Starting phenix.real_space_refine on Fri Mar 6 07:23:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vxb_32174/03_2026/7vxb_32174.map" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.126 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 145 5.16 5 C 19069 2.51 5 N 5002 2.21 5 O 5672 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29888 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8354 Classifications: {'peptide': 1068} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "A" Number of atoms: 8310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8310 Classifications: {'peptide': 1062} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1009} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8354 Classifications: {'peptide': 1068} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1015} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.93, per 1000 atoms: 0.23 Number of scatterers: 29888 At special positions: 0 Unit cell: (161.764, 150.834, 239.367, 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 145 16.00 O 5672 8.00 N 5002 7.00 C 19069 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.02 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.33 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.3 seconds 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7118 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 52 sheets defined 30.5% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'D' and resid 294 through 304 removed outlier: 3.610A pdb=" N THR D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 344 removed outlier: 3.668A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 386 through 390 Processing helix chain 'D' and resid 406 through 410 Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 737 through 743 removed outlier: 3.678A pdb=" N CYS D 743 " --> pdb=" O THR D 739 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 755 removed outlier: 3.508A pdb=" N LEU D 752 " --> pdb=" O GLU D 748 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 753 " --> pdb=" O CYS D 749 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 754 " --> pdb=" O SER D 750 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 780 removed outlier: 4.590A pdb=" N THR D 761 " --> pdb=" O GLY D 757 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG D 765 " --> pdb=" O THR D 761 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.985A pdb=" N LEU D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 849 through 856 removed outlier: 3.694A pdb=" N GLN D 853 " --> pdb=" O LEU D 849 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 856 " --> pdb=" O ALA D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 removed outlier: 3.512A pdb=" N THR D 874 " --> pdb=" O ILE D 870 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 909 removed outlier: 3.709A pdb=" N MET D 902 " --> pdb=" O PHE D 898 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA D 903 " --> pdb=" O ALA D 899 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 905 " --> pdb=" O GLN D 901 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 907 " --> pdb=" O ALA D 903 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 913 through 941 removed outlier: 3.718A pdb=" N TYR D 917 " --> pdb=" O GLN D 913 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU D 918 " --> pdb=" O ASN D 914 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS D 921 " --> pdb=" O TYR D 917 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N LEU D 922 " --> pdb=" O GLU D 918 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ASN D 925 " --> pdb=" O LYS D 921 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.974A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 984 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 3.573A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG D 995 " --> pdb=" O VAL D 991 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D1024 " --> pdb=" O ALA D1020 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D1030 " --> pdb=" O ALA D1026 " (cutoff:3.500A) Processing helix chain 'D' and resid 1142 through 1147 removed outlier: 3.638A pdb=" N ASP D1146 " --> pdb=" O PRO D1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.553A pdb=" N GLN C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 81 removed outlier: 3.564A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR C 78 " --> pdb=" O LYS C 74 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.948A pdb=" N GLU C 87 " --> pdb=" O PRO C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.811A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.965A pdb=" N VAL C 107 " --> pdb=" O GLY C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 removed outlier: 3.963A pdb=" N ASN C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 155 removed outlier: 3.617A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN C 154 " --> pdb=" O GLU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 removed outlier: 3.692A pdb=" N ALA C 164 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG C 169 " --> pdb=" O TRP C 165 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU C 171 " --> pdb=" O SER C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 194 removed outlier: 4.298A pdb=" N LEU C 179 " --> pdb=" O GLN C 175 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.524A pdb=" N TYR C 202 " --> pdb=" O ASP C 198 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TRP C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'C' and resid 220 through 248 removed outlier: 4.060A pdb=" N GLU C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU C 232 " --> pdb=" O HIS C 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 233 " --> pdb=" O THR C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.559A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.131A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 301 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.711A pdb=" N PHE C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 314 " --> pdb=" O GLU C 