Details of bonding type rmsd covalent geometry : bond 0.00423 (38616) covalent geometry : angle 0.62776 (52404) hydrogen bonds : bond 0.03698 ( 1158) hydrogen bonds : angle 6.84910 ( 2898) *********************** 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 610 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 490 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.5498 (ttp) cc_final: 0.5162 (ttt) REVERT: A 108 PHE cc_start: 0.8769 (m-80) cc_final: 0.8399 (m-10) REVERT: A 239 LYS cc_start: 0.5731 (ttmt) cc_final: 0.5315 (tttp) REVERT: A 240 LEU cc_start: 0.7780 (tt) cc_final: 0.7434 (tp) REVERT: A 397 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9051 (pp) REVERT: A 477 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7268 (pt) REVERT: A 716 GLN cc_start: 0.8610 (tt0) cc_final: 0.8274 (pt0) REVERT: A 804 ASN cc_start: 0.7122 (m110) cc_final: 0.6569 (m-40) REVERT: B 120 VAL cc_start: 0.8496 (p) cc_final: 0.8247 (m) REVERT: B 145 PHE cc_start: 0.8329 (m-80) cc_final: 0.7365 (m-80) REVERT: B 224 VAL cc_start: 0.8694 (OUTLIER) cc_final: 0.8464 (m) REVERT: B 240 LEU cc_start: 0.7891 (tt) cc_final: 0.7466 (tp) REVERT: B 397 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8710 (pp) REVERT: B 411 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8452 (mt) REVERT: B 477 ILE cc_start: 0.7192 (OUTLIER) cc_final: 0.6829 (pp) REVERT: B 518 SER cc_start: 0.9123 (m) cc_final: 0.8749 (p) REVERT: B 556 ASP cc_start: 0.8734 (m-30) cc_final: 0.8478 (m-30) REVERT: B 687 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8308 (tm-30) REVERT: B 804 ASN cc_start: 0.7002 (m110) cc_final: 0.6682 (m-40) REVERT: C 54 MET cc_start: 0.5147 (ttm) cc_final: 0.4714 (ttm) REVERT: C 135 MET cc_start: 0.7363 (ttp) cc_final: 0.6985 (ttp) REVERT: C 240 LEU cc_start: 0.7922 (tt) cc_final: 0.7484 (tp) REVERT: C 352 ASP cc_start: 0.5308 (m-30) cc_final: 0.5064 (t0) REVERT: C 491 MET cc_start: 0.8388 (mmt) cc_final: 0.8088 (mmt) REVERT: C 503 LYS cc_start: 0.9112 (mttt) cc_final: 0.8911 (mtpp) REVERT: C 518 SER cc_start: 0.8870 (m) cc_final: 0.8490 (p) REVERT: C 716 GLN cc_start: 0.8645 (tt0) cc_final: 0.8415 (pt0) REVERT: C 795 SER cc_start: 0.8713 (m) cc_final: 0.8379 (t) REVERT: C 804 ASN cc_start: 0.6952 (m110) cc_final: 0.6535 (m110) REVERT: C 858 PHE cc_start: 0.7689 (m-10) cc_final: 0.7444 (m-10) REVERT: D 54 MET cc_start: 0.5634 (ttp) cc_final: 0.5262 (ttt) REVERT: D 108 PHE cc_start: 0.8668 (m-80) cc_final: 0.8307 (m-10) REVERT: D 239 LYS cc_start: 0.5988 (ttmt) cc_final: 0.5589 (tttp) REVERT: D 240 LEU cc_start: 0.7750 (tt) cc_final: 0.7352 (tp) REVERT: D 383 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8107 (mm-30) REVERT: D 397 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9032 (pp) REVERT: D 477 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.7195 (pt) REVERT: D 716 GLN cc_start: 0.8824 (tt0) cc_final: 0.8390 (pt0) REVERT: D 785 SER cc_start: 0.7959 (m) cc_final: 0.7627 (p) REVERT: E 145 PHE cc_start: 0.8300 (m-80) cc_final: 0.7435 (m-80) REVERT: E 224 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8674 (m) REVERT: E 240 LEU cc_start: 0.7752 (tt) cc_final: 0.7303 (tp) REVERT: E 324 GLU cc_start: 0.7999 (pt0) cc_final: 0.7638 (pt0) REVERT: E 397 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8693 (pp) REVERT: E 411 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8385 (mt) REVERT: E 503 LYS cc_start: 0.9043 (mttt) cc_final: 0.8707 (mtpp) REVERT: E 518 SER cc_start: 0.9121 (m) cc_final: 0.8749 (p) REVERT: E 556 ASP cc_start: 0.8752 (m-30) cc_final: 0.8460 (m-30) REVERT: E 672 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.8045 (ptt180) REVERT: E 801 LEU cc_start: 0.9052 (mp) cc_final: 0.8788 (mp) REVERT: E 804 ASN cc_start: 0.7127 (m110) cc_final: 0.6778 (m-40) REVERT: E 830 PHE cc_start: 0.7167 (p90) cc_final: 0.6646 (p90) REVERT: E 858 PHE cc_start: 0.7417 (m-10) cc_final: 0.7213 (m-80) REVERT: F 98 MET cc_start: 0.7845 (mmt) cc_final: 0.7558 (mmp) REVERT: F 107 GLN cc_start: 0.8722 (mp10) cc_final: 0.8223 (mp10) REVERT: F 239 LYS cc_start: 0.7120 (ttmt) cc_final: 0.6367 (tttp) REVERT: F 240 LEU cc_start: 0.7930 (tt) cc_final: 0.7547 (tp) REVERT: F 352 ASP cc_start: 0.5625 (m-30) cc_final: 0.5204 (t0) REVERT: F 411 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8910 (tt) REVERT: F 503 LYS cc_start: 0.9058 (mttt) cc_final: 0.8790 (mtpp) REVERT: F 518 SER cc_start: 0.9048 (m) cc_final: 0.8714 (p) REVERT: F 731 ASP cc_start: 0.8885 (t0) cc_final: 0.8011 (p0) REVERT: F 795 SER cc_start: 0.8560 (m) cc_final: 0.8265 (t) REVERT: F 804 ASN cc_start: 0.6947 (m110) cc_final: 0.6383 (m110) REVERT: F 830 PHE cc_start: 0.6790 (p90) cc_final: 0.6511 (p90) outliers start: 120 outliers final: 92 residues processed: 572 average time/residue: 0.2452 time to fit residues: 224.8641 Evaluate side-chains 569 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 465 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 752 VAL Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 247 optimal weight: 0.3980 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.5980 chunk 114 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 429 optimal weight: 1.9990 chunk 228 optimal weight: 9.9990 chunk 445 optimal weight: 2.9990 chunk 411 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 831 ASN ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 673 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.184651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.134286 restraints weight = 49594.987| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.03 r_work: 0.3251 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 38616 Z= 0.148 Angle : 0.618 15.892 52404 Z= 0.308 Chirality : 0.046 0.174 6060 Planarity : 0.004 0.062 6822 Dihedral : 4.764 19.635 5358 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.78 % Allowed : 14.47 % Favored : 82.75 % 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 aren not related in a simple way. whole: -1.82 (0.11), residues: 4980 helix: -2.14 (0.22), residues: 474 sheet: -1.03 (0.12), residues: 1614 loop : -1.10 (0.11), residues: 2892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 725 TYR 0.013 0.001 TYR E 154 PHE 0.021 0.001 PHE B 858 TRP 0.010 0.001 TRP C 574 HIS 0.003 0.001 HIS E 558 Details of bonding type rmsd covalent geometry : bond 0.00354 (38616) covalent geometry : angle 0.61778 (52404) hydrogen bonds : bond 0.03546 ( 1158) hydrogen bonds : angle 6.76072 ( 2898) *********************** 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 604 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 490 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.5412 (ttp) cc_final: 0.5046 (ttt) REVERT: A 108 PHE cc_start: 0.8708 (m-80) cc_final: 0.8407 (m-10) REVERT: A 239 LYS cc_start: 0.5713 (ttmt) cc_final: 0.5295 (tttp) REVERT: A 240 LEU cc_start: 0.7691 (tt) cc_final: 0.7366 (tp) REVERT: A 397 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9042 (pp) REVERT: A 411 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 477 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7242 (pt) REVERT: A 678 LYS cc_start: 0.8837 (ttpp) cc_final: 0.8573 (ttpp) REVERT: A 716 GLN cc_start: 0.8621 (tt0) cc_final: 0.8242 (pt0) REVERT: A 722 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 804 ASN cc_start: 0.7124 (m110) cc_final: 0.6584 (m-40) REVERT: B 120 VAL cc_start: 0.8498 (p) cc_final: 0.8242 (m) REVERT: B 145 PHE cc_start: 0.8297 (m-80) cc_final: 0.7349 (m-80) REVERT: B 224 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8481 (m) REVERT: B 240 LEU cc_start: 0.7772 (tt) cc_final: 0.7367 (tp) REVERT: B 397 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8630 (pp) REVERT: B 411 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 518 SER cc_start: 0.9121 (m) cc_final: 0.8748 (p) REVERT: B 556 ASP cc_start: 0.8740 (m-30) cc_final: 0.8507 (m-30) REVERT: B 687 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8319 (tm-30) REVERT: B 785 SER cc_start: 0.7966 (m) cc_final: 0.7494 (p) REVERT: B 804 ASN cc_start: 0.7008 (m110) cc_final: 0.6689 (m-40) REVERT: C 54 MET cc_start: 0.5204 (ttm) cc_final: 0.4757 (ttm) REVERT: C 135 MET cc_start: 0.7351 (ttp) cc_final: 0.6977 (ttp) REVERT: C 240 LEU cc_start: 0.7901 (tt) cc_final: 0.7474 (tp) REVERT: C 352 ASP cc_start: 0.5628 (m-30) cc_final: 0.5319 (t0) REVERT: C 491 MET cc_start: 0.8307 (mmt) cc_final: 0.7958 (mmt) REVERT: C 503 LYS cc_start: 0.9133 (mttt) cc_final: 0.8855 (mtpp) REVERT: C 518 SER cc_start: 0.8816 (m) cc_final: 0.8427 (p) REVERT: C 687 GLN cc_start: 0.8433 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 716 GLN cc_start: 0.8637 (tt0) cc_final: 0.8422 (pt0) REVERT: C 795 SER cc_start: 0.8613 (m) cc_final: 0.8307 (t) REVERT: C 804 ASN cc_start: 0.6964 (m110) cc_final: 0.6541 (m110) REVERT: D 54 MET cc_start: 0.5628 (ttp) cc_final: 0.5249 (ttt) REVERT: D 108 PHE cc_start: 0.8582 (m-80) cc_final: 0.8239 (m-10) REVERT: D 239 LYS cc_start: 0.5908 (ttmt) cc_final: 0.5497 (tttp) REVERT: D 240 LEU cc_start: 0.7777 (tt) cc_final: 0.7391 (tp) REVERT: D 383 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8171 (mm-30) REVERT: D 397 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9049 (pp) REVERT: D 477 ILE cc_start: 0.7437 (OUTLIER) cc_final: 0.7166 (pt) REVERT: D 716 GLN cc_start: 0.8672 (tt0) cc_final: 0.8214 (pt0) REVERT: D 785 SER cc_start: 0.7960 (m) cc_final: 0.7660 (p) REVERT: D 804 ASN cc_start: 0.8564 (t0) cc_final: 0.8344 (m-40) REVERT: E 224 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 240 LEU cc_start: 0.7711 (tt) cc_final: 0.7305 (tp) REVERT: E 324 GLU cc_start: 0.8013 (pt0) cc_final: 0.7734 (pt0) REVERT: E 397 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8618 (pp) REVERT: E 411 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8369 (mt) REVERT: E 503 LYS cc_start: 0.9034 (mttt) cc_final: 0.8705 (mtpp) REVERT: E 518 SER cc_start: 0.9052 (m) cc_final: 0.8731 (p) REVERT: E 556 ASP cc_start: 0.8750 (m-30) cc_final: 0.8466 (m-30) REVERT: E 672 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8008 (ptt180) REVERT: E 787 ARG cc_start: 0.7429 (mmt180) cc_final: 0.7107 (mmp80) REVERT: E 801 LEU cc_start: 0.9043 (mp) cc_final: 0.8773 (mp) REVERT: E 804 ASN cc_start: 0.7064 (m110) cc_final: 0.6788 (m-40) REVERT: E 858 PHE cc_start: 0.7514 (m-10) cc_final: 0.7283 (m-80) REVERT: F 107 GLN cc_start: 0.8729 (mp10) cc_final: 0.8210 (mp10) REVERT: F 239 LYS cc_start: 0.7119 (ttmt) cc_final: 0.6388 (tttp) REVERT: F 240 LEU cc_start: 0.7914 (tt) cc_final: 0.7522 (tp) REVERT: F 352 ASP cc_start: 0.5323 (m-30) cc_final: 0.5055 (t0) REVERT: F 503 LYS cc_start: 0.9073 (mttt) cc_final: 0.8801 (mtpp) REVERT: F 518 SER cc_start: 0.9027 (m) cc_final: 0.8684 (p) REVERT: F 687 GLN cc_start: 0.8389 (tm-30) cc_final: 0.8051 (tm-30) REVERT: F 731 ASP cc_start: 0.8897 (t0) cc_final: 0.7789 (p0) REVERT: F 795 SER cc_start: 0.8580 (m) cc_final: 0.8288 (t) REVERT: F 804 ASN cc_start: 0.6984 (m110) cc_final: 0.6455 (m110) REVERT: F 830 PHE cc_start: 0.6762 (p90) cc_final: 0.6483 (p90) outliers start: 114 outliers final: 91 residues processed: 567 average time/residue: 0.2496 time to fit residues: 227.6051 Evaluate side-chains 568 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 466 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 477 ILE Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 670 THR Chi-restraints excluded: chain E residue 675 VAL Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 123 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 477 ILE Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 670 THR Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 37 optimal weight: 3.9990 chunk 457 optimal weight: 9.9990 chunk 233 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 399 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 180 optimal weight: 0.7980 chunk 274 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 673 ASN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 831 ASN ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN ** F 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 673 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.186383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136374 restraints weight = 48339.015| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.06 r_work: 0.3247 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38616 Z= 0.119 Angle : 0.607 14.401 52404 Z= 0.302 Chirality : 0.045 0.173 6060 Planarity : 0.004 0.046 6822 Dihedral : 4.589 24.154 5358 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.44 % Allowed : 15.15 % Favored : 82.41 % 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 aren not related in a simple way. whole: -1.87 (0.11), residues: 4980 helix: -2.23 (0.21), residues: 510 sheet: -0.98 (0.12), residues: 1644 loop : -1.15 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 725 TYR 0.013 0.001 TYR B 154 PHE 0.022 0.001 PHE C 858 TRP 0.010 0.001 TRP C 574 HIS 0.004 0.001 HIS D 800 Details of bonding type rmsd covalent geometry : bond 0.00286 (38616) covalent geometry : angle 0.60729 (52404) hydrogen bonds : bond 0.03365 ( 1158) hydrogen bonds : angle 6.68003 ( 2898) ********************** 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 579 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 479 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.5478 (ttp) cc_final: 0.5111 (ttt) REVERT: A 239 LYS cc_start: 0.5676 (ttmt) cc_final: 0.5228 (tttp) REVERT: A 240 LEU cc_start: 0.7720 (tt) cc_final: 0.7382 (tp) REVERT: A 397 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9017 (pp) REVERT: A 411 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 678 LYS cc_start: 0.8802 (ttpp) cc_final: 0.8478 (ttmm) REVERT: A 716 GLN cc_start: 0.8639 (tt0) cc_final: 0.8227 (pt0) REVERT: A 722 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 804 ASN cc_start: 0.7190 (m110) cc_final: 0.6685 (m-40) REVERT: B 67 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8151 (mmt180) REVERT: B 120 VAL cc_start: 0.8504 (p) cc_final: 0.8256 (m) REVERT: B 145 PHE cc_start: 0.8244 (m-80) cc_final: 0.7253 (m-80) REVERT: B 224 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8469 (m) REVERT: B 240 LEU cc_start: 0.7657 (tt) cc_final: 0.7249 (tp) REVERT: B 397 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8526 (pp) REVERT: B 411 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8441 (mt) REVERT: B 518 SER cc_start: 0.9038 (m) cc_final: 