Starting phenix.real_space_refine on Wed Aug 27 00:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.map" model { file = "/net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fnt_29323/08_2025/8fnt_29323.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.122 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 217 5.16 5 C 27833 2.51 5 N 7578 2.21 5 O 8240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 352 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: 43868 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "C" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "D" Number of atoms: 6264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6264 Classifications: {'peptide': 784} Link IDs: {'PTRANS': 21, 'TRANS': 762} Chain breaks: 9 Chain: "F" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "G" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "E" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6239 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 20, 'TRANS': 760} Chain breaks: 9 Chain: "A" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Time building chain proxies: 10.23, per 1000 atoms: 0.23 Number of scatterers: 43868 At special positions: 0 Unit cell: (155.925, 160.875, 131.175, 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 217 16.00 O 8240 8.00 N 7578 7.00 C 27833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 1.2 microseconds 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10434 Finding SS restraints... Secondary structure from input PDB file: 259 helices and 14 sheets defined 63.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 removed outlier: 4.128A pdb=" N HIS B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.107A pdb=" N THR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.640A pdb=" N SER B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 3.592A pdb=" N CYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 607 removed outlier: 3.857A pdb=" N SER B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 632 Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 723 " --> pdb=" O ASN B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 730 through 752 removed outlier: 3.585A pdb=" N ASN B 746 " --> pdb=" O TYR B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 756 removed outlier: 4.027A pdb=" N LEU B 756 " --> pdb=" O LYS B 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 753 through 756' Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.583A pdb=" N MET B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 847 Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.928A pdb=" N ASN B 869 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 870 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 873 " --> pdb=" O ASN B 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 877 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 removed outlier: 4.705A pdb=" N TYR B 894 " --> pdb=" O GLU B 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 895 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.502A pdb=" N ILE C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 4.072A pdb=" N ASP C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 344 through 357 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 472 through 490 removed outlier: 3.518A pdb=" N ILE C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE C 511 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.707A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER C 607 " --> pdb=" O ALA C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 632 Processing helix chain 'C' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL C 649 " --> pdb=" O ALA C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 723 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN C 746 " --> pdb=" O TYR C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 756 removed outlier: 4.027A pdb=" N LEU C 756 " --> pdb=" O LYS C 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 753 through 756' Processing helix chain 'C' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 831 removed outlier: 3.560A pdb=" N LYS C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 827 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 830 " --> pdb=" O GLU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 870 " --> pdb=" O LYS C 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 873 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 877 " --> pdb=" O SER C 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR C 894 " --> pdb=" O GLU C 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 895 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER D 178 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 443 through 457 removed outlier: 3.686A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 Processing helix chain 'D' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 516 " --> pdb=" O ASN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 540 Processing helix chain 'D' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER D 607 " --> pdb=" O ALA D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 632 Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 723 " --> pdb=" O ASN D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN D 746 " --> pdb=" O TYR D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU D 756 " --> pdb=" O LYS D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 753 through 756' Processing helix chain 'D' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 829 " --> pdb=" O GLY D 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 830 " --> pdb=" O GLU D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 847 Processing helix chain 'D' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 873 " --> pdb=" O ASN D 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 876 " --> pdb=" O THR D 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 896 removed outlier: 4.705A pdb=" N TYR D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 895 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER F 178 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 181 " --> pdb=" O SER F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 240 removed outlier: 4.073A pdb=" N ASP F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 279 through 302 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 312 through 317 Processing helix chain 'F' and resid 344 through 357 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR F 387 " --> pdb=" O LEU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 425 through 433 Processing helix chain 'F' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 466 Processing helix chain 'F' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE F 511 " --> pdb=" O SER F 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 540 Processing helix chain 'F' and resid 546 through 559 removed outlier: 3.707A pdb=" N ALA F 556 " --> pdb=" O ASN F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 607 removed outlier: 3.857A pdb=" N SER F 607 " --> pdb=" O ALA F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 632 Processing helix chain 'F' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL F 649 " --> pdb=" O ALA F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR F 711 " --> pdb=" O SER F 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 723 " --> pdb=" O ASN F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 727 No H-bonds generated for 'chain 'F' and resid 725 through 727' Processing helix chain 'F' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN F 746 " --> pdb=" O TYR F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 756 removed outlier: 4.028A pdb=" N LEU F 756 " --> pdb=" O LYS F 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 753 through 756' Processing helix chain 'F' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F 794 " --> pdb=" O GLU F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 831 removed outlier: 3.560A pdb=" N LYS F 822 " --> pdb=" O GLU F 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS F 829 " --> pdb=" O GLY F 825 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 830 " --> pdb=" O GLU F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 847 Processing helix chain 'F' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE F 856 " --> pdb=" O HIS F 852 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 883 removed outlier: 3.926A pdb=" N ASN F 869 " --> pdb=" O VAL F 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS F 870 " --> pdb=" O LYS F 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 873 " --> pdb=" O ASN F 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 876 " --> pdb=" O THR F 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 877 " --> pdb=" O SER F 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 878 " --> pdb=" O PHE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR F 894 " --> pdb=" O GLU F 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 897 " --> pdb=" O ASP F 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS G 156 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.107A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.640A pdb=" N SER G 178 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE G 199 " --> pdb=" O ASP G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR G 257 " --> pdb=" O ASP G 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR G 269 " --> pdb=" O GLN G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 277 Processing helix chain 'G' and resid 279 through 302 Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 344 through 357 Processing helix chain 'G' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP G 365 " --> pdb=" O GLY G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR G 387 " --> pdb=" O LEU G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 425 Processing helix chain 'G' and resid 425 through 433 Processing helix chain 'G' and resid 443 through 457 removed outlier: 3.686A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 466 Processing helix chain 'G' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS G 505 " --> pdb=" O LEU G 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE G 511 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR G 516 " --> pdb=" O ASN G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 540 Processing helix chain 'G' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 632 Processing helix chain 'G' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL G 649 " --> pdb=" O ALA G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR G 711 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 723 " --> pdb=" O ASN G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 727 No H-bonds generated for 'chain 'G' and resid 725 through 727' Processing helix chain 'G' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN G 746 " --> pdb=" O TYR G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU G 756 " --> pdb=" O LYS G 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 753 through 756' Processing helix chain 'G' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS G 794 " --> pdb=" O GLU G 790 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS G 822 " --> pdb=" O GLU G 818 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 827 " --> pdb=" O ILE G 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS G 829 " --> pdb=" O GLY G 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 830 " --> pdb=" O GLU G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 839 through 847 Processing helix chain 'G' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE G 856 " --> pdb=" O HIS G 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN G 869 " --> pdb=" O VAL G 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS G 870 " --> pdb=" O LYS G 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 876 " --> pdb=" O THR G 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU G 877 " --> pdb=" O SER G 873 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 878 " --> pdb=" O PHE G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 897 removed outlier: 4.707A pdb=" N TYR G 894 " --> pdb=" O GLU G 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU G 895 " --> pdb=" O GLU G 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 120 through 139 removed outlier: 3.519A pdb=" N THR E 124 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 163 removed outlier: 4.128A pdb=" N HIS E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 181 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 279 through 302 Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 344 through 357 Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 425 Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 516 " --> pdb=" O ASN E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 540 Processing helix chain 'E' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER E 607 " --> pdb=" O ALA E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 632 Processing helix chain 'E' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL E 649 " --> pdb=" O