310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.625A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.565A pdb=" N PHE C 369 " --> pdb=" O THR C 365 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS C 373 " --> pdb=" O PHE C 369 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 379 " --> pdb=" O GLU C 375 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 384 " --> pdb=" O GLN C 380 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 399 through 413 removed outlier: 4.143A pdb=" N GLY C 405 " --> pdb=" O HIS C 401 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.559A pdb=" N ILE C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 447 removed outlier: 3.722A pdb=" N ASN C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 438 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR C 445 " --> pdb=" O LYS C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 465 removed outlier: 3.961A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 485 removed outlier: 3.937A pdb=" N GLU C 483 " --> pdb=" O GLU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 503 removed outlier: 4.107A pdb=" N SER C 502 " --> pdb=" O CYS C 498 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 498 through 503' Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.824A pdb=" N THR C 519 " --> pdb=" O TYR C 515 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU C 520 " --> pdb=" O TYR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.654A pdb=" N GLN C 552 " --> pdb=" O THR C 548 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN C 556 " --> pdb=" O GLN C 552 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 572 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 588 through 599 removed outlier: 3.770A pdb=" N ASP C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.793A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.669A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.809A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 817 through 826 removed outlier: 3.778A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.173A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 5.800A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.701A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.509A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.617A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.763A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.063A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.545A pdb=" N ARG B 408 " --> pdb=" O GLY B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 404 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.579A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.605A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 removed outlier: 3.604A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.605A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 5.768A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.864A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.636A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1145 removed outlier: 3.820A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 28 through 29 removed outlier: 3.877A pdb=" N VAL D 267 " --> pdb=" O THR D 63 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE D 65 " --> pdb=" O TYR D 265 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR D 265 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA D 264 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 187 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 191 " --> pdb=" O LYS D 206 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N PHE D 201 " --> pdb=" O ASP D 228 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ASP D 228 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 203 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.614A pdb=" N THR D 51 " --> pdb=" O PHE D 275 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE D 275 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS D 278 " --> pdb=" O THR D 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 83 through 84 removed outlier: 3.626A pdb=" N LEU D 84 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA D 243 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE D 101 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG D 102 " --> pdb=" O ASN D 121 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASN D 121 " --> pdb=" O ARG D 102 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N CYS D 131 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU D 118 " --> pdb=" O LYS D 129 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS D 129 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL D 126 " --> pdb=" O TYR D 170 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR D 170 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE D 128 " --> pdb=" O PHE D 168 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE D 168 " --> pdb=" O ILE D 128 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL D 130 " --> pdb=" O CYS D 166 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N CYS D 166 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN D 164 " --> pdb=" O GLU D 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 141 through 144 removed outlier: 3.551A pdb=" N LEU D 141 " --> pdb=" O LEU D 242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.491A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 324 through 328 removed outlier: 4.209A pdb=" N GLU D 324 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG D 328 " --> pdb=" O ASN D 542 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL D 539 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN D 394 " --> pdb=" O GLU D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'D' and resid 565 through 566 removed outlier: 6.844A pdb=" N PHE D 565 " --> pdb=" O PHE B 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.015A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'D' and resid 718 through 728 removed outlier: 3.502A pdb=" N ALA D1056 