0.8656 (p) REVERT: B 556 ASP cc_start: 0.8684 (m-30) cc_final: 0.8420 (m-30) REVERT: B 687 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8516 (tm-30) REVERT: B 804 ASN cc_start: 0.6950 (m110) cc_final: 0.6639 (m-40) REVERT: C 54 MET cc_start: 0.5165 (ttm) cc_final: 0.4720 (ttm) REVERT: C 135 MET cc_start: 0.7187 (ttp) cc_final: 0.6797 (ttp) REVERT: C 240 LEU cc_start: 0.7737 (tt) cc_final: 0.7337 (tp) REVERT: C 312 LYS cc_start: 0.8823 (tttt) cc_final: 0.8565 (ttpt) REVERT: C 352 ASP cc_start: 0.5482 (m-30) cc_final: 0.5234 (t0) REVERT: C 477 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7378 (tp) REVERT: C 491 MET cc_start: 0.8231 (mmt) cc_final: 0.7884 (mmt) REVERT: C 503 LYS cc_start: 0.9068 (mttt) cc_final: 0.8867 (mtpp) REVERT: C 518 SER cc_start: 0.8692 (m) cc_final: 0.8311 (p) REVERT: C 687 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8115 (tm-30) REVERT: C 716 GLN cc_start: 0.8620 (tt0) cc_final: 0.8415 (pt0) REVERT: C 731 ASP cc_start: 0.8766 (t0) cc_final: 0.7628 (p0) REVERT: C 804 ASN cc_start: 0.7033 (m110) cc_final: 0.6590 (m110) REVERT: C 858 PHE cc_start: 0.7679 (m-10) cc_final: 0.7404 (m-80) REVERT: D 54 MET cc_start: 0.5585 (ttp) cc_final: 0.5210 (ttt) REVERT: D 108 PHE cc_start: 0.8540 (m-80) cc_final: 0.8294 (m-10) REVERT: D 239 LYS cc_start: 0.5943 (ttmt) cc_final: 0.5510 (tttp) REVERT: D 240 LEU cc_start: 0.7736 (tt) cc_final: 0.7391 (tp) REVERT: D 383 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8062 (mm-30) REVERT: D 397 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.9017 (pp) REVERT: D 678 LYS cc_start: 0.8775 (ttpp) cc_final: 0.8452 (ttmm) REVERT: D 716 GLN cc_start: 0.8629 (tt0) cc_final: 0.8197 (pt0) REVERT: D 785 SER cc_start: 0.7895 (m) cc_final: 0.7586 (p) REVERT: E 224 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8672 (m) REVERT: E 240 LEU cc_start: 0.7854 (tt) cc_final: 0.7422 (tp) REVERT: E 324 GLU cc_start: 0.8065 (pt0) cc_final: 0.7814 (pt0) REVERT: E 397 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8502 (pp) REVERT: E 411 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8411 (mt) REVERT: E 503 LYS cc_start: 0.9024 (mttt) cc_final: 0.8705 (mtpp) REVERT: E 518 SER cc_start: 0.8982 (m) cc_final: 0.8667 (p) REVERT: E 556 ASP cc_start: 0.8700 (m-30) cc_final: 0.8397 (m-30) REVERT: E 672 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8011 (ptt180) REVERT: E 787 ARG cc_start: 0.7481 (mmt180) cc_final: 0.6980 (mmp80) REVERT: E 801 LEU cc_start: 0.9028 (mp) cc_final: 0.8742 (mp) REVERT: E 804 ASN cc_start: 0.7074 (m110) cc_final: 0.6805 (m-40) REVERT: E 858 PHE cc_start: 0.7487 (m-10) cc_final: 0.7238 (m-80) REVERT: F 107 GLN cc_start: 0.8642 (mp10) cc_final: 0.8106 (mp10) REVERT: F 162 MET cc_start: 0.8361 (tpp) cc_final: 0.7848 (ttt) REVERT: F 239 LYS cc_start: 0.6746 (ttmt) cc_final: 0.6399 (tttp) REVERT: F 240 LEU cc_start: 0.7944 (tt) cc_final: 0.7644 (tp) REVERT: F 352 ASP cc_start: 0.5264 (m-30) cc_final: 0.5019 (t0) REVERT: F 503 LYS cc_start: 0.9004 (mttt) cc_final: 0.8733 (mtpp) REVERT: F 518 SER cc_start: 0.8959 (m) cc_final: 0.8626 (p) REVERT: F 687 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8146 (tm-30) REVERT: F 731 ASP cc_start: 0.8868 (t0) cc_final: 0.7947 (p0) REVERT: F 795 SER cc_start: 0.8605 (m) cc_final: 0.8307 (t) REVERT: F 804 ASN cc_start: 0.7002 (m110) cc_final: 0.6475 (m110) REVERT: F 858 PHE cc_start: 0.7204 (m-10) cc_final: 0.6962 (m-10) outliers start: 100 outliers final: 83 residues processed: 545 average time/residue: 0.2525 time to fit residues: 220.4004 Evaluate side-chains 551 residues out of total 4098 