ALA E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 724 removed outlier: 3.550A pdb=" N THR E 711 " --> pdb=" O SER E 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE E 723 " --> pdb=" O ASN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 727 No H-bonds generated for 'chain 'E' and resid 725 through 727' Processing helix chain 'E' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN E 746 " --> pdb=" O TYR E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU E 756 " --> pdb=" O LYS E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 753 through 756' Processing helix chain 'E' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS E 794 " --> pdb=" O GLU E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 831 removed outlier: 3.562A pdb=" N LYS E 822 " --> pdb=" O GLU E 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 827 " --> pdb=" O ILE E 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 829 " --> pdb=" O GLY E 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 830 " --> pdb=" O GLU E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 847 Processing helix chain 'E' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN E 869 " --> pdb=" O VAL E 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS E 870 " --> pdb=" O LYS E 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 873 " --> pdb=" O ASN E 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 876 " --> pdb=" O THR E 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 877 " --> pdb=" O SER E 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 878 " --> pdb=" O PHE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 896 removed outlier: 4.706A pdb=" N TYR E 894 " --> pdb=" O GLU E 890 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 895 " --> pdb=" O GLU E 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 120 through 139 removed outlier: 3.521A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.073A pdb=" N ASP A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU A 756 " --> pdb=" O LYS A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.583A pdb=" N MET A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 105 through 106 removed outlier: 7.250A pdb=" N LYS B 105 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR B 219 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 216 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 249 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 218 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR B 251 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 308 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE B 73 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP B 618 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 611 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS B 655 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR B 610 " --> pdb=" O CYS B 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 106 removed outlier: 7.252A pdb=" N LYS C 105 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR C 219 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 308 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE C 73 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 611 " --> pdb=" O MET C 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS C 655 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 610 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS D 105 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR D 219 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 216 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 249 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 218 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR D 251 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 576 removed outlier: 4.296A pdb=" N ASP D 618 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 611 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS D 655 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 610 " --> pdb=" O CYS D 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 105 through 106 removed outlier: 7.250A pdb=" N LYS F 105 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR F 219 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE F 216 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 249 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 218 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR F 251 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE F 308 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE F 73 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP F 618 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 611 " --> pdb=" O MET F 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS F 655 " --> pdb=" O LEU F 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR F 610 " --> pdb=" O CYS F 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS G 105 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR G 219 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP G 618 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL G 611 " --> pdb=" O MET G 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS G 655 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR G 610 " --> pdb=" O CYS G 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS E 105 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR E 219 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 611 " --> pdb=" O MET E 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS E 655 " --> pdb=" O LEU E 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 610 " --> pdb=" O CYS E 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS A 105 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR A 219 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE A 308 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A 73 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 611 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS A 655 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 610 " --> pdb=" O CYS A 655 " (cutoff:3.500A) 2245 hydrogen bonds defined for protein. 6588 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.32 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11579 1.33 - 1.47: 12942 1.47 - 1.60: 19730 1.60 - 1.73: 8 1.73 - 1.86: 322 Bond restraints: 44581 Sorted by residual: bond pdb=" CA VAL D 413 " pdb=" CB VAL D 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 9.00e+01 bond pdb=" CA VAL E 413 " pdb=" CB VAL E 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 8.93e+01 bond pdb=" CA VAL B 413 " pdb=" CB VAL B 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 8.77e+01 bond pdb=" CA VAL F 413 " pdb=" CB VAL F 413 " ideal model delta sigma weight residual 1.539 1.489 0.050 5.40e-03 3.43e+04 8.66e+01 bond pdb=" CA VAL G 413 " pdb=" CB VAL G 413 " ideal model delta sigma weight residual 1.539 1.489 0.050 5.40e-03 3.43e+04 8.62e+01 ... (remaining 44576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.38: 59185 6.38 - 12.76: 609 12.76 - 19.14: 194 19.14 - 25.53: 35 25.53 - 31.91: 21 Bond angle restraints: 60044 Sorted by residual: angle pdb=" CB LYS G 311 " pdb=" CG LYS G 311 " pdb=" CD LYS G 311 " ideal model delta sigma weight residual 111.30 137.27 -25.97 2.30e+00 1.89e-01 1.28e+02 angle pdb=" CB LYS F 311 " pdb=" CG LYS F 311 " pdb=" CD LYS F 311 " ideal model delta sigma weight residual 111.30 137.24 -25.94 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS C 311 " pdb=" CG LYS C 311 " pdb=" CD LYS C 311 " ideal model delta sigma weight residual 111.30 137.22 -25.92 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS A 311 " pdb=" CG LYS A 311 " pdb=" CD LYS A 311 " ideal model delta sigma weight residual 111.30 137.21 -25.91 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS E 311 " pdb=" CG LYS E 311 " pdb=" CD LYS E 311 " ideal model delta sigma weight residual 111.30 137.20 -25.90 2.30e+00 1.89e-01 1.27e+02 ... (remaining 60039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22595 17.97 - 35.93: 3101 35.93 - 53.90: 1087 53.90 - 71.86: 331 71.86 - 89.83: 84 Dihedral angle restraints: 27198 sinusoidal: 11162 harmonic: 16036 Sorted by residual: dihedral pdb=" CD ARG B 38 " pdb=" NE ARG B 38 " pdb=" CZ ARG B 38 " pdb=" NH1 ARG B 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.27 -89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " pdb=" CZ ARG A 38 " pdb=" NH1 ARG A 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CD ARG C 38 " pdb=" NE ARG C 38 " pdb=" CZ ARG C 38 " pdb=" NH1 ARG C 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 ... (remaining 27195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.522: 6770 0.522 - 1.044: 7 1.044 - 1.566: 0 1.566 - 2.087: 0 2.087 - 2.609: 7 Chirality restraints: 6784 Sorted by residual: chirality pdb=" CG LEU G 502 " pdb=" CB LEU G 502 " pdb=" CD1 LEU G 502 " pdb=" CD2 LEU G 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 chirality pdb=" CG LEU B 502 " pdb=" CB LEU B 502 " pdb=" CD1 LEU B 502 " pdb=" CD2 LEU B 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 chirality pdb=" CG LEU A 502 " pdb=" CB LEU A 502 " pdb=" CD1 LEU A 502 " pdb=" CD2 LEU A 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 ... (remaining 6781 not shown) Planarity restraints: 7672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG A 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG B 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 38 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG G 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG G 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG G 38 " -0.013 2.00e-02 2.50e+03 ... (remaining 7669 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 16 1.81 - 2.59: 694 2.59 - 3.36: 58726 3.36 - 4.13: 110456 4.13 - 4.90: 203934 Nonbonded interactions: 373826 Sorted by model distance: nonbonded pdb=" OD1 ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.042 3.040 nonbonded pdb=" OD1 ASN F 759 " pdb=" CG ASP F 930 " model vdw 1.152 3.270 nonbonded pdb=" CG ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.200 3.270 nonbonded pdb=" NH1 ARG F 758 " pdb=" O ASP F 928 " model vdw 1.492 3.120 nonbonded pdb=" ND2 ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.603 3.120 ... (remaining 373821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'B' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'C' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'D' and resid 35 through 930) selection = (chain 'E' and (resid 35 through 76 or resid 81 through 930)) selection = (chain 'F' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'G' and (resid 35 through 896 or resid 910 through 930)) } 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: 4.390 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 37.260 Find NCS groups from input model: 1.040 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:6.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.010 0.159 44581 Z= 0.449 Angle : 1.798 31.906 60044 Z= 0.856 Chirality : 0.106 2.609 6784 Planarity : 0.025 0.448 7672 Dihedral : 19.926 89.828 16764 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.95 % Favored : 89.79 % Rotamer: Outliers : 10.57 % Allowed : 19.43 % Favored : 70.00 % 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: -2.16 (0.11), residues: 5350 helix: -0.90 (0.09), residues: 3048 sheet: -0.07 (0.39), residues: 224 loop : -2.32 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.005 ARG G 740 TYR 0.140 0.006 TYR G 436 PHE 0.036 0.003 PHE G 177 TRP 0.015 0.002 TRP E 660 HIS 0.027 0.004 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00993 (44581) covalent geometry : angle 1.79760 (60044) hydrogen bonds : bond 0.19439 ( 2245) hydrogen bonds : angle 7.38604 ( 6588) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 515 poor density : 812 time to evaluate : 1.619 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: B 170 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6577 (mmtt) REVERT: B 209 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 311 LYS cc_start: 0.3903 (OUTLIER) cc_final: 0.3552 (mttp) REVERT: B 431 ARG cc_start: 0.7266 (tpt170) cc_final: 0.7025 (tpt170) REVERT: B 617 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3740 (mmm) REVERT: B 621 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6801 (p) REVERT: B 648 LYS cc_start: 0.7193 (mtpm) cc_final: 0.6983 (tppt) REVERT: B 868 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4417 (tp) REVERT: C 496 LYS cc_start: 0.8377 (mttp) cc_final: 0.8066 (mttt) REVERT: C 617 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.3583 (mmm) REVERT: D 38 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5978 (ttp-170) REVERT: D 75 ASP cc_start: 0.6203 (m-30) cc_final: 0.5989 (m-30) REVERT: D 346 GLN cc_start: 0.7182 (tt0) cc_final: 0.6920 (mt0) REVERT: D 494 LEU cc_start: 0.7633 (tm) cc_final: 0.7398 (tp) REVERT: D 540 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7389 (t) REVERT: D 617 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4770 (mtm) REVERT: D 633 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 775 MET cc_start: 0.6186 (mmm) cc_final: 0.5957 (mmm) REVERT: D 873 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7610 (p) REVERT: D 893 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5514 (t0) REVERT: F 336 MET cc_start: 0.6220 (mtt) cc_final: 0.5781 (mtt) REVERT: F 338 ASP cc_start: 0.5062 (OUTLIER) cc_final: 0.4587 (t70) REVERT: F 340 ASP cc_start: 0.4952 (OUTLIER) cc_final: 0.4635 (p0) REVERT: F 392 HIS cc_start: 0.4576 (OUTLIER) cc_final: 0.4374 (t-90) REVERT: F 431 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6497 (tpt170) REVERT: F 617 MET cc_start: 0.3426 (OUTLIER) cc_final: 0.1360 (tpp) REVERT: F 934 ARG cc_start: 0.0980 (OUTLIER) cc_final: 0.0780 (mmp80) REVERT: G 270 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8850 (p) REVERT: G 527 LYS cc_start: 0.7537 (mttm) cc_final: 0.7150 (ptmt) REVERT: E 170 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6196 (mppt) REVERT: E 171 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: E 380 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5079 (mtm) REVERT: E 387 TYR cc_start: 0.5623 (m-80) cc_final: 0.5148 (m-80) REVERT: E 497 PHE cc_start: 0.5196 (t80) cc_final: 0.4758 (t80) REVERT: E 620 CYS cc_start: 0.4633 (t) cc_final: 0.4077 (t) REVERT: E 639 ARG cc_start: 0.6095 (ttt-90) cc_final: 0.5048 (ttp80) REVERT: E 715 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: E 740 ARG cc_start: 0.6190 (ttm-80) cc_final: 0.5975 (tpp80) REVERT: E 745 LEU cc_start: 0.6461 (mt) cc_final: 0.6229 (tt) REVERT: E 765 MET cc_start: 0.3191 (OUTLIER) cc_final: 0.2628 (ttt) REVERT: A 40 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5537 (tp40) REVERT: A 198 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 338 ASP cc_start: 0.4852 (OUTLIER) cc_final: 0.3599 (t70) REVERT: A 340 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4659 (p0) REVERT: A 617 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4334 (mtm) REVERT: A 765 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4312 (ttp) outliers start: 515 outliers final: 72 residues processed: 1160 average time/residue: 0.7050 time to fit residues: 1009.3585 Evaluate side-chains 609 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 509 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 392 HIS Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 723 ILE Chi-restraints excluded: chain F residue 834 THR Chi-restraints excluded: chain F residue 934 ARG Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 270 SER Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 621 SER Chi-restraints excluded: chain G residue 633 SER Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 621 SER Chi-restraints excluded: chain E residue 715 GLN Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain E residue 834 THR Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 798 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 0.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 0.6980 chunk 488 optimal weight: 1.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 456 GLN B 461 ASN B 512 ASN B 624 ASN B 751 GLN C 268 ASN C 512 ASN C 513 GLN C 759 ASN C 875 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN D 374 GLN D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN F 268 ASN F 309 GLN ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 ASN F 652 GLN ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 156 HIS G 159 GLN G 337 GLN G 374 GLN G 512 ASN G 597 ASN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 ASN G 875 ASN E 154 GLN E 159 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 156 HIS A 374 GLN A 456 GLN A 491 GLN A 512 ASN ** A 549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN A 875 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.207405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.163113 restraints weight = 47349.997| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.62 r_work: 0.3609 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44581 Z= 0.190 Angle : 0.712 10.001 60044 Z= 0.374 Chirality : 0.044 0.244 6784 Planarity : 0.005 0.068 7672 Dihedral : 7.532 123.183 6101 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.04 % Favored : 93.51 % Rotamer: Outliers : 5.11 % Allowed : 22.53 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.11), residues: 5350 helix: 0.33 (0.09), residues: 3163 sheet: 0.03 (0.36), residues: 229 loop : -2.13 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 38 TYR 0.034 0.002 TYR B 176 PHE 0.023 0.002 PHE A 441 TRP 0.018 0.002 TRP B 892 HIS 0.009 0.002 HIS G 794 Details of bonding type rmsd covalent geometry : bond 0.00425 (44581) covalent geometry : angle 0.71150 (60044) hydrogen bonds : bond 0.04783 ( 2245) hydrogen bonds : angle 5.01063 ( 6588) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 685 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8332 (mt) REVERT: B 214 LYS cc_start: 0.7574 (mtmt) cc_final: 0.7214 (mmtm) REVERT: B 244 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7835 (mtt-85) REVERT: B 311 LYS cc_start: 0.6462 (OUTLIER) cc_final: 0.5984 (pmtt) REVERT: B 333 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: B 431 ARG cc_start: 0.8315 (tpt170) cc_final: 0.8073 (tpt-90) REVERT: B 438 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7625 (mt0) REVERT: B 570 PHE cc_start: 0.7510 (m-10) cc_final: 0.7224 (m-10) REVERT: B 584 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6098 (mtm) REVERT: B 617 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.4694 (mmm) REVERT: B 625 LEU cc_start: 0.7243 (tt) cc_final: 0.6246 (mt) REVERT: B 728 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6605 (ptp-170) REVERT: C 173 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7768 (ptpp) REVERT: C 206 ARG cc_start: 0.7932 (mmm160) cc_final: 0.7639 (mmm-85) REVERT: C 331 LYS cc_start: 0.6983 (ttpt) cc_final: 0.5999 (pmtt) REVERT: C 461 ASN cc_start: 0.7684 (t0) cc_final: 0.7432 (m-40) REVERT: C 470 SER cc_start: 0.7581 (t) cc_final: 0.7360 (p) REVERT: C 496 LYS cc_start: 0.8774 (mttp) cc_final: 0.8327 (mttt) REVERT: C 636 ARG cc_start: 0.6274 (mmm-85) cc_final: 0.5816 (mtm-85) REVERT: D 40 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6723 (tt0) REVERT: D 244 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7501 (mtt90) REVERT: D 271 LYS cc_start: 0.8517 (mptt) cc_final: 0.8238 (mmtt) REVERT: D 291 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7883 (mm-30) REVERT: D 346 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.6901 (mt0) REVERT: D 350 ASP cc_start: 0.8109 (m-30) cc_final: 0.7748 (m-30) REVERT: D 436 TYR cc_start: 0.7331 (t80) cc_final: 0.7130 (t80) REVERT: D 718 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6976 (mmpt) REVERT: D 802 ILE cc_start: 0.8154 (tt) cc_final: 0.7937 (tt) REVERT: D 893 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5422 (t0) REVERT: F 132 MET cc_start: 0.8434 (mtp) cc_final: 0.8180 (mtp) REVERT: F 331 LYS cc_start: 0.6888 (ttpt) cc_final: 0.5754 (pmtt) REVERT: G 132 MET cc_start: 0.8610 (mtm) cc_final: 0.8334 (mtm) REVERT: G 526 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.5591 (pp20) REVERT: G 527 LYS cc_start: 0.7678 (mttm) cc_final: 0.7189 (ptmt) REVERT: G 646 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7232 (t80) REVERT: G 721 ASN cc_start: 0.8898 (m-40) cc_final: 0.8690 (m110) REVERT: G 815 ASP cc_start: 0.7909 (m-30) cc_final: 0.7476 (p0) REVERT: G 836 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6351 (mppt) REVERT: E 82 LYS cc_start: 0.4990 (OUTLIER) cc_final: 0.4482 (ptmt) REVERT: E 224 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6735 (p0) REVERT: E 266 TYR cc_start: 0.7654 (OUTLIER) cc_final: 0.7271 (t80) REVERT: E 314 LEU cc_start: 0.7458 (tp) cc_final: 0.7192 (tt) REVERT: E 336 MET cc_start: 0.3878 (mtt) cc_final: 0.3606 (mtt) REVERT: E 366 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5549 (ttm) REVERT: E 431 ARG cc_start: 0.6035 (tpt170) cc_final: 0.5730 (tpp-160) REVERT: E 443 MET cc_start: 0.4224 (OUTLIER) cc_final: 0.4007 (ttm) REVERT: E 454 VAL cc_start: 0.6953 (p) cc_final: 0.6603 (t) REVERT: E 497 PHE cc_start: 0.5111 (t80) cc_final: 0.4506 (t80) REVERT: E 554 CYS cc_start: 0.4493 (t) cc_final: 0.3453 (p) REVERT: E 715 GLN cc_start: 0.6962 (mm-40) cc_final: 0.6728 (mm110) REVERT: E 740 ARG cc_start: 0.6217 (ttm-80) cc_final: 0.5926 (tpp80) REVERT: E 745 LEU cc_start: 0.6500 (mt) cc_final: 0.6053 (tt) REVERT: A 164 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 271 LYS cc_start: 0.8462 (mptt) cc_final: 0.8130 (mppt) REVERT: A 429 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8194 (mt) REVERT: A 584 MET cc_start: 0.5630 (mpp) cc_final: 0.5396 (mtt) REVERT: A 755 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.7560 (mtt180) REVERT: A 819 LYS cc_start: 0.7470 (mtpp) cc_final: 0.7238 (tppt) REVERT: A 871 GLU cc_start: 0.6395 (tt0) cc_final: 0.6109 (tt0) REVERT: A 876 LYS cc_start: 0.7239 (OUTLIER) cc_final: 0.7038 (mmtm) REVERT: A 889 ASP cc_start: 0.6324 (m-30) cc_final: 0.6114 (m-30) outliers start: 249 outliers final: 54 residues processed: 859 average time/residue: 0.8439 time to fit residues: 877.3829 Evaluate side-chains 590 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 512 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 441 PHE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 441 PHE Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 646 PHE Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain G residue 800 GLU Chi-restraints excluded: chain G residue 836 LYS Chi-restraints excluded: chain E residue 82 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 443 MET Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 739 SER Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 876 LYS Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 376 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 256 optimal weight: 0.8980 chunk 150 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 429 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 513 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS B 159 GLN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN B 259 GLN B 456 GLN B 549 HIS B 624 ASN C 159 GLN C 161 GLN C 512 ASN C 875 ASN D 118 HIS D 156 HIS D 159 GLN D 268 ASN D 374 GLN D 499 GLN D 875 ASN F 154 GLN F 259 GLN F 268 ASN F 315 GLN F 513 GLN F 560 ASN F 744 ASN G 159 GLN G 276 GLN G 489 ASN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 GLN E 194 GLN E 259 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 461 ASN E 512 ASN A 560 ASN A 582 GLN A 770 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.197311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151419 restraints weight = 46305.047| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.72 r_work: 0.3500 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 44581 Z= 0.165 Angle : 0.627 8.740 60044 Z= 0.333 Chirality : 0.042 0.209 6784 Planarity : 0.005 0.058 7672 Dihedral : 5.169 62.834 5923 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.83 % Favored : 93.74 % Rotamer: Outliers : 4.92 % Allowed : 22.06 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.11), residues: 5350 helix: 0.74 (0.09), residues: 3193 sheet: 0.33 (0.36), residues: 229 loop : -1.93 (0.14), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 740 TYR 0.022 0.002 TYR G 801 PHE 0.050 0.002 PHE F 782 TRP 0.019 0.002 TRP G 738 HIS 0.008 0.002 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00368 (44581) covalent geometry : angle 0.62732 (60044) hydrogen bonds : bond 0.04586 ( 2245) hydrogen bonds : angle 4.62624 ( 6588) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 240 poor density : 627 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 159 GLN cc_start: 0.7919 (pt0) cc_final: 0.7694 (pt0) REVERT: B 175 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7668 (pp20) REVERT: B 214 LYS cc_start: 0.8092 (mtmt) cc_final: 0.7562 (mmtm) REVERT: B 244 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8248 (mtt-85) REVERT: B 291 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7756 (mm-30) REVERT: B 333 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.6369 (mp0) REVERT: B 342 ILE cc_start: 0.6195 (OUTLIER) cc_final: 0.5517 (tp) REVERT: B 431 ARG cc_start: 0.8098 (tpt170) cc_final: 0.7891 (tpt170) REVERT: B 438 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7980 (mt0) REVERT: B 473 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: B 570 PHE cc_start: 0.7529 (m-10) cc_final: 0.7312 (m-10) REVERT: B 584 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5769 (mpp) REVERT: B 625 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6337 (mt) REVERT: B 636 ARG cc_start: 0.5419 (OUTLIER) cc_final: 0.5137 (mtt180) REVERT: B 728 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6685 (ptp-170) REVERT: B 742 TYR cc_start: 0.7322 (t80) cc_final: 0.7059 (t80) REVERT: B 762 HIS cc_start: 0.6124 (OUTLIER) cc_final: 0.5808 (m-70) REVERT: B 808 LEU cc_start: 0.8365 (mp) cc_final: 0.8096 (mm) REVERT: B 826 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.6071 (pm20) REVERT: C 138 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6295 (mtmp) REVERT: C 151 GLU cc_start: 0.7373 (pp20) cc_final: 0.7055 (pp20) REVERT: C 271 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8497 (ttmm) REVERT: C 311 LYS cc_start: 0.6989 (pmtt) cc_final: 0.6479 (ptpp) REVERT: C 331 LYS cc_start: 0.7223 (ttpt) cc_final: 0.6274 (pmtt) REVERT: C 350 ASP cc_start: 0.7835 (m-30) cc_final: 0.7609 (m-30) REVERT: C 443 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7279 (mmm) REVERT: C 470 SER cc_start: 0.8485 (t) cc_final: 0.8169 (p) REVERT: C 496 LYS cc_start: 0.8775 (mttp) cc_final: 0.8336 (mttt) REVERT: C 596 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: C 617 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.7296 (mtm) REVERT: C 636 ARG cc_start: 0.6126 (mmm-85) cc_final: 0.5485 (mtm-85) REVERT: C 715 GLN cc_start: 0.6999 (tt0) cc_final: 0.6367 (tm-30) REVERT: C 750 ASP cc_start: 0.6488 (OUTLIER) cc_final: 0.6279 (t70) REVERT: C 775 MET cc_start: 0.7371 (mmm) cc_final: 0.7130 (mmm) REVERT: D 117 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7421 (tpp-160) REVERT: D 214 LYS cc_start: 0.6820 (pttt) cc_final: 0.6567 (ptpp) REVERT: D 291 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8061 (mm-30) REVERT: D 310 LEU cc_start: 0.7243 (OUTLIER) cc_final: 0.6429 (mp) REVERT: D 346 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: D 350 ASP cc_start: 0.8123 (m-30) cc_final: 0.7766 (m-30) REVERT: D 717 LEU cc_start: 0.7955 (tp) cc_final: 0.7478 (mt) REVERT: D 718 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6971 (mmpt) REVERT: D 798 ASP cc_start: 0.7764 (m-30) cc_final: 0.7419 (p0) REVERT: D 836 LYS cc_start: 0.7330 (mttm) cc_final: 0.6689 (mppt) REVERT: D 893 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5510 (t0) REVERT: F 102 VAL cc_start: 0.3009 (OUTLIER) cc_final: 0.2453 (p) REVERT: F 132 MET cc_start: 0.8536 (mtp) cc_final: 0.8309 (mtp) REVERT: F 222 ASP cc_start: 0.6498 (p0) cc_final: 0.5918 (p0) REVERT: F 279 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6971 (pm20) REVERT: F 291 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: F 312 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7610 (t) REVERT: F 328 ILE cc_start: 0.5800 (OUTLIER) cc_final: 0.5568 (pt) REVERT: F 331 LYS cc_start: 0.7485 (ttpt) cc_final: 0.6394 (pmtt) REVERT: F 354 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7293 (mt-10) REVERT: F 431 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8146 (tpt-90) REVERT: F 437 GLU cc_start: 0.8584 (mp0) cc_final: 0.8272 (mp0) REVERT: F 715 GLN cc_start: 0.6997 (tp-100) cc_final: 0.6567 (tm-30) REVERT: F 818 GLU cc_start: 0.4922 (OUTLIER) cc_final: 0.4678 (tp30) REVERT: G 206 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7823 (tpp-160) REVERT: G 310 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7480 (mp) REVERT: G 526 GLU cc_start: 0.5892 (OUTLIER) cc_final: 0.5634 (pp20) REVERT: G 573 MET cc_start: 0.8905 (ptp) cc_final: 0.8661 (ptt) REVERT: G 719 ASN cc_start: 0.8920 (m-40) cc_final: 0.8564 (m-40) REVERT: G 742 TYR cc_start: 0.8752 (t80) cc_final: 0.8438 (t80) REVERT: G 815 ASP cc_start: 0.8027 (m-30) cc_final: 0.7669 (p0) REVERT: E 86 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7682 (mp) REVERT: E 154 GLN cc_start: 0.7679 (mm110) cc_final: 0.7324 (mm110) REVERT: E 170 LYS cc_start: 0.7568 (mmtt) cc_final: 0.7133 (mppt) REVERT: E 206 ARG cc_start: 0.7468 (mmp-170) cc_final: 0.7174 (mmp80) REVERT: E 224 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7037 (p0) REVERT: E 235 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8393 (tp30) REVERT: E 245 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8262 (mmtm) REVERT: E 253 ASP cc_start: 0.8377 (p0) cc_final: 0.8136 (t0) REVERT: E 366 MET cc_start: 0.6208 (tpp) cc_final: 0.5946 (ttm) REVERT: E 391 TYR cc_start: 0.5783 (t80) cc_final: 0.5544 (t80) REVERT: E 425 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.6443 (mmt) REVERT: E 431 ARG cc_start: 0.6816 (tpt170) cc_final: 0.6455 (tpp-160) REVERT: E 473 GLU cc_start: 0.6517 (pt0) cc_final: 0.6230 (tt0) REVERT: E 497 PHE cc_start: 0.5321 (t80) cc_final: 0.4610 (t80) REVERT: E 646 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5414 (m-80) REVERT: E 714 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5779 (tm-30) REVERT: E 715 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6913 (mm110) REVERT: E 740 ARG cc_start: 0.6193 (ttm-80) cc_final: 0.5759 (tpp80) REVERT: E 745 LEU cc_start: 0.6245 (mt) cc_final: 0.5638 (tt) REVERT: A 214 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6673 (mttp) REVERT: A 271 LYS cc_start: 0.8674 (mptt) cc_final: 0.8371 (mppt) REVERT: A 391 TYR cc_start: 0.7568 (t80) cc_final: 0.7101 (t80) REVERT: A 595 THR cc_start: 0.7647 (p) cc_final: 0.7376 (t) REVERT: A 715 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6996 (mm-40) REVERT: A 819 LYS cc_start: 0.7616 (mtpp) cc_final: 0.7299 (tppt) REVERT: A 826 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6769 (mm-30) outliers start: 240 outliers final: 68 residues processed: 798 average time/residue: 0.8227 time to fit residues: 798.1447 Evaluate side-chains 630 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 522 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 636 ARG Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 762 HIS Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 443 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 279 GLU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 561 SER Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 818 GLU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 206 ARG Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 545 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 646 PHE Chi-restraints excluded: chain E residue 714 GLU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 739 SER Chi-restraints excluded: chain E residue 770 ASN Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 214 LYS Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 931 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 52 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 479 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 469 optimal weight: 0.9990 chunk 531 optimal weight: 5.9990 chunk 58 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 223 optimal weight: 8.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS B 268 ASN B 456 GLN B 549 HIS ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 875 ASN C 47 ASN C 155 ASN C 159 GLN C 415 ASN C 875 ASN D 875 ASN F 159 GLN F 469 GLN F 513 GLN G 40 GLN G 159 GLN G 161 GLN G 624 ASN G 747 ASN E 155 ASN E 159 GLN E 226 GLN E 309 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN A 159 GLN A 161 GLN A 721 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.193994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147896 restraints weight = 45916.570| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.75 r_work: 0.3446 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 44581 Z= 0.172 Angle : 0.609 9.491 60044 Z= 0.324 Chirality : 0.042 0.214 6784 Planarity : 0.004 0.056 7672 Dihedral : 4.833 55.061 5901 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.34 % Favored : 93.38 % Rotamer: Outliers : 4.27 % Allowed : 22.92 % Favored : 72.81 % 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: -0.18 (0.11), residues: 5350 helix: 0.88 (0.09), residues: 3199 sheet: 0.46 (0.35), residues: 230 loop : -1.91 (0.14), residues: 1921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 117 TYR 0.023 0.002 TYR C 176 PHE 0.034 0.002 PHE C 782 TRP 0.019 0.002 TRP G 738 HIS 0.008 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00390 (44581) covalent geometry : angle 0.60877 (60044) hydrogen bonds : bond 0.04483 ( 2245) hydrogen bonds : angle 4.55334 ( 6588) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 583 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7788 (tp40) REVERT: B 164 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8563 (mt) REVERT: B 214 LYS cc_start: 0.8248 (mtmt) cc_final: 0.7708 (mmtm) REVERT: B 291 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: B 333 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: B 342 ILE cc_start: 0.6254 (OUTLIER) cc_final: 0.5577 (tp) REVERT: B 431 ARG cc_start: 0.8209 (tpt170) cc_final: 0.7979 (tpt170) REVERT: B 438 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: B 473 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.6849 (tm-30) REVERT: B 584 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.5877 (mpp) REVERT: B 625 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6316 (mt) REVERT: B 719 ASN cc_start: 0.6051 (p0) cc_final: 0.5596 (t0) REVERT: B 728 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.6836 (ptp-170) REVERT: B 808 LEU cc_start: 0.8437 (mp) cc_final: 0.8227 (mm) REVERT: C 138 LYS cc_start: 0.7295 (OUTLIER) cc_final: 0.6569 (mtmp) REVERT: C 151 GLU cc_start: 0.7398 (pp20) cc_final: 0.7177 (pp20) REVERT: C 173 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7811 (mtmm) REVERT: C 244 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.8132 (tpt-90) REVERT: C 311 LYS cc_start: 0.7182 (pmtt) cc_final: 0.6593 (ptpp) REVERT: C 331 LYS cc_start: 0.7384 (ttpt) cc_final: 0.6398 (pmtt) REVERT: C 336 MET cc_start: 0.5853 (mmt) cc_final: 0.5180 (mmt) REVERT: C 337 GLN cc_start: 0.5408 (OUTLIER) cc_final: 0.5037 (pm20) REVERT: C 350 ASP cc_start: 0.7984 (m-30) cc_final: 0.7776 (m-30) REVERT: C 496 LYS cc_start: 0.8801 (mttp) cc_final: 0.8356 (mttt) REVERT: C 596 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: C 715 GLN cc_start: 0.7076 (tt0) cc_final: 0.6546 (tm-30) REVERT: C 750 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.6138 (t0) REVERT: C 775 MET cc_start: 0.7553 (mmm) cc_final: 0.7291 (mmm) REVERT: D 105 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8145 (mptt) REVERT: D 117 ARG cc_start: 0.7743 (ttm110) cc_final: 0.7382 (tpp-160) REVERT: D 151 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6242 (pm20) REVERT: D 291 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8044 (mm-30) REVERT: D 346 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7555 (tt0) REVERT: D 350 ASP cc_start: 0.8147 (m-30) cc_final: 0.7834 (m-30) REVERT: D 431 ARG cc_start: 0.8552 (tpt170) cc_final: 0.8216 (ttt180) REVERT: D 440 ARG cc_start: 0.7350 (ptm160) cc_final: 0.7019 (ptp-110) REVERT: D 717 LEU cc_start: 0.7931 (tp) cc_final: 0.7600 (mt) REVERT: D 718 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7015 (mmpt) REVERT: D 798 ASP cc_start: 0.7889 (m-30) cc_final: 0.7535 (p0) REVERT: D 836 LYS cc_start: 0.7397 (mttm) cc_final: 0.6783 (mppt) REVERT: D 893 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5497 (t0) REVERT: F 102 VAL cc_start: 0.2931 (OUTLIER) cc_final: 0.2722 (p) REVERT: F 132 MET cc_start: 0.8590 (mtp) cc_final: 0.8356 (mtp) REVERT: F 267 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8206 (mt-10) REVERT: F 279 GLU cc_start: 0.7318 (pm20) cc_final: 0.7043 (pm20) REVERT: F 330 VAL cc_start: 0.7592 (OUTLIER) cc_final: 0.7262 (m) REVERT: F 331 LYS cc_start: 0.7756 (ttpt) cc_final: 0.6573 (pmtt) REVERT: F 354 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7464 (mt-10) REVERT: F 431 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8199 (tpt-90) REVERT: F 437 GLU cc_start: 0.8643 (mp0) cc_final: 0.8395 (mp0) REVERT: F 529 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6694 (tt0) REVERT: F 530 GLN cc_start: 0.7175 (mm-40) cc_final: 0.6588 (tm-30) REVERT: F 715 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.6876 (tm-30) REVERT: F 721 ASN cc_start: 0.8141 (m-40) cc_final: 0.7588 (m110) REVERT: F 818 GLU cc_start: 0.5115 (OUTLIER) cc_final: 0.4825 (tp30) REVERT: G 311 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7536 (mtpm) REVERT: G 380 MET cc_start: 0.9136 (mmm) cc_final: 0.8916 (mmp) REVERT: G 526 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5507 (pp20) REVERT: G 573 MET cc_start: 0.9060 (ptp) cc_final: 0.8820 (ptt) REVERT: G 719 ASN cc_start: 0.8935 (m-40) cc_final: 0.8639 (m-40) REVERT: G 815 ASP cc_start: 0.8136 (m-30) cc_final: 0.7903 (p0) REVERT: E 86 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7879 (mp) REVERT: E 235 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8409 (tp30) REVERT: E 271 LYS cc_start: 0.8596 (mppt) cc_final: 0.8235 (mttm) REVERT: E 285 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: E 291 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: E 366 MET cc_start: 0.6519 (tpp) cc_final: 0.6264 (ttm) REVERT: E 391 TYR cc_start: 0.5986 (t80) cc_final: 0.5774 (t80) REVERT: E 425 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.6726 (mmt) REVERT: E 431 ARG cc_start: 0.7042 (tpt170) cc_final: 0.6670 (tpp-160) REVERT: E 473 GLU cc_start: 0.6816 (pt0) cc_final: 0.6614 (tt0) REVERT: E 497 PHE cc_start: 0.5649 (t80) cc_final: 0.4915 (t80) REVERT: E 584 MET cc_start: 0.2014 (mtm) cc_final: 0.1027 (pp-130) REVERT: E 608 LEU cc_start: 0.3967 (OUTLIER) cc_final: 0.3747 (mm) REVERT: E 745 LEU cc_start: 0.6399 (mt) cc_final: 0.5838 (tt) REVERT: A 262 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8756 (ttp80) REVERT: A 271 LYS cc_start: 0.8760 (mptt) cc_final: 0.8477 (mppt) REVERT: A 346 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: A 496 LYS cc_start: 0.8666 (mttp) cc_final: 0.8383 (mttm) REVERT: A 715 GLN cc_start: 0.7407 (mm-40) cc_final: 0.7171 (mm-40) REVERT: A 819 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7374 (tppt) REVERT: A 826 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6849 (mm-30) REVERT: A 929 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7600 (mptp) outliers start: 208 outliers final: 63 residues processed: 737 average time/residue: 0.8150 time to fit residues: 728.2267 Evaluate side-chains 624 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 525 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 573 MET Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 635 CYS Chi-restraints excluded: chain F residue 643 THR Chi-restraints excluded: chain F residue 715 GLN Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 818 GLU Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 311 LYS Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 566 LYS Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 186 optimal weight: 0.9990 chunk 463 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 453 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 346 GLN B 435 ASN B 456 GLN B 549 HIS B 560 ASN ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 155 ASN C 159 GLN C 268 ASN C 768 GLN C 875 ASN D 40 GLN D 94 ASN D 226 GLN D 469 GLN D 560 ASN D 875 ASN F 159 GLN F 513 GLN G 47 ASN G 392 HIS G 747 ASN E 159 GLN E 226 GLN A 159 GLN A 374 GLN A 582 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.188905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.142873 restraints weight = 45871.029| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 1.67 r_work: 0.3389 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 44581 Z= 0.272 Angle : 0.736 8.765 60044 Z= 0.389 Chirality : 0.048 0.243 6784 Planarity : 0.006 0.061 7672 Dihedral : 5.202 59.213 5895 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.73 % Favored : 92.99 % Rotamer: Outliers : 5.11 % Allowed : 22.12 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.11), residues: 5350 helix: 0.59 (0.09), residues: 3230 sheet: 0.33 (0.31), residues: 260 loop : -1.86 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 639 TYR 0.031 0.003 TYR G 176 PHE 0.043 0.003 PHE C 782 TRP 0.023 0.002 TRP G 738 HIS 0.010 0.002 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00631 (44581) covalent geometry : angle 0.73615 (60044) hydrogen bonds : bond 0.05379 ( 2245) hydrogen bonds : angle 4.84136 ( 6588) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 249 poor density : 574 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7879 (tp40) REVERT: B 214 LYS cc_start: 0.8386 (mtmt) cc_final: 0.7835 (mmtm) REVERT: B 244 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8135 (mtt-85) REVERT: B 291 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: B 342 ILE cc_start: 0.6493 (OUTLIER) cc_final: 0.6025 (tp) REVERT: B 390 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8451 (tttm) REVERT: B 392 HIS cc_start: 0.7045 (m90) cc_final: 0.6651 (t70) REVERT: B 431 ARG cc_start: 0.8336 (tpt170) cc_final: 0.8058 (tpt-90) REVERT: B 461 ASN cc_start: 0.7817 (t0) cc_final: 0.7450 (t0) REVERT: B 473 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: B 584 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5843 (mpp) REVERT: B 617 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7735 (mtm) REVERT: B 625 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6544 (mt) REVERT: B 728 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.6691 (ptp-170) REVERT: B 929 LYS cc_start: 0.7513 (mttm) cc_final: 0.7029 (tttm) REVERT: C 75 ASP cc_start: 0.7406 (m-30) cc_final: 0.7072 (m-30) REVERT: C 151 GLU cc_start: 0.7414 (pp20) cc_final: 0.7138 (pp20) REVERT: C 155 ASN cc_start: 0.7977 (m110) cc_final: 0.7754 (m-40) REVERT: C 191 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8036 (mm) REVERT: C 214 LYS cc_start: 0.7652 (mttt) cc_final: 0.7390 (mttp) REVERT: C 244 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8215 (tpt-90) REVERT: C 245 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8426 (mptt) REVERT: C 331 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.6921 (pptt) REVERT: C 336 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5618 (mmt) REVERT: C 337 GLN cc_start: 0.5772 (OUTLIER) cc_final: 0.5381 (pm20) REVERT: C 392 HIS cc_start: 0.7172 (m-70) cc_final: 0.6916 (t-90) REVERT: C 431 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8003 (tmt170) REVERT: C 571 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7358 (tp) REVERT: C 715 GLN cc_start: 0.7176 (tt0) cc_final: 0.6750 (tm-30) REVERT: C 716 TRP cc_start: 0.7575 (t60) cc_final: 0.7314 (t60) REVERT: C 930 ASP cc_start: 0.7732 (m-30) cc_final: 0.7389 (m-30) REVERT: D 201 GLU cc_start: 0.8304 (tt0) cc_final: 0.8094 (tp30) REVERT: D 206 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.7626 (mmt-90) REVERT: D 244 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.7933 (mtt90) REVERT: D 280 SER cc_start: 0.8412 (p) cc_final: 0.8173 (m) REVERT: D 285 GLU cc_start: 0.7726 (pp20) cc_final: 0.7378 (pt0) REVERT: D 310 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6691 (mp) REVERT: D 440 ARG cc_start: 0.7562 (ptm160) cc_final: 0.7261 (ptp-110) REVERT: D 473 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7144 (tp30) REVERT: D 717 LEU cc_start: 0.8051 (tp) cc_final: 0.7794 (mt) REVERT: D 718 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7209 (mmtm) REVERT: D 723 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7257 (tp) REVERT: D 753 LYS cc_start: 0.7979 (ttmm) cc_final: 0.7324 (ttpp) REVERT: D 775 MET cc_start: 0.7414 (mmm) cc_final: 0.7047 (mmm) REVERT: D 798 ASP cc_start: 0.7879 (m-30) cc_final: 0.7599 (p0) REVERT: D 836 LYS cc_start: 0.7547 (mttm) cc_final: 0.7155 (mtpm) REVERT: D 893 ASP cc_start: 0.6134 (OUTLIER) cc_final: 0.5583 (t0) REVERT: F 102 VAL cc_start: 0.3055 (OUTLIER) cc_final: 0.2689 (p) REVERT: F 132 MET cc_start: 0.8636 (mtp) cc_final: 0.8405 (mtp) REVERT: F 171 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8424 (pm20) REVERT: F 182 LYS cc_start: 0.7077 (pttt) cc_final: 0.6454 (mptt) REVERT: F 330 VAL cc_start: 0.7956 (OUTLIER) cc_final: 0.7629 (m) REVERT: F 336 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6522 (mtt) REVERT: F 392 HIS cc_start: 0.7174 (t70) cc_final: 0.6568 (t-90) REVERT: F 431 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8218 (tpt-90) REVERT: F 530 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6980 (tm-30) REVERT: F 584 MET cc_start: 0.6067 (mmt) cc_final: 0.5536 (mmm) REVERT: F 719 ASN cc_start: 0.7566 (t0) cc_final: 0.7229 (m-40) REVERT: F 747 ASN cc_start: 0.6542 (OUTLIER) cc_final: 0.5761 (m-40) REVERT: G 182 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7935 (ptpt) REVERT: G 282 ARG cc_start: 0.8244 (mmt90) cc_final: 0.7804 (mmt-90) REVERT: G 310 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7683 (mp) REVERT: G 526 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5677 (pp20) REVERT: G 573 MET cc_start: 0.9133 (ptp) cc_final: 0.8875 (ptt) REVERT: G 578 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8059 (ptm160) REVERT: G 590 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8418 (ttmt) REVERT: G 719 ASN cc_start: 0.8993 (m-40) cc_final: 0.8736 (m-40) REVERT: G 747 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8900 (t0) REVERT: G 815 ASP cc_start: 0.8102 (m-30) cc_final: 0.7887 (p0) REVERT: G 829 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7737 (ptpp) REVERT: E 271 LYS cc_start: 0.8728 (mppt) cc_final: 0.8414 (mttm) REVERT: E 277 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: E 285 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: E 391 TYR cc_start: 0.6146 (t80) cc_final: 0.5935 (t80) REVERT: E 425 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6722 (mmt) REVERT: E 431 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6846 (tpp-160) REVERT: E 465 TYR cc_start: 0.6715 (m-80) cc_final: 0.6482 (m-80) REVERT: E 497 PHE cc_start: 0.6050 (t80) cc_final: 0.5276 (t80) REVERT: A 38 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7184 (ttp-170) REVERT: A 151 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7211 (pp20) REVERT: A 271 LYS cc_start: 0.8844 (mptt) cc_final: 0.8585 (mppt) REVERT: A 291 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7819 (tp30) REVERT: A 346 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 360 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: A 617 MET cc_start: 0.7898 (mtt) cc_final: 0.7543 (mtt) REVERT: A 715 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: A 819 LYS cc_start: 0.7613 (mtpp) cc_final: 0.7358 (tppt) REVERT: A 826 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: A 871 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7111 (tp30) REVERT: A 929 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7828 (mptp) outliers start: 249 outliers final: 89 residues processed: 756 average time/residue: 0.6883 time to fit residues: 634.1932 Evaluate side-chains 662 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 526 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 244 ARG Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 244 ARG Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 431 ARG Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 244 ARG Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 723 ILE Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 171 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 561 SER Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 635 CYS Chi-restraints excluded: chain F residue 643 THR Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 747 ASN Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 152 GLN Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 382 VAL Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 718 LYS Chi-restraints excluded: chain G residue 747 ASN Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 277 GLU Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 826 GLU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 258 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 498 optimal weight: 0.7980 chunk 236 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 157 optimal weight: 0.3980 chunk 193 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 194 GLN B 456 GLN B 489 ASN B 549 HIS B 746 ASN C 40 GLN C 159 GLN C 259 GLN C 268 ASN C 309 GLN C 489 ASN C 875 ASN D 94 ASN D 159 GLN D 226 GLN D 489 ASN D 875 ASN F 159 GLN G 47 ASN G 159 GLN G 392 HIS G 499 GLN E 346 GLN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN E 597 ASN E 875 ASN A 159 GLN A 259 GLN A 309 GLN A 721 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.194347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149961 restraints weight = 46377.834| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.64 r_work: 0.3491 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 44581 Z= 0.121 Angle : 0.548 8.771 60044 Z= 0.292 Chirality : 0.039 0.171 6784 Planarity : 0.004 0.058 7672 Dihedral : 4.567 58.304 5895 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.17 % Rotamer: Outliers : 3.57 % Allowed : 23.94 % Favored : 72.49 % 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: 0.09 (0.12), residues: 5350 helix: 1.04 (0.09), residues: 3238 sheet: 0.82 (0.34), residues: 230 loop : -1.79 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 934 TYR 0.019 0.001 TYR B 391 PHE 0.019 0.001 PHE F 646 TRP 0.021 0.002 TRP G 738 HIS 0.008 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00263 (44581) covalent geometry : angle 0.54832 (60044) hydrogen bonds : bond 0.03872 ( 2245) hydrogen bonds : angle 4.38193 ( 6588) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 586 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7829 (tp40) REVERT: B 214 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7741 (mmtm) REVERT: B 291 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8156 (mm-30) REVERT: B 342 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5769 (tp) REVERT: B 392 HIS cc_start: 0.6866 (m90) cc_final: 0.6498 (t70) REVERT: B 473 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6834 (tm-30) REVERT: B 584 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5975 (mpp) REVERT: B 617 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7381 (mtm) REVERT: B 622 VAL cc_start: 0.7506 (t) cc_final: 0.7219 (p) REVERT: B 625 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6275 (mt) REVERT: B 728 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.6761 (ptp-170) REVERT: B 929 LYS cc_start: 0.7488 (mttm) cc_final: 0.7049 (tttm) REVERT: C 151 GLU cc_start: 0.7270 (pp20) cc_final: 0.6976 (pp20) REVERT: C 155 ASN cc_start: 0.7897 (m110) cc_final: 0.7632 (m-40) REVERT: C 191 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7935 (mm) REVERT: C 244 ARG cc_start: 0.8463 (ptp-170) cc_final: 0.8147 (tpt-90) REVERT: C 311 LYS cc_start: 0.7166 (pmtt) cc_final: 0.6533 (pttm) REVERT: C 331 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6732 (pptt) REVERT: C 336 MET cc_start: 0.6357 (OUTLIER) cc_final: 