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N TYR D1067 " --> pdb=" O HIS D1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS D1048 " --> pdb=" O TYR D1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 735 through 736 Processing sheet with id=AB6, first strand: chain 'D' and resid 788 through 789 removed outlier: 5.942A pdb=" N ILE D 788 " --> pdb=" O ASN A 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.660A pdb=" N LEU C 142 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.445A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 347 through 352 removed outlier: 3.725A pdb=" N THR C 347 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 359 " --> pdb=" O THR C 347 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU C 351 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 35 through 37 removed outlier: 8.110A pdb=" N ASN A 68 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N TYR A 269 " --> pdb=" O ASN A 68 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL A 267 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 54 through 62 removed outlier: 3.580A pdb=" N VAL A 54 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 60 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.044A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 83 through 85 removed outlier: 7.417A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL A 126 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TYR A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.522A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AC9, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AD1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.286A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.537A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AD8, first strand: chain 'A' and resid 807 through 808 removed outlier: 4.451A pdb=" N ARG A 815 " --> pdb=" O ASP A 808 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AE1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'B' and resid 34 through 37 removed outlier: 4.160A pdb=" N ALA B 34 " --> pdb=" O TRP B 71 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ASN B 68 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 269 " --> pdb=" O ASN B 68 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 267 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 55 through 62 removed outlier: 7.429A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.388A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 156 " --> pdb=" O ASP B 142 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.925A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 126 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR B 170 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.538A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AE8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.574A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.306A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AF4, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.662A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AF6, first strand: chain 'B' and resid 807 through 808 removed outlier: 4.117A pdb=" N ARG B 815 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1120 through 1122 1169 hydrogen bonds defined for protein. 3276 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: 7.81 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9686 1.35 - 1.47: 7578 1.47 - 1.59: 13141 1.59 - 1.71: 0 1.71 - 1.83: 196 Bond restraints: 30601 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.440 -0.106 2.34e-02 1.83e+03 2.06e+01 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.411 -0.077 2.34e-02 1.83e+03 1.09e+01 bond pdb=" C LEU B 229 " pdb=" N PRO B 230 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.57e+00 bond pdb=" C PRO D 25 " pdb=" N PRO D 26 " ideal model delta sigma weight residual 1.334 1.396 -0.062 2.34e-02 1.83e+03 7.08e+00 bond pdb=" N GLN A 21 " pdb=" CA GLN A 21 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.16e+00 ... (remaining 30596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 40723 1.12 - 2.24: 689 2.24 - 3.36: 152 3.36 - 4.48: 47 4.48 - 5.60: 7 Bond angle restraints: 41618 Sorted by residual: angle pdb=" C ASP A 215 " pdb=" CA ASP A 215 " pdb=" CB ASP A 215 " ideal model delta sigma weight residual 116.63 111.52 5.11 1.16e+00 7.43e-01 1.94e+01 angle pdb=" O PRO B 32 " pdb=" C PRO B 32 " pdb=" N PRO B 33 " ideal model delta sigma weight residual 121.15 122.80 -1.65 4.70e-01 4.53e+00 1.23e+01 angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.34 111.47 4.87 1.40e+00 5.10e-01 1.21e+01 angle pdb=" C ASN B 544 " pdb=" CA ASN B 544 " pdb=" CB ASN B 544 " ideal model delta sigma weight residual 110.42 116.02 -5.60 1.99e+00 2.53e-01 7.91e+00 angle pdb=" C LEU B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta sigma weight residual 119.66 121.56 -1.90 7.20e-01 1.93e+00 6.95e+00 ... (remaining 41613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.05: 17820 16.05 - 32.10: 299 32.10 - 48.14: 86 48.14 - 64.19: 21 64.19 - 80.24: 5 Dihedral angle restraints: 18231 sinusoidal: 7171 harmonic: 11060 Sorted by residual: dihedral pdb=" SG CYS A 738 " pdb=" CB CYS A 760 " pdb=" SG CYS A 760 " pdb=" CA CYS A 760 " ideal model delta sinusoidal sigma weight residual 79.00 5.94 73.06 1 2.00e+01 2.50e-03 1.70e+01 dihedral pdb=" SG CYS B 738 " pdb=" CB CYS B 760 " pdb=" SG CYS B 760 " pdb=" CA CYS B 760 " ideal model delta sinusoidal sigma weight residual -73.00 -3.34 -69.66 1 2.00e+01 2.50e-03 1.57e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 18228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3077 0.030 - 0.060: 1052 0.060 - 0.090: 204 0.090 - 0.120: 264 0.120 - 0.150: 50 Chirality restraints: 4647 Sorted by residual: chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE B 235 " pdb=" N ILE B 235 " pdb=" C ILE B 235 " pdb=" CB ILE B 235 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 4644 not shown) Planarity restraints: 