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 458 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 829 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 700 THR Chi-restraints excluded: chain B residue 846 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 524 LEU Chi-restraints excluded: chain C residue 567 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 675 VAL Chi-restraints excluded: chain C residue 697 SER Chi-restraints excluded: chain C residue 748 LEU Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 PHE Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 524 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 569 SER Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 637 ILE Chi-restraints excluded: chain D residue 670 THR Chi-restraints excluded: chain D residue 697 SER Chi-restraints excluded: chain D residue 700 THR Chi-restraints excluded: chain D residue 773 VAL Chi-restraints excluded: chain D residue 829 THR Chi-restraints excluded: chain D residue 830 PHE Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 331 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 397 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 467 GLU Chi-restraints excluded: chain E residue 524 LEU Chi-restraints excluded: chain E residue 697 SER Chi-restraints excluded: chain E residue 700 THR Chi-restraints excluded: chain E residue 748 LEU Chi-restraints excluded: chain E residue 846 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 502 GLU Chi-restraints excluded: chain F residue 509 LEU Chi-restraints excluded: chain F residue 524 LEU Chi-restraints excluded: chain F residue 567 LEU Chi-restraints excluded: chain F residue 626 SER Chi-restraints excluded: chain F residue 669 ILE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 697 SER Chi-restraints excluded: chain F residue 748 LEU Chi-restraints excluded: chain F residue 829 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 498 random chunks: chunk 196 optimal weight: 5.9990 chunk 251 optimal weight: 0.0370 chunk 450 optimal weight: 0.9980 chunk 326 optimal weight: 50.0000 chunk 128 optimal weight: 0.6980 chunk 218 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 408 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 406 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 overall best weight: 1.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN ** A 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 ASN F 636 GLN F 673 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135629 restraints weight = 48449.556| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.22 r_work: 0.3192 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 38616 Z= 0.173 Angle : 0.635 15.459 52404 Z= 0.316 Chirality : 0.046 0.173 6060 Planarity : 0.004 0.055 6822 Dihedral : 4.730 22.709 5358 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.59 % Allowed : 15.20 % Favored : 82.21 % 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 aren not related in a simple way. whole: -1.81 (0.11), residues: 4980 helix: -2.11 (0.22), residues: 474 sheet: -1.06 (0.12), residues: 1680 loop : -1.06 (0.11), residues: 2826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 725 TYR 0.014 0.001 TYR F 154 PHE 0.020 0.002 PHE D 858 TRP 0.011 0.001 TRP D 222 HIS 0.003 0.001 HIS D 558 Details of bonding type rmsd covalent geometry : bond 0.00417 (38616) covalent geometry : angle 0.63462 (52404) hydrogen bonds : bond 0.03577 ( 1158) hydrogen bonds : angle 6.71487 ( 2898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10662.55 seconds wall clock time: 182 minutes 36.33 seconds (10956.33 seconds total)