0.5909 (mmt) REVERT: C 337 GLN cc_start: 0.5697 (OUTLIER) cc_final: 0.5488 (pm20) REVERT: C 392 HIS cc_start: 0.7187 (m-70) cc_final: 0.6894 (t-90) REVERT: C 496 LYS cc_start: 0.8808 (mttm) cc_final: 0.8356 (mttt) REVERT: C 500 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7875 (tpt) REVERT: C 571 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7249 (tp) REVERT: C 750 ASP cc_start: 0.6240 (OUTLIER) cc_final: 0.5847 (t70) REVERT: D 195 ASP cc_start: 0.7927 (p0) cc_final: 0.7667 (p0) REVERT: D 201 GLU cc_start: 0.8277 (tt0) cc_final: 0.8063 (tp30) REVERT: D 206 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7616 (mmt-90) REVERT: D 214 LYS cc_start: 0.6908 (ptpp) cc_final: 0.6145 (ptmt) REVERT: D 285 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7239 (pt0) REVERT: D 346 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7377 (tp40) REVERT: D 350 ASP cc_start: 0.8240 (m-30) cc_final: 0.7968 (m-30) REVERT: D 431 ARG cc_start: 0.8558 (ttt180) cc_final: 0.8142 (ttt90) REVERT: D 440 ARG cc_start: 0.7412 (ptm160) cc_final: 0.7136 (ptp-110) REVERT: D 473 GLU cc_start: 0.7253 (tm-30) cc_final: 0.6960 (tp30) REVERT: D 717 LEU cc_start: 0.7928 (tp) cc_final: 0.7618 (mt) REVERT: D 718 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6982 (mmpt) REVERT: D 753 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7183 (ttpp) REVERT: D 775 MET cc_start: 0.7381 (mmm) cc_final: 0.7009 (mmm) REVERT: D 798 ASP cc_start: 0.7793 (m-30) cc_final: 0.7544 (p0) REVERT: D 836 LYS cc_start: 0.7402 (mttm) cc_final: 0.6725 (mppt) REVERT: D 893 ASP cc_start: 0.6006 (OUTLIER) cc_final: 0.5435 (t0) REVERT: F 132 MET cc_start: 0.8542 (mtp) cc_final: 0.8317 (mtp) REVERT: F 182 LYS cc_start: 0.7068 (pttt) cc_final: 0.6445 (mptt) REVERT: F 330 VAL cc_start: 0.7541 (OUTLIER) cc_final: 0.7275 (m) REVERT: F 336 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6187 (mtt) REVERT: F 425 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8609 (mpp) REVERT: F 431 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8102 (tpt-90) REVERT: F 530 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6996 (tm-30) REVERT: F 584 MET cc_start: 0.5766 (mmt) cc_final: 0.5398 (mmm) REVERT: F 592 ASN cc_start: 0.7419 (t0) cc_final: 0.7128 (t0) REVERT: F 715 GLN cc_start: 0.7459 (tp40) cc_final: 0.7167 (tt0) REVERT: F 719 ASN cc_start: 0.7456 (t0) cc_final: 0.7154 (m-40) REVERT: G 253 ASP cc_start: 0.8663 (t70) cc_final: 0.8459 (t70) REVERT: G 282 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7864 (mmt-90) REVERT: G 526 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5596 (pp20) REVERT: G 573 MET cc_start: 0.8981 (ptp) cc_final: 0.8694 (ptt) REVERT: G 719 ASN cc_start: 0.8994 (m-40) cc_final: 0.8723 (m-40) REVERT: E 151 GLU cc_start: 0.6859 (pm20) cc_final: 0.6475 (mm-30) REVERT: E 235 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8431 (tp30) REVERT: E 271 LYS cc_start: 0.8643 (mppt) cc_final: 0.8347 (mttm) REVERT: E 285 GLU cc_start: 0.7827 (pt0) cc_final: 0.7592 (pp20) REVERT: E 291 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: E 391 TYR cc_start: 0.6205 (t80) cc_final: 0.5973 (t80) REVERT: E 425 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.6445 (mmt) REVERT: E 437 GLU cc_start: 0.8103 (mp0) cc_final: 0.7603 (mm-30) REVERT: E 497 PHE cc_start: 0.5996 (t80) cc_final: 0.5244 (t80) REVERT: E 584 MET cc_start: 0.2432 (mtm) cc_final: 0.1352 (pp-130) REVERT: E 765 MET cc_start: 0.3816 (mtm) cc_final: 0.3035 (tpp) REVERT: A 271 LYS cc_start: 0.8722 (mptt) cc_final: 0.8512 (mptt) REVERT: A 291 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: A 617 MET cc_start: 0.7853 (OUTLIER) cc_final: 0.7607 (mtt) REVERT: A 871 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6846 (tp30) REVERT: A 929 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7768 (mptp) outliers start: 174 outliers final: 55 residues processed: 711 average time/residue: 0.6916 time to fit residues: 602.2950 Evaluate side-chains 623 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 538 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 500 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 646 PHE Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 159 GLN Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 477 optimal weight: 3.9990 chunk 349 optimal weight: 2.9990 chunk 439 optimal weight: 2.9990 chunk 497 optimal weight: 2.9990 chunk 534 optimal weight: 5.9990 chunk 78 optimal weight: 9.9990 chunk 535 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 453 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 152 GLN B 456 GLN B 549 HIS ** B 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN C 268 ASN C 499 GLN C 644 ASN C 875 ASN D 40 GLN D 154 GLN D 159 GLN D 226 GLN D 875 ASN F 159 GLN F 469 GLN F 513 GLN G 47 ASN G 152 GLN G 560 ASN G 768 GLN A 374 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.189332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143896 restraints weight = 45734.705| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.60 r_work: 0.3385 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 44581 Z= 0.232 Angle : 0.674 9.681 60044 Z= 0.356 Chirality : 0.045 0.209 6784 Planarity : 0.005 0.058 7672 Dihedral : 4.863 58.727 5893 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 4.02 % Allowed : 23.78 % Favored : 72.20 % 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: -0.06 (0.11), residues: 5350 helix: 0.87 (0.09), residues: 3239 sheet: 0.63 (0.31), residues: 260 loop : -1.78 (0.15), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 934 TYR 0.037 0.002 TYR G 176 PHE 0.082 0.002 PHE G 441 TRP 0.020 0.002 TRP G 738 HIS 0.009 0.002 HIS C 165 Details of bonding type rmsd covalent geometry : bond 0.00536 (44581) covalent geometry : angle 0.67440 (60044) hydrogen bonds : bond 0.04998 ( 2245) hydrogen bonds : angle 4.66452 ( 6588) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 558 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7850 (tp40) REVERT: B 175 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7770 (pp20) REVERT: B 214 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7818 (mmtm) REVERT: B 291 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8220 (tp30) REVERT: B 342 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5538 (tp) REVERT: B 346 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: B 390 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8400 (tttm) REVERT: B 392 HIS cc_start: 0.7239 (m90) cc_final: 0.6805 (t-90) REVERT: B 473 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7172 (tm-30) REVERT: B 584 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6153 (mpp) REVERT: B 617 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (mtm) REVERT: B 622 VAL cc_start: 0.7567 (t) cc_final: 0.7194 (p) REVERT: B 625 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6373 (mt) REVERT: B 728 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.6751 (ptp-170) REVERT: B 929 LYS cc_start: 0.7495 (mttm) cc_final: 0.7009 (tttm) REVERT: C 154 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7581 (mp10) REVERT: C 191 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.8050 (mm) REVERT: C 244 ARG cc_start: 0.8513 (ptp-170) cc_final: 0.8194 (tpt-90) REVERT: C 245 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8626 (mttt) REVERT: C 311 LYS cc_start: 0.7390 (pmtt) cc_final: 0.6706 (ptpp) REVERT: C 331 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.6955 (pptt) REVERT: C 336 MET cc_start: 0.6337 (OUTLIER) cc_final: 0.5842 (mmt) REVERT: C 337 GLN cc_start: 0.5975 (OUTLIER) cc_final: 0.5709 (pm20) REVERT: C 392 HIS cc_start: 0.7217 (m-70) cc_final: 0.6937 (t-90) REVERT: C 571 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7372 (tp) REVERT: C 750 ASP cc_start: 0.6420 (OUTLIER) cc_final: 0.5924 (p0) REVERT: C 819 LYS cc_start: 0.7114 (mptp) cc_final: 0.6895 (mmtt) REVERT: C 930 ASP cc_start: 0.7698 (m-30) cc_final: 0.7350 (m-30) REVERT: D 195 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7802 (p0) REVERT: D 201 GLU cc_start: 0.8411 (tt0) cc_final: 0.8181 (tp30) REVERT: D 206 ARG cc_start: 0.7877 (tpp-160) cc_final: 0.7638 (mmt-90) REVERT: D 214 LYS cc_start: 0.7229 (ptpp) cc_final: 0.6508 (ptmt) REVERT: D 285 GLU cc_start: 0.7782 (pp20) cc_final: 0.7443 (pt0) REVERT: D 346 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: D 350 ASP cc_start: 0.8356 (m-30) cc_final: 0.8066 (m-30) REVERT: D 431 ARG cc_start: 0.8647 (ttt180) cc_final: 0.8039 (ttt90) REVERT: D 440 ARG cc_start: 0.7487 (ptm160) cc_final: 0.7176 (ptp-110) REVERT: D 473 GLU cc_start: 0.7425 (tm-30) cc_final: 0.7090 (tp30) REVERT: D 717 LEU cc_start: 0.8015 (tp) cc_final: 0.7769 (mt) REVERT: D 718 LYS cc_start: 0.7436 (OUTLIER) cc_final: 0.7204 (mmtm) REVERT: D 753 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7309 (ttpp) REVERT: D 798 ASP cc_start: 0.7921 (m-30) cc_final: 0.7641 (p0) REVERT: D 836 LYS cc_start: 0.7500 (mttm) cc_final: 0.6798 (mppt) REVERT: D 893 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5911 (m-30) REVERT: F 132 MET cc_start: 0.8681 (mtp) cc_final: 0.8418 (mtp) REVERT: F 182 LYS cc_start: 0.7277 (pttt) cc_final: 0.6689 (mptt) REVERT: F 330 VAL cc_start: 0.8019 (OUTLIER) cc_final: 0.7649 (m) REVERT: F 336 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6405 (mtt) REVERT: F 392 HIS cc_start: 0.7255 (t70) cc_final: 0.6646 (t-90) REVERT: F 431 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.8200 (tpt-90) REVERT: F 440 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7011 (ptp-110) REVERT: F 471 GLU cc_start: 0.7056 (mp0) cc_final: 0.6849 (pt0) REVERT: F 530 GLN cc_start: 0.7502 (mm-40) cc_final: 0.7089 (tm-30) REVERT: F 584 MET cc_start: 0.5824 (mmt) cc_final: 0.5387 (mmm) REVERT: F 715 GLN cc_start: 0.7626 (tp40) cc_final: 0.6901 (tm-30) REVERT: F 719 ASN cc_start: 0.7563 (t0) cc_final: 0.7202 (m-40) REVERT: G 182 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7566 (ptpt) REVERT: G 253 ASP cc_start: 0.8830 (t70) cc_final: 0.8611 (t0) REVERT: G 279 GLU cc_start: 0.7253 (mp0) cc_final: 0.7016 (pm20) REVERT: G 526 GLU cc_start: 0.6058 (OUTLIER) cc_final: 0.5675 (pp20) REVERT: G 573 MET cc_start: 0.9107 (ptp) cc_final: 0.8842 (ptt) REVERT: G 590 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: G 719 ASN cc_start: 0.9013 (m-40) cc_final: 0.8747 (m-40) REVERT: E 40 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6895 (tp40) REVERT: E 191 ILE cc_start: 0.7812 (tp) cc_final: 0.7591 (tt) REVERT: E 235 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8397 (tp30) REVERT: E 271 LYS cc_start: 0.8751 (mppt) cc_final: 0.8388 (mttm) REVERT: E 285 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (pp20) REVERT: E 291 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7747 (tp30) REVERT: E 329 LYS cc_start: 0.5933 (tppp) cc_final: 0.5709 (tppp) REVERT: E 391 TYR cc_start: 0.6379 (t80) cc_final: 0.6100 (t80) REVERT: E 425 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.6689 (mmt) REVERT: E 437 GLU cc_start: 0.8131 (mp0) cc_final: 0.7575 (mm-30) REVERT: E 497 PHE cc_start: 0.5970 (t80) cc_final: 0.5193 (t80) REVERT: E 584 MET cc_start: 0.2353 (mtm) cc_final: 0.1412 (pp-130) REVERT: E 800 GLU cc_start: 0.4622 (OUTLIER) cc_final: 0.4162 (pt0) REVERT: A 38 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7329 (ttp-170) REVERT: A 271 LYS cc_start: 0.8809 (mptt) cc_final: 0.8588 (mptt) REVERT: A 291 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7824 (tp30) REVERT: A 310 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 346 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8006 (tm-30) REVERT: A 455 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8831 (ttmt) REVERT: A 761 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.6320 (pt0) REVERT: A 871 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: A 929 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7813 (mptp) outliers start: 196 outliers final: 89 residues processed: 699 average time/residue: 0.6265 time to fit residues: 537.4628 Evaluate side-chains 662 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 530 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 346 GLN Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 337 GLN Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 646 PHE Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 336 MET Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 635 CYS Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 813 SER Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 527 LYS Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 718 LYS Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 887 LEU Chi-restraints excluded: chain G residue 889 ASP Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 800 GLU Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 761 GLU Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 487 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 540 optimal weight: 0.8980 chunk 275 optimal weight: 6.9990 chunk 249 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 472 optimal weight: 0.9980 chunk 543 optimal weight: 0.6980 chunk 213 optimal weight: 3.9990 chunk 316 