5403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 31 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C LEU B 31 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 31 " 0.013 2.00e-02 2.50e+03 pdb=" N PRO B 32 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 335 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 336 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 336 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 336 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 294 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO A 295 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.019 5.00e-02 4.00e+02 ... (remaining 5400 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 230 2.62 - 3.19: 26690 3.19 - 3.76: 43722 3.76 - 4.33: 63995 4.33 - 4.90: 104570 Nonbonded interactions: 239207 Sorted by model distance: nonbonded pdb=" OG SER D 813 " pdb=" OE1 GLU D 868 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR D 599 " pdb=" O GLN D 607 " model vdw 2.069 3.040 nonbonded pdb=" OG1 THR C 276 " pdb=" OG1 THR C 445 " model vdw 2.088 3.040 nonbonded pdb=" OG1 THR A 40 " pdb=" O GLY A 219 " model vdw 2.101 3.040 nonbonded pdb=" OG SER D 98 " pdb=" O GLU D 180 " model vdw 2.126 3.040 ... (remaining 239202 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' selection = (chain 'B' and (resid 21 through 827 or resid 854 through 1147)) selection = (chain 'D' and (resid 14 through 827 or resid 854 through 1147)) } 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 group one per residue 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 29.900 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.300 30643 Z= 0.132 Angle : 0.408 6.428 41702 Z= 0.241 Chirality : 0.040 0.150 4647 Planarity : 0.002 0.036 5403 Dihedral : 7.201 80.240 10987 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.85 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.11), residues: 3757 helix: -2.05 (0.13), residues: 969 sheet: -0.78 (0.15), residues: 764 loop : -0.98 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 158 TYR 0.014 0.001 TYR A 145 PHE 0.016 0.001 PHE A 392 TRP 0.016 0.001 TRP D 436 HIS 0.002 0.000 HIS C 535 Details of bonding type rmsd covalent geometry : bond 0.00184 (30601) covalent geometry : angle 0.40589 (41618) SS BOND : bond 0.04630 ( 42) SS BOND : angle 1.03405 ( 84) hydrogen bonds : bond 0.26723 ( 1165) hydrogen bonds : angle 9.55960 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1034 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 269 TYR cc_start: 0.3838 (p90) cc_final: 0.3620 (p90) REVERT: D 456 PHE cc_start: 0.2979 (m-10) cc_final: 0.2439 (m-80) REVERT: D 1061 VAL cc_start: 0.8747 (t) cc_final: 0.8425 (t) REVERT: D 1118 ASP cc_start: 0.6913 (m-30) cc_final: 0.6685 (m-30) REVERT: C 117 ASN cc_start: 0.7601 (m-40) cc_final: 0.7010 (p0) REVERT: C 270 MET cc_start: 0.2884 (tpt) cc_final: 0.2132 (tpt) REVERT: C 305 GLN cc_start: 0.8231 (mt0) cc_final: 0.7749 (tm-30) REVERT: C 579 MET cc_start: 0.4014 (mtm) cc_final: 0.3546 (pmm) REVERT: A 62 PHE cc_start: 0.6784 (m-10) cc_final: 0.6544 (m-80) REVERT: A 81 ASN cc_start: 0.6770 (p0) cc_final: 0.6321 (p0) REVERT: A 177 MET cc_start: 0.2375 (mmm) cc_final: 0.0551 (mtm) REVERT: A 598 ILE cc_start: 0.8061 (mt) cc_final: 0.7583 (mt) REVERT: A 739 THR cc_start: 0.8159 (m) cc_final: 0.7957 (m) REVERT: A 805 ILE cc_start: 0.8446 (mt) cc_final: 0.8107 (mt) REVERT: A 816 SER cc_start: 0.7902 (p) cc_final: 0.7436 (t) REVERT: A 1012 LEU cc_start: 0.9202 (mt) cc_final: 0.8875 (mt) REVERT: B 582 LEU cc_start: 0.7677 (tp) cc_final: 0.6985 (tt) REVERT: B 730 SER cc_start: 0.8586 (t) cc_final: 0.8316 (p) outliers start: 0 outliers final: 0 residues processed: 1034 average time/residue: 0.2099 time to fit residues: 341.1687 Evaluate side-chains 497 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS D 69 HIS D 165 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN D 484 GLN D 498 GLN D 641 ASN D 655 HIS ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 895 GLN ** D 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 GLN D1106 GLN C 103 ASN C 241 HIS C 345 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS C 417 HIS C 508 ASN C 526 GLN ** A 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 536 ASN A 580 GLN A 613 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 907 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN B 414 GLN B 644 GLN B 655 HIS B 710 ASN B 856 ASN B 957 GLN B1048 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.145103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.111085 restraints weight = 93426.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.112084 restraints weight = 59795.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.112163 restraints weight = 43809.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.113387 restraints weight = 37523.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.112726 restraints weight = 33826.326| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 30643 Z= 0.292 Angle : 0.817 11.893 41702 Z= 0.427 Chirality : 0.050 0.253 4647 Planarity : 0.005 0.049 5403 Dihedral : 4.639 23.117 4071 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.64 % Favored : 97.34 % Rotamer: Outliers : 3.91 % Allowed : 9.91 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.12), residues: 3757 helix: -0.11 (0.15), residues: 1017 sheet: -0.42 (0.16), residues: 779 loop : -0.73 (0.13), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1039 TYR 0.033 0.003 TYR D 365 PHE 0.032 0.003 PHE B 275 TRP 0.033 0.003 TRP C 328 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00651 (30601) covalent geometry : angle 0.81155 (41618) SS BOND : bond 0.01303 ( 42) SS BOND : angle 2.26815 ( 84) hydrogen bonds : bond 0.05549 ( 1165) hydrogen bonds : angle 6.33175 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 514 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 215 ASP cc_start: 0.5198 (t70) cc_final: 0.4950 (t70) REVERT: D 758 SER cc_start: 0.9156 (OUTLIER) cc_final: 0.8922 (p) REVERT: D 820 ASP cc_start: 