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 456 GLN B 549 HIS B 751 GLN C 40 GLN C 875 ASN D 40 GLN D 152 GLN D 154 GLN D 226 GLN D 875 ASN F 159 GLN ** F 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 47 ASN G 392 HIS G 560 ASN G 869 ASN E 156 HIS ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN A 721 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.192660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148185 restraints weight = 46294.874| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.66 r_work: 0.3464 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 44581 Z= 0.130 Angle : 0.561 10.792 60044 Z= 0.298 Chirality : 0.040 0.189 6784 Planarity : 0.004 0.055 7672 Dihedral : 4.501 55.850 5893 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 3.22 % Allowed : 24.87 % Favored : 71.91 % 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: 0.23 (0.12), residues: 5350 helix: 1.12 (0.09), residues: 3237 sheet: 0.90 (0.34), residues: 230 loop : -1.68 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 934 TYR 0.022 0.001 TYR B 391 PHE 0.030 0.001 PHE G 441 TRP 0.021 0.002 TRP C 716 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00289 (44581) covalent geometry : angle 0.56119 (60044) hydrogen bonds : bond 0.03996 ( 2245) hydrogen bonds : angle 4.39178 ( 6588) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 571 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7800 (tp40) REVERT: B 175 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7672 (pp20) REVERT: B 214 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7771 (mmtm) REVERT: B 291 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8082 (mm-30) REVERT: B 333 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5973 (mp0) REVERT: B 342 ILE cc_start: 0.5985 (OUTLIER) cc_final: 0.5428 (tp) REVERT: B 390 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8347 (tttm) REVERT: B 392 HIS cc_start: 0.7088 (m90) cc_final: 0.6730 (t-90) REVERT: B 473 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: B 584 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6256 (mpp) REVERT: B 622 VAL cc_start: 0.7535 (t) cc_final: 0.7269 (p) REVERT: B 625 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6309 (mt) REVERT: B 728 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6796 (ptp-170) REVERT: B 875 ASN cc_start: 0.4852 (OUTLIER) cc_final: 0.4368 (m-40) REVERT: B 929 LYS cc_start: 0.7474 (mttm) cc_final: 0.7004 (tttm) REVERT: C 39 ASP cc_start: 0.6663 (m-30) cc_final: 0.6297 (m-30) REVERT: C 40 GLN cc_start: 0.6451 (tp40) cc_final: 0.6200 (tp-100) REVERT: C 182 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7317 (mtpt) REVERT: C 191 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7981 (mm) REVERT: C 244 ARG cc_start: 0.8523 (ptp-170) cc_final: 0.8191 (tpt-90) REVERT: C 245 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8539 (mttt) REVERT: C 311 LYS cc_start: 0.7250 (pmtt) cc_final: 0.6623 (ptpp) REVERT: C 331 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6712 (pttm) REVERT: C 392 HIS cc_start: 0.7220 (m-70) cc_final: 0.6923 (t-90) REVERT: C 496 LYS cc_start: 0.8838 (mttm) cc_final: 0.8336 (mttt) REVERT: C 571 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7296 (tp) REVERT: C 750 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5769 (t70) REVERT: D 43 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7485 (mm-30) REVERT: D 162 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7653 (ptp90) REVERT: D 195 ASP cc_start: 0.7953 (p0) cc_final: 0.7679 (p0) REVERT: D 201 GLU cc_start: 0.8344 (tt0) cc_final: 0.8130 (tp30) REVERT: D 214 LYS cc_start: 0.7118 (ptpp) cc_final: 0.6408 (ptmt) REVERT: D 285 GLU cc_start: 0.7588 (pp20) cc_final: 0.7272 (pt0) REVERT: D 346 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7636 (tp40) REVERT: D 431 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8112 (ttm-80) REVERT: D 440 ARG cc_start: 0.7420 (ptm160) cc_final: 0.7147 (ptp-110) REVERT: D 473 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7050 (tp30) REVERT: D 717 LEU cc_start: 0.7982 (tp) cc_final: 0.7740 (mt) REVERT: D 718 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7198 (mmtm) REVERT: D 753 LYS cc_start: 0.7889 (ttmm) cc_final: 0.7270 (mtpp) REVERT: D 775 MET cc_start: 0.7354 (mmm) cc_final: 0.6960 (mmm) REVERT: D 798 ASP cc_start: 0.7827 (m-30) cc_final: 0.7592 (p0) REVERT: D 836 LYS cc_start: 0.7426 (mttm) cc_final: 0.6719 (mppt) REVERT: D 893 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5780 (m-30) REVERT: F 132 MET cc_start: 0.8627 (mtp) cc_final: 0.8359 (mtp) REVERT: F 182 LYS cc_start: 0.7294 (pttt) cc_final: 0.6726 (mptt) REVERT: F 222 ASP cc_start: 0.6339 (p0) cc_final: 0.6056 (p0) REVERT: F 330 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7385 (m) REVERT: F 425 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8654 (mpp) REVERT: F 431 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8190 (tpt-90) REVERT: F 440 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7005 (ptp-110) REVERT: F 530 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7104 (tm-30) REVERT: F 584 MET cc_start: 0.5772 (mmt) cc_final: 0.5437 (mmm) REVERT: F 715 GLN cc_start: 0.7525 (tp40) cc_final: 0.6785 (tm-30) REVERT: F 719 ASN cc_start: 0.7461 (t0) cc_final: 0.7128 (m-40) REVERT: G 182 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7372 (mmtm) REVERT: G 205 LYS cc_start: 0.8593 (mtmt) cc_final: 0.8330 (mttp) REVERT: G 253 ASP cc_start: 0.8735 (t70) cc_final: 0.8517 (t0) REVERT: G 282 ARG cc_start: 0.8243 (mmt90) cc_final: 0.7861 (mmt-90) REVERT: G 425 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.7977 (mmt) REVERT: G 526 GLU cc_start: 0.6012 (OUTLIER) cc_final: 0.5629 (pp20) REVERT: G 573 MET cc_start: 0.8980 (ptp) cc_final: 0.8670 (ptt) REVERT: G 640 SER cc_start: 0.7882 (p) cc_final: 0.7665 (t) REVERT: G 719 ASN cc_start: 0.8999 (m-40) cc_final: 0.8736 (m-40) REVERT: E 235 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8335 (tp30) REVERT: E 271 LYS cc_start: 0.8707 (mppt) cc_final: 0.8418 (mttm) REVERT: E 285 GLU cc_start: 0.7955 (pt0) cc_final: 0.7712 (pp20) REVERT: E 291 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7726 (tp30) REVERT: E 391 TYR cc_start: 0.6360 (t80) cc_final: 0.6046 (t80) REVERT: E 425 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.6500 (mmt) REVERT: E 437 GLU cc_start: 0.8082 (mp0) cc_final: 0.7532 (mm-30) REVERT: E 497 PHE cc_start: 0.5933 (t80) cc_final: 0.5218 (t80) REVERT: E 500 MET cc_start: 0.5273 (tpt) cc_final: 0.4986 (mmm) REVERT: E 584 MET cc_start: 0.2193 (mtm) cc_final: 0.1313 (pp-130) REVERT: E 765 MET cc_start: 0.3839 (mtm) cc_final: 0.3010 (tpp) REVERT: A 271 LYS cc_start: 0.8760 (mptt) cc_final: 0.8557 (mptt) REVERT: A 279 GLU cc_start: 0.7860 (mp0) cc_final: 0.7647 (mp0) REVERT: A 291 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7737 (tp30) REVERT: A 337 GLN cc_start: 0.6014 (OUTLIER) cc_final: 0.5675 (pm20) REVERT: A 346 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: A 455 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8840 (ttmt) REVERT: A 617 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7579 (mtt) REVERT: A 871 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6933 (tp30) REVERT: A 929 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7753 (mptp) outliers start: 157 outliers final: 68 residues processed: 683 average time/residue: 0.6644 time to fit residues: 554.6777 Evaluate side-chains 645 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 542 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 441 PHE Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 425 MET Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 813 SER Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 566 LYS Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 136 optimal weight: 6.9990 chunk 501 optimal weight: 5.9990 chunk 423 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 411 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 487 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 543 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 152 GLN B 456 GLN B 549 HIS D 40 GLN D 152 GLN D 154 GLN D 159 GLN D 875 ASN F 159 GLN F 242 ASN G 47 ASN G 87 ASN G 159 GLN G 560 ASN G 768 GLN G 869 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.190418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.145056 restraints weight = 45913.610| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.63 r_work: 0.3395 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 44581 Z= 0.182 Angle : 0.625 10.498 60044 Z= 0.330 Chirality : 0.042 0.210 6784 Planarity : 0.004 0.056 7672 Dihedral : 4.651 57.187 5893 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.50 % Favored : 93.33 % Rotamer: Outliers : 3.04 % Allowed : 25.11 % Favored : 71.85 % 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: 0.16 (0.11), residues: 5350 helix: 1.04 (0.09), residues: 3247 sheet: 0.75 (0.32), residues: 261 loop : -1.70 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 636 TYR 0.028 0.002 TYR B 391 PHE 0.040 0.002 PHE G 441 TRP 0.031 0.002 TRP C 716 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00418 (44581) covalent geometry : angle 0.62499 (60044) hydrogen bonds : bond 0.04545 ( 2245) hydrogen bonds : angle 4.51168 ( 6588) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 547 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.7877 (tp40) REVERT: B 175 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7727 (pp20) REVERT: B 214 LYS cc_start: 0.8392 (mtmt) cc_final: 0.7789 (mmtm) REVERT: B 291 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: B 342 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5572 (tp) REVERT: B 390 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8374 (tttm) REVERT: B 392 HIS cc_start: 0.7264 (m90) cc_final: 0.6852 (t-90) REVERT: B 473 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: B 622 VAL cc_start: 0.7528 (t) cc_final: 0.7180 (p) REVERT: B 625 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6338 (mt) REVERT: B 728 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.6929 (ptp-170) REVERT: B 875 ASN cc_start: 0.4888 (OUTLIER) cc_final: 0.4364 (m-40) REVERT: B 929 LYS cc_start: 0.7492 (mttm) cc_final: 0.6993 (tttm) REVERT: C 154 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: C 182 LYS cc_start: 0.7865 (ptpt) cc_final: 0.7366 (mtpt) REVERT: C 191 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.8045 (mm) REVERT: C 244 ARG cc_start: 0.8524 (ptp-170) cc_final: 0.8194 (tpt-90) REVERT: C 245 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8568 (mttt) REVERT: C 331 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.6867 (pttm) REVERT: C 392 HIS cc_start: 0.7352 (m-70) cc_final: 0.6973 (t-90) REVERT: C 496 LYS cc_start: 0.8858 (mttm) cc_final: 0.8385 (mttt) REVERT: C 571 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7412 (tp) REVERT: C 750 ASP cc_start: 0.6284 (OUTLIER) cc_final: 0.5823 (t70) REVERT: C 930 ASP cc_start: 0.7642 (m-30) cc_final: 0.7314 (m-30) REVERT: D 159 GLN cc_start: 0.7715 (pt0) cc_final: 0.7364 (tt0) REVERT: D 162 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7658 (ptp90) REVERT: D 195 ASP cc_start: 0.8070 (p0) cc_final: 0.7761 (p0) REVERT: D 201 GLU cc_start: 0.8421 (tt0) cc_final: 0.8194 (tp30) REVERT: D 244 ARG cc_start: 0.8335 (mtp180) cc_final: 0.7882 (mtt90) REVERT: D 285 GLU cc_start: 0.7751 (pp20) cc_final: 0.7447 (pt0) REVERT: D 346 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7707 (tp40) REVERT: D 431 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8168 (ttm-80) REVERT: D 440 ARG cc_start: 0.7437 (ptm160) cc_final: 0.7135 (ptp-110) REVERT: D 473 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7044 (tp30) REVERT: D 717 LEU cc_start: 0.7982 (tp) cc_final: 0.7743 (mt) REVERT: D 718 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7144 (mmtm) REVERT: D 753 LYS cc_start: 0.7915 (ttmm) cc_final: 0.7273 (mtpp) REVERT: D 775 MET cc_start: 0.7427 (mmm) cc_final: 0.7004 (mmm) REVERT: D 798 ASP cc_start: 0.7833 (m-30) cc_final: 0.7585 (p0) REVERT: D 802 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8308 (mm) REVERT: D 836 LYS cc_start: 0.7485 (mttm) cc_final: 0.6764 (mppt) REVERT: F 132 MET cc_start: 0.8694 (mtp) cc_final: 0.8430 (mtp) REVERT: F 182 LYS cc_start: 0.7394 (pttt) cc_final: 0.6786 (mptt) REVERT: F 224 ASP cc_start: 0.7879 (m-30) cc_final: 0.7574 (p0) REVERT: F 330 VAL cc_start: 0.7963 (OUTLIER) cc_final: 0.7638 (m) REVERT: F 431 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7922 (tpt-90) REVERT: F 440 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7135 (ptp-110) REVERT: F 530 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7101 (tm-30) REVERT: F 584 MET cc_start: 0.5642 (mmt) cc_final: 0.5299 (mmm) REVERT: F 715 GLN cc_start: 0.7649 (tp40) cc_final: 0.6887 (tm-30) REVERT: F 719 ASN cc_start: 0.7575 (t0) cc_final: 0.7224 (m-40) REVERT: G 182 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7410 (mmtm) REVERT: G 205 LYS cc_start: 0.8606 (mtmt) cc_final: 0.8317 (mttp) REVERT: G 253 ASP cc_start: 0.8810 (t70) cc_final: 0.8589 (t0) REVERT: G 282 