0.9115 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: D 1050 MET cc_start: 0.7726 (ptp) cc_final: 0.7499 (ptp) REVERT: D 1144 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8244 (mp0) REVERT: C 117 ASN cc_start: 0.7435 (m-40) cc_final: 0.6888 (p0) REVERT: C 250 ASN cc_start: 0.5665 (m-40) cc_final: 0.5236 (p0) REVERT: C 305 GLN cc_start: 0.8040 (mt0) cc_final: 0.7598 (tm-30) REVERT: C 323 MET cc_start: -0.0960 (mmt) cc_final: -0.1333 (mmt) REVERT: A 135 PHE cc_start: 0.8126 (t80) cc_final: 0.7903 (m-80) REVERT: A 387 LEU cc_start: 0.8454 (mt) cc_final: 0.8031 (mt) REVERT: A 515 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6446 (p90) REVERT: A 816 SER cc_start: 0.8521 (p) cc_final: 0.7852 (m) REVERT: A 900 MET cc_start: 0.8421 (mtt) cc_final: 0.8125 (mtt) REVERT: A 916 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8282 (tp) REVERT: A 1017 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 1038 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8475 (mmmt) REVERT: A 1040 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8164 (m) REVERT: B 61 LEU cc_start: 0.8677 (mt) cc_final: 0.8407 (pp) REVERT: B 62 PHE cc_start: 0.7595 (m-10) cc_final: 0.7269 (m-10) REVERT: B 153 MET cc_start: 0.4928 (ppp) cc_final: 0.4194 (ppp) REVERT: B 196 ASN cc_start: 0.8095 (m-40) cc_final: 0.7597 (m-40) REVERT: B 695 TYR cc_start: 0.8710 (p90) cc_final: 0.8205 (p90) REVERT: B 730 SER cc_start: 0.8946 (t) cc_final: 0.8692 (p) REVERT: B 773 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 968 SER cc_start: 0.9374 (m) cc_final: 0.8441 (p) REVERT: B 970 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: B 1050 MET cc_start: 0.6865 (mtp) cc_final: 0.6507 (mtm) outliers start: 130 outliers final: 78 residues processed: 608 average time/residue: 0.1869 time to fit residues: 186.7957 Evaluate side-chains 436 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 351 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 PHE Chi-restraints excluded: chain D residue 266 TYR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 729 VAL Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 758 SER Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 951 VAL Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 980 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 345 HIS Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 555 PHE Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 698 SER Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 299 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 267 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 339 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 30 optimal weight: 0.0670 chunk 201 optimal weight: 0.7980 chunk 259 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN D 920 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 HIS C 524 GLN A 125 ASN A 245 HIS ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.139335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.107398 restraints weight = 112426.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.108670 restraints weight = 69125.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108967 restraints weight = 41935.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.109309 restraints weight = 39977.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.109649 restraints weight = 32390.762| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30643 Z= 0.126 Angle : 0.595 8.510 41702 Z= 0.306 Chirality : 0.044 0.193 4647 Planarity : 0.004 0.037 5403 Dihedral : 4.160 21.676 4071 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.74 % Favored : 97.23 % Rotamer: Outliers : 2.83 % Allowed : 13.64 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.13), residues: 3757 helix: 0.53 (0.16), residues: 1027 sheet: -0.03 (0.17), residues: 731 loop : -0.66 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 273 TYR 0.024 0.001 TYR A 707 PHE 0.032 0.002 PHE A 643 TRP 0.016 0.001 TRP A 71 HIS 0.011 0.001 HIS C 345 Details of bonding type rmsd covalent geometry : bond 0.00269 (30601) covalent geometry : angle 0.58786 (41618) SS BOND : bond 0.00336 ( 42) SS BOND : angle 2.10084 ( 84) hydrogen bonds : bond 0.04643 ( 1165) hydrogen bonds : angle 5.60784 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 420 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 55 PHE cc_start: 0.7692 (m-80) cc_final: 0.7481 (m-10) REVERT: D 820 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8684 (m-30) REVERT: D 894 LEU cc_start: 0.7381 (tt) cc_final: 0.7019 (mm) REVERT: D 1144 GLU cc_start: 0.8807 (mm-30) cc_final: 0.7957 (mp0) REVERT: C 117 ASN cc_start: 0.7446 (m-40) cc_final: 0.7036 (p0) REVERT: C 250 ASN cc_start: 0.5562 (m-40) cc_final: 0.5171 (p0) REVERT: C 305 GLN cc_start: 0.7899 (mt0) cc_final: 0.7559 (tm-30) REVERT: A 62 PHE cc_start: 0.7316 (m-80) cc_final: 0.6486 (m-80) REVERT: A 223 LEU cc_start: 0.9104 (mp) cc_final: 0.8901 (mp) REVERT: A 387 LEU cc_start: 0.8518 (mt) cc_final: 0.8107 (mt) REVERT: A 708 SER cc_start: 0.8652 (t) cc_final: 0.8074 (m) REVERT: A 816 SER cc_start: 0.8663 (p) cc_final: 0.8189 (m) REVERT: A 900 MET cc_start: 0.8374 (mtt) cc_final: 0.8131 (mtt) REVERT: A 955 ASN cc_start: 0.8921 (m-40) cc_final: 0.8620 (t0) REVERT: A 1017 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7564 (tm-30) REVERT: A 1038 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8487 (mmmt) REVERT: A 1109 PHE cc_start: 0.7682 (t80) cc_final: 0.7427 (t80) REVERT: B 153 MET cc_start: 0.4803 (ppp) cc_final: 0.4577 (ppp) REVERT: B 177 MET cc_start: 0.3739 (tmm) cc_final: 0.3201 (ppp) REVERT: B 196 ASN cc_start: 0.8532 (m-40) cc_final: 0.7970 (m-40) REVERT: B 242 LEU cc_start: 0.7707 (mt) cc_final: 0.7332 (mm) REVERT: B 695 TYR cc_start: 0.8758 (p90) cc_final: 0.8208 (p90) REVERT: B 774 GLN cc_start: 0.8715 (mm-40) cc_final: 0.8502 (mm-40) REVERT: B 775 ASP cc_start: 0.7983 (t0) cc_final: 0.7715 (t0) REVERT: B 1050 MET cc_start: 0.6732 (mtp) cc_final: 0.6493 (mtm) outliers start: 94 outliers final: 52 residues processed: 483 average time/residue: 0.1741 time to fit residues: 141.3746 Evaluate side-chains 395 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 HIS Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 562 PHE Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 645 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 71 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 0.0570 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 210 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.111520 restraints weight = 84106.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.112157 restraints weight = 58848.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.112109 restraints weight = 47206.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.112354 restraints weight = 39047.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112388 restraints weight = 35475.124| |-----------------------------------------------------------------------------| r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30643 Z= 0.189 Angle : 0.624 14.305 41702 Z= 0.325 Chirality : 0.045 0.234 4647 Planarity : 0.004 0.044 5403 Dihedral : 4.302 20.033 4071 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 3.40 % Allowed : 14.00 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.13), residues: 3757 helix: 0.61 (0.16), residues: 1033 sheet: 0.03 (0.17), residues: 718 loop : -0.66 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.020 0.002 TYR B 369 PHE 0.027 0.002 PHE A 106 TRP 0.021 0.002 TRP D 258 HIS 0.008 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00430 (30601) covalent geometry : angle 0.61465 (41618) SS BOND : bond 0.00709 ( 42) SS BOND : angle 2.50665 ( 84) hydrogen bonds : bond 0.04498 ( 1165) hydrogen bonds : angle 5.57912 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 384 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 177 MET cc_start: -0.1470 (tpp) cc_final: -0.1747 (tpt) REVERT: D 319 ARG cc_start: 0.7365 (ttm170) cc_final: 0.6912 (mtp85) REVERT: D 820 ASP cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (m-30) REVERT: D 913 GLN cc_start: 0.7810 (pt0) cc_final: 0.7574 (pt0) REVERT: D 1144 GLU cc_start: 0.8868 (mm-30) cc_final: 0.7974 (mp0) REVERT: C 117 ASN cc_start: 0.7494 (m-40) cc_final: 0.7027 (p0) REVERT: C 250 ASN cc_start: 0.5754 (m-40) cc_final: 0.5226 (p0) REVERT: C 305 GLN cc_start: 0.7992 (mt0) cc_final: 0.7495 (tm-30) REVERT: C 341 LYS cc_start: 0.4518 (OUTLIER) cc_final: 0.3801 (pttm) REVERT: A 104 TRP cc_start: 0.7811 (m-90) cc_final: 0.7476 (m-90) REVERT: A 135 PHE cc_start: 0.7936 (m-80) cc_final: 0.7600 (m-80) REVERT: A 223 LEU cc_start: 0.8725 (mp) cc_final: 0.8446 (mp) REVERT: A 290 ASP cc_start: 0.7625 (t0) cc_final: 0.7218 (p0) REVERT: A 318 PHE cc_start: 0.8216 (t80) cc_final: 0.7849 (t80) REVERT: A 515 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6414 (p90) REVERT: A 708 SER cc_start: 0.8392 (t) cc_final: 0.7761 (m) REVERT: A 900 MET cc_start: 0.8429 (mtt) cc_final: 0.8083 (mtt) REVERT: A 1017 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7744 (tm-30) REVERT: A 1038 LYS cc_start: 0.9067 (ttmm) cc_final: 0.8610 (mmmt) REVERT: B 153 MET cc_start: 0.5220 (ppp) cc_final: 0.4882 (ppp) REVERT: B 196 ASN cc_start: 0.7876 (m-40) cc_final: 0.7389 (m-40) REVERT: B 695 TYR cc_start: 0.8982 (p90) cc_final: 0.8539 (p90) REVERT: B 970 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.7865 (m-10) outliers start: 113 outliers final: 80 residues processed: 463 average time/residue: 0.1758 time to fit residues: 137.6468 Evaluate side-chains 401 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 317 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 60 ASP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 536 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain B residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 149 optimal weight: 20.0000 chunk 351 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 856 ASN D 957 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.150382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118116 restraints weight = 112311.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.120381 restraints weight = 64876.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121676 restraints weight = 36815.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.121615 restraints weight = 27058.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.122162 restraints weight = 26910.665| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30643 Z= 0.156 Angle : 0.585 11.522 41702 Z= 0.302 Chirality : 0.044 0.235 4647 Planarity : 0.004 0.040 5403 Dihedral : 4.315 28.202 4071 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.41 % Favored : 96.54 % Rotamer: Outliers : 3.10 % Allowed : 15.30 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.13), residues: 3757 helix: 0.79 (0.16), residues: 1031 sheet: 0.04 (0.18), residues: 697 loop : -0.69 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG A 346 TYR 0.030 0.002 TYR B 45 PHE 0.034 0.002 PHE B1075 TRP 0.025 0.001 TRP D 258 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00350 (30601) covalent geometry : angle 0.57954 (41618) SS BOND : bond 0.00314 ( 42) SS BOND : angle 1.86555 ( 84) hydrogen bonds : bond 0.04244 ( 1165) hydrogen bonds : angle 5.41897 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 361 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6771 (mtp85) REVERT: D 774 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8532 (mm-40) REVERT: D 779 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 820 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8746 (m-30) REVERT: D 913 GLN cc_start: 0.8020 (pt0) cc_final: 0.7798 (pt0) REVERT: D 969 ASN cc_start: 0.8053 (m-40) cc_final: 0.7838 (m-40) REVERT: D 994 ASP cc_start: 0.8851 (m-30) cc_final: 0.8604 (m-30) REVERT: C 117 ASN cc_start: 0.7470 (m-40) cc_final: 0.7088 (p0) REVERT: C 250 ASN cc_start: 0.5703 (m-40) cc_final: 0.5243 (p0) REVERT: C 305 GLN cc_start: 0.8065 (mt0) cc_final: 0.7588 (tm-30) REVERT: C 341 LYS cc_start: 0.4397 (OUTLIER) cc_final: 0.3594 (pttm) REVERT: C 366 MET cc_start: -0.1059 (tpt) cc_final: -0.1378 (tpt) REVERT: A 62 PHE cc_start: 0.7205 (m-80) cc_final: 0.6988 (m-80) REVERT: A 104 TRP cc_start: 0.7647 (m-90) cc_final: 0.7369 (m-90) REVERT: A 223 LEU cc_start: 0.8690 (mp) cc_final: 0.8444 (mp) REVERT: A 318 PHE cc_start: 0.7904 (t80) cc_final: 0.7502 (t80) REVERT: A 674 TYR cc_start: 0.7383 (t80) cc_final: 0.7155 (t80) REVERT: A 708 SER cc_start: 0.8561 (t) cc_final: 0.7944 (m) REVERT: A 900 MET cc_start: 0.8462 (mtt) cc_final: 0.8125 (mtt) REVERT: A 1017 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7765 (tm-30) REVERT: A 1038 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8613 (mmmt) REVERT: A 1084 ASP cc_start: 0.7378 (t0) cc_final: 0.7134 (t0) REVERT: B 62 PHE cc_start: 0.7567 (m-10) cc_final: 0.7244 (m-10) REVERT: B 153 MET cc_start: 0.4884 (ppp) cc_final: 0.4618 (ppp) REVERT: B 177 MET cc_start: 0.3557 (tmm) cc_final: 0.1609 (ptt) REVERT: B 196 ASN cc_start: 0.8446 (m-40) cc_final: 0.7969 (m-40) REVERT: B 242 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6984 (mm) REVERT: B 695 TYR cc_start: 0.8990 (p90) cc_final: 0.8700 (p90) REVERT: B 740 MET cc_start: 0.8591 (tmm) cc_final: 0.8382 (tmm) REVERT: B 776 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9065 (ttpp) outliers start: 103 outliers final: 79 residues processed: 436 average time/residue: 0.1741 time to fit residues: 129.1139 Evaluate side-chains 406 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1061 VAL Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1121 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 297 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 374 optimal weight: 0.0020 chunk 330 optimal weight: 0.0050 chunk 230 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 372 optimal weight: 4.9990 chunk 156 optimal weight: 6.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.134327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.102547 restraints weight = 110804.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.103756 restraints weight = 68551.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.103974 restraints weight = 41271.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.104181 restraints weight = 40891.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.104575 restraints weight = 34997.534| |-----------------------------------------------------------------------------| r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30643 Z= 0.183 Angle : 0.614 12.952 41702 Z= 0.318 Chirality : 0.045 0.208 4647 Planarity : 0.004 0.054 5403 Dihedral : 4.399 22.275 4071 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 3.61 % Allowed : 15.18 % Favored : 81.21 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3757 helix: 0.77 (0.16), residues: 1043 sheet: 0.08 (0.18), residues: 711 loop : -0.70 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1107 TYR 0.022 0.002 TYR B 369 PHE 0.024 0.002 PHE A 92 TRP 0.031 0.001 TRP D 258 HIS 0.007 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00418 (30601) covalent geometry : angle 0.60666 (41618) SS BOND : bond 0.00357 ( 42) SS BOND : angle 2.17631 ( 84) hydrogen bonds : bond 0.04306 ( 1165) hydrogen bonds : angle 5.44422 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 342 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 774 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8607 (mm-40) REVERT: D 779 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8083 (tm-30) REVERT: D 789 TYR cc_start: 0.9113 (m-10) cc_final: 0.8845 (m-10) REVERT: D 820 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8784 (m-30) REVERT: D 913 GLN cc_start: 0.8266 (pt0) cc_final: 0.8030 (pt0) REVERT: D 994 ASP cc_start: 0.8894 (m-30) cc_final: 0.8693 (m-30) REVERT: C 117 ASN cc_start: 0.7629 (m-40) cc_final: 0.7183 (p0) REVERT: C 250 ASN cc_start: 0.5698 (m-40) cc_final: 0.5188 (p0) REVERT: C 305 GLN cc_start: 0.8274 (mt0) cc_final: 0.7733 (tm-30) REVERT: C 341 LYS cc_start: 0.4499 (OUTLIER) cc_final: 0.3615 (pttm) REVERT: A 104 TRP cc_start: 0.7932 (m-90) cc_final: 0.7655 (m-90) REVERT: A 177 MET cc_start: 0.3147 (mmm) cc_final: 0.2809 (mmm) REVERT: A 318 PHE cc_start: 0.8139 (t80) cc_final: 0.7885 (t80) REVERT: A 515 PHE cc_start: 0.7594 (OUTLIER) cc_final: 0.6557 (p90) REVERT: A 708 SER cc_start: 0.8568 (t) cc_final: 0.7957 (m) REVERT: A 900 MET cc_start: 0.8614 (mtt) cc_final: 0.8269 (mtt) REVERT: A 902 MET cc_start: 0.9146 (tpp) cc_final: 0.8732 (tpt) REVERT: A 1017 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7728 (tm-30) REVERT: A 1038 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8655 (mmmt) REVERT: A 1084 ASP cc_start: 0.7715 (t0) cc_final: 0.7441 (t0) REVERT: B 62 PHE cc_start: 0.7352 (m-10) cc_final: 0.7026 (m-10) REVERT: B 196 ASN cc_start: 0.8503 (m-40) cc_final: 0.8034 (m-40) REVERT: B 242 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7078 (mm) REVERT: B 695 TYR cc_start: 0.9076 (p90) cc_final: 0.8726 (p90) REVERT: B 764 ASN cc_start: 0.8446 (t0) cc_final: 0.8168 (t0) REVERT: B 776 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9112 (ttpp) REVERT: B 777 ASN cc_start: 0.9384 (t0) cc_final: 0.9030 (t0) REVERT: B 970 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.8021 (m-10) outliers start: 120 outliers final: 85 residues processed: 432 average time/residue: 0.1697 time to fit residues: 124.8159 Evaluate side-chains 407 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 315 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 959 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 548 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 822 LEU Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 259 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 317 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 146 optimal weight: 10.0000 chunk 299 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 346 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 GLN ** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 501 ASN ** D 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 474 GLN A 536 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.128030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095752 restraints weight = 113648.