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7684 (mmt180) REVERT: G 291 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: G 328 ILE cc_start: 0.6729 (OUTLIER) cc_final: 0.6483 (pp) REVERT: G 526 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5698 (pp20) REVERT: G 573 MET cc_start: 0.9053 (ptp) cc_final: 0.8767 (ptt) REVERT: G 590 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8340 (ttmt) REVERT: G 640 SER cc_start: 0.7941 (p) cc_final: 0.7682 (t) REVERT: G 719 ASN cc_start: 0.9033 (m-40) cc_final: 0.8772 (m-40) REVERT: G 866 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7753 (mppt) REVERT: E 40 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6905 (tp40) REVERT: E 235 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8457 (tp30) REVERT: E 271 LYS cc_start: 0.8798 (mppt) cc_final: 0.8419 (mttm) REVERT: E 291 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7781 (tp30) REVERT: E 391 TYR cc_start: 0.6432 (t80) cc_final: 0.6099 (t80) REVERT: E 425 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.6591 (mmt) REVERT: E 437 GLU cc_start: 0.8115 (mp0) cc_final: 0.7569 (mm-30) REVERT: E 497 PHE cc_start: 0.5977 (t80) cc_final: 0.5217 (t80) REVERT: E 584 MET cc_start: 0.2249 (mtm) cc_final: 0.1294 (pp-130) REVERT: E 765 MET cc_start: 0.3874 (mtm) cc_final: 0.3021 (tpp) REVERT: A 271 LYS cc_start: 0.8838 (mptt) cc_final: 0.8604 (mptt) REVERT: A 291 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7821 (tp30) REVERT: A 337 GLN cc_start: 0.6020 (OUTLIER) cc_final: 0.5716 (pm20) REVERT: A 346 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: A 455 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8847 (ttmt) REVERT: A 617 MET cc_start: 0.7889 (mtt) cc_final: 0.7556 (mtt) REVERT: A 871 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7060 (tp30) REVERT: A 929 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7759 (mptp) outliers start: 148 outliers final: 74 residues processed: 656 average time/residue: 0.5653 time to fit residues: 454.2147 Evaluate side-chains 645 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 535 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 154 GLN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 802 ILE Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 175 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 813 SER Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 182 LYS Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 566 LYS Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 913 THR Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 532 ILE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 311 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 455 optimal weight: 2.9990 chunk 374 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 152 GLN B 456 GLN B 549 HIS D 40 GLN D 152 GLN D 154 GLN D 159 GLN D 875 ASN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 ASN G 159 GLN G 560 ASN ** E 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.192423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147823 restraints weight = 46307.452| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.65 r_work: 0.3435 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 44581 Z= 0.137 Angle : 0.575 11.748 60044 Z= 0.303 Chirality : 0.040 0.236 6784 Planarity : 0.004 0.052 7672 Dihedral : 4.454 56.055 5891 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.91 % Favored : 93.93 % Rotamer: Outliers : 2.61 % Allowed : 25.61 % Favored : 71.79 % 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: 0.35 (0.12), residues: 5350 helix: 1.19 (0.09), residues: 3238 sheet: 0.88 (0.33), residues: 251 loop : -1.60 (0.15), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 636 TYR 0.024 0.001 TYR B 391 PHE 0.026 0.002 PHE G 441 TRP 0.038 0.002 TRP C 716 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00309 (44581) covalent geometry : angle 0.57543 (60044) hydrogen bonds : bond 0.04048 ( 2245) hydrogen bonds : angle 4.38161 ( 6588) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 561 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 214 LYS cc_start: 0.8383 (mtmt) cc_final: 0.7820 (mmtm) REVERT: B 291 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: B 342 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5401 (tp) REVERT: B 390 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8375 (tttm) REVERT: B 392 HIS cc_start: 0.7203 (m90) cc_final: 0.6790 (t-90) REVERT: B 473 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7091 (tm-30) REVERT: B 584 MET cc_start: 0.6375 (mpp) cc_final: 0.6150 (mpm) REVERT: B 622 VAL cc_start: 0.7510 (t) cc_final: 0.7211 (p) REVERT: B 625 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6313 (mt) REVERT: B 728 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.6869 (ptp-170) REVERT: B 875 ASN cc_start: 0.4890 (OUTLIER) cc_final: 0.4386 (m-40) REVERT: B 929 LYS cc_start: 0.7537 (mttm) cc_final: 0.7063 (tttm) REVERT: C 39 ASP cc_start: 0.6659 (m-30) cc_final: 0.6226 (m-30) REVERT: C 182 LYS cc_start: 0.7872 (ptpt) cc_final: 0.7448 (mtpt) REVERT: C 191 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7982 (mm) REVERT: C 244 ARG cc_start: 0.8563 (ptp-170) cc_final: 0.8187 (tpt-90) REVERT: C 245 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8544 (mttt) REVERT: C 311 LYS cc_start: 0.7278 (pmtt) cc_final: 0.6615 (ptpp) REVERT: C 331 LYS cc_start: 0.7523 (OUTLIER) cc_final: 0.6859 (pttm) REVERT: C 392 HIS cc_start: 0.7375 (m-70) cc_final: 0.6988 (t-90) REVERT: C 496 LYS cc_start: 0.8831 (mttm) cc_final: 0.8374 (mttt) REVERT: C 571 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7383 (tp) REVERT: C 750 ASP cc_start: 0.6167 (OUTLIER) cc_final: 0.5814 (t70) REVERT: D 159 GLN cc_start: 0.7620 (pt0) cc_final: 0.7301 (tt0) REVERT: D 162 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7617 (ptp90) REVERT: D 195 ASP cc_start: 0.7991 (p0) cc_final: 0.7689 (p0) REVERT: D 201 GLU cc_start: 0.8386 (tt0) cc_final: 0.8158 (tp30) REVERT: D 214 LYS cc_start: 0.6904 (ptpp) cc_final: 0.6162 (ptmt) REVERT: D 244 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7893 (mtt90) REVERT: D 285 GLU cc_start: 0.7646 (pp20) cc_final: 0.7320 (pt0) REVERT: D 346 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7567 (tp40) REVERT: D 431 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8135 (ttm-80) REVERT: D 440 ARG cc_start: 0.7428 (ptm160) cc_final: 0.7127 (ptp-110) REVERT: D 473 GLU cc_start: 0.7381 (tm-30) cc_final: 0.7071 (tp30) REVERT: D 717 LEU cc_start: 0.8010 (tp) cc_final: 0.7780 (mt) REVERT: D 718 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.7126 (mmtm) REVERT: D 753 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7253 (mtpp) REVERT: D 802 ILE cc_start: 0.8605 (mt) cc_final: 0.8354 (mm) REVERT: D 836 LYS cc_start: 0.7427 (mttm) cc_final: 0.6671 (mppt) REVERT: F 91 LYS cc_start: 0.6824 (mtmt) cc_final: 0.6509 (mttt) REVERT: F 132 MET cc_start: 0.8644 (mtp) cc_final: 0.8376 (mtp) REVERT: F 182 LYS cc_start: 0.7467 (pttt) cc_final: 0.6779 (mptt) REVERT: F 330 VAL cc_start: 0.7852 (OUTLIER) cc_final: 0.7538 (m) REVERT: F 384 GLN cc_start: 0.8643 (tt0) cc_final: 0.8325 (mt0) REVERT: F 431 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8038 (tpt-90) REVERT: F 440 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7022 (ptp-110) REVERT: F 530 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7155 (tm-30) REVERT: F 584 MET cc_start: 0.5662 (mmt) cc_final: 0.5441 (mmm) REVERT: F 719 ASN cc_start: 0.7516 (t0) cc_final: 0.7219 (m-40) REVERT: G 182 LYS cc_start: 0.8219 (ptpt) cc_final: 0.7442 (mmtm) REVERT: G 205 LYS cc_start: 0.8577 (mtmt) cc_final: 0.8320 (mttp) REVERT: G 253 ASP cc_start: 0.8756 (t70) cc_final: 0.8533 (t0) REVERT: G 282 ARG cc_start: 0.8235 (mmt90) cc_final: 0.7975 (mmt-90) REVERT: G 291 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8033 (tp30) REVERT: G 526 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5807 (pp20) REVERT: G 573 MET cc_start: 0.8989 (ptp) cc_final: 0.8674 (ptt) REVERT: G 640 SER cc_start: 0.7936 (p) cc_final: 0.7730 (t) REVERT: G 719 ASN cc_start: 0.9002 (m-40) cc_final: 0.8733 (m-40) REVERT: G 890 GLU cc_start: 0.7516 (pp20) cc_final: 0.7264 (tm-30) REVERT: E 191 ILE cc_start: 0.7417 (tp) cc_final: 0.7031 (tp) REVERT: E 235 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8429 (tp30) REVERT: E 271 LYS cc_start: 0.8750 (mppt) cc_final: 0.8432 (mttm) REVERT: E 291 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: E 391 TYR cc_start: 0.6410 (t80) cc_final: 0.6110 (t80) REVERT: E 425 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.6484 (mmt) REVERT: E 437 GLU cc_start: 0.8144 (mp0) cc_final: 0.7596 (mm-30) REVERT: E 497 PHE cc_start: 0.5904 (t80) cc_final: 0.5217 (t80) REVERT: E 500 MET cc_start: 0.5113 (tpt) cc_final: 0.4699 (mmm) REVERT: E 584 MET cc_start: 0.2246 (mtm) cc_final: 0.1287 (pp-130) REVERT: E 765 MET cc_start: 0.3838 (mtm) cc_final: 0.2998 (tpp) REVERT: A 271 LYS cc_start: 0.8806 (mptt) cc_final: 0.8578 (mptt) REVERT: A 291 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 337 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: A 346 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8020 (tm-30) REVERT: A 455 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8850 (ttmt) REVERT: A 617 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7606 (mtt) REVERT: A 871 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: A 929 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7742 (mptp) outliers start: 127 outliers final: 76 residues processed: 651 average time/residue: 0.5070 time to fit residues: 405.2980 Evaluate side-chains 645 residues out of total 4874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 540 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 GLU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 390 LYS Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 657 VAL Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 750 ASP Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain B residue 875 ASN Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 214 LYS Chi-restraints excluded: chain C residue 245 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 509 SER Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 571 LEU Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 162 ARG Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 864 SER Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 214 LYS Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 431 ARG Chi-restraints excluded: chain F residue 440 ARG Chi-restraints excluded: chain F residue 532 ILE Chi-restraints excluded: chain F residue 633 SER Chi-restraints excluded: chain F residue 644 ASN Chi-restraints excluded: chain F residue 707 SER Chi-restraints excluded: chain F residue 739 SER Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain G residue 222 ASP Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 291 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 566 LYS Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 727 ILE Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 635 CYS Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 346 GLN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 718 LYS Chi-restraints excluded: chain A residue 739 SER Chi-restraints excluded: chain A residue 871 GLU Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 929 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 314 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 409 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 389 optimal weight: 4.9990 chunk 382 optimal weight: 0.7980 chunk 124 optimal weight: 0.0370 chunk 512 optimal weight: 7.9990 chunk 362 optimal weight: 3.9990 chunk 468 optimal weight: 5.9990 chunk 365 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 152 GLN B 456 GLN B 549 HIS D 40 GLN D 152 GLN D 154 GLN D 875 ASN ** F 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 47 ASN G 309 GLN G 560 ASN E 374 GLN A 159 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.194465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.149778 restraints weight = 46273.459| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.68 r_work: 0.3473 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 44581 Z= 0.119 Angle : 0.559 11.853 60044 Z= 0.295 Chirality : 0.039 0.189 6784 Planarity : 0.004 0.049 7672 Dihedral : 4.333 54.725 5891 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.00 % Favored : 93.83 % Rotamer: Outliers : 2.65 % Allowed : 25.58 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.12), residues: 5350 helix: 1.31 (0.09), residues: 3238 sheet: 0.91 (0.32), residues: 257 loop : -1.57 (0.15), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 636 TYR 0.024 0.001 TYR B 391 PHE 0.019 0.001 PHE F 646 TRP 0.041 0.002 TRP C 716 HIS 0.009 0.001 HIS B 549 Details of bonding type rmsd covalent geometry : bond 0.00263 (44581) covalent geometry : angle 0.55924 (60044) hydrogen bonds : bond 0.03804 ( 2245) hydrogen bonds : angle 4.29738 ( 6588) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18668.20 seconds wall clock time: 317 minutes 43.07 seconds (19063.07 seconds total)