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.097570 restraints weight = 61979.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.098846 restraints weight = 40236.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.099451 restraints weight = 29533.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.100235 restraints weight = 24399.337| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.7758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 30643 Z= 0.264 Angle : 0.724 12.067 41702 Z= 0.380 Chirality : 0.048 0.221 4647 Planarity : 0.005 0.068 5403 Dihedral : 5.054 38.281 4071 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 4.34 % Allowed : 15.18 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 3757 helix: 0.47 (0.16), residues: 1051 sheet: -0.23 (0.18), residues: 718 loop : -0.98 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.021 0.002 TYR D 365 PHE 0.023 0.002 PHE D 377 TRP 0.045 0.002 TRP D 258 HIS 0.011 0.002 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00599 (30601) covalent geometry : angle 0.71873 (41618) SS BOND : bond 0.00490 ( 42) SS BOND : angle 2.04757 ( 84) hydrogen bonds : bond 0.04938 ( 1165) hydrogen bonds : angle 5.85872 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 349 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 319 ARG cc_start: 0.7392 (ttm170) cc_final: 0.7047 (mtp85) REVERT: D 730 SER cc_start: 0.9062 (p) cc_final: 0.8477 (t) REVERT: D 774 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8399 (mm-40) REVERT: D 779 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8292 (tm-30) REVERT: D 820 ASP cc_start: 0.9054 (OUTLIER) cc_final: 0.8780 (m-30) REVERT: D 823 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7959 (m-10) REVERT: D 894 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6848 (mm) REVERT: D 913 GLN cc_start: 0.8439 (pt0) cc_final: 0.8223 (pt0) REVERT: D 994 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8503 (t70) REVERT: C 62 MET cc_start: 0.4950 (OUTLIER) cc_final: 0.3792 (tpt) REVERT: C 117 ASN cc_start: 0.7575 (m-40) cc_final: 0.7300 (p0) REVERT: C 250 ASN cc_start: 0.5652 (m-40) cc_final: 0.5220 (p0) REVERT: C 305 GLN cc_start: 0.8298 (mt0) cc_final: 0.7673 (tm-30) REVERT: C 366 MET cc_start: -0.1532 (tpt) cc_final: -0.1881 (tpt) REVERT: C 383 MET cc_start: 0.6568 (tpp) cc_final: 0.6260 (mpp) REVERT: A 515 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6465 (p90) REVERT: A 708 SER cc_start: 0.8519 (t) cc_final: 0.7896 (m) REVERT: A 900 MET cc_start: 0.8790 (mtt) cc_final: 0.8186 (mtm) REVERT: A 902 MET cc_start: 0.9253 (tpp) cc_final: 0.8912 (tpt) REVERT: A 926 GLN cc_start: 0.8431 (mt0) cc_final: 0.7826 (mp10) REVERT: A 1017 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7712 (tm-30) REVERT: A 1038 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8578 (mmmt) REVERT: A 1084 ASP cc_start: 0.7706 (t0) cc_final: 0.7447 (t0) REVERT: B 86 PHE cc_start: 0.8823 (t80) cc_final: 0.8562 (t80) REVERT: B 177 MET cc_start: 0.3072 (tmm) cc_final: 0.1569 (ptt) REVERT: B 196 ASN cc_start: 0.8334 (m-40) cc_final: 0.7899 (m-40) REVERT: B 214 ARG cc_start: 0.5018 (OUTLIER) cc_final: 0.4330 (tpm170) REVERT: B 695 TYR cc_start: 0.9201 (p90) cc_final: 0.8610 (p90) REVERT: B 764 ASN cc_start: 0.8523 (t0) cc_final: 0.8219 (t0) REVERT: B 776 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9133 (ttpp) REVERT: B 803 SER cc_start: 0.8740 (t) cc_final: 0.8500 (p) REVERT: B 970 PHE cc_start: 0.8784 (OUTLIER) cc_final: 0.8135 (m-10) outliers start: 144 outliers final: 106 residues processed: 460 average time/residue: 0.1781 time to fit residues: 137.8397 Evaluate side-chains 414 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 298 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 894 LEU Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1027 THR Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 435 GLU Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1049 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1121 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 346 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 247 optimal weight: 0.6980 chunk 252 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 254 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 957 GLN ** D1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.096760 restraints weight = 112540.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.098921 restraints weight = 62764.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099193 restraints weight = 37777.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.099960 restraints weight = 27807.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.099956 restraints weight = 24393.023| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.7798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30643 Z= 0.132 Angle : 0.610 10.062 41702 Z= 0.312 Chirality : 0.045 0.349 4647 Planarity : 0.004 0.043 5403 Dihedral : 4.602 27.575 4071 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.35 % Favored : 96.57 % Rotamer: Outliers : 2.74 % Allowed : 17.86 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.13), residues: 3757 helix: 0.83 (0.16), residues: 1040 sheet: -0.13 (0.18), residues: 705 loop : -0.85 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1039 TYR 0.035 0.002 TYR D 365 PHE 0.033 0.001 PHE D 541 TRP 0.047 0.002 TRP D 258 HIS 0.004 0.001 HIS D1048 Details of bonding type rmsd covalent geometry : bond 0.00297 (30601) covalent geometry : angle 0.60584 (41618) SS BOND : bond 0.00375 ( 42) SS BOND : angle 1.73894 ( 84) hydrogen bonds : bond 0.04277 ( 1165) hydrogen bonds : angle 5.45137 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 353 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 386 LYS cc_start: 0.8638 (pttt) cc_final: 0.8141 (ttmt) REVERT: D 582 LEU cc_start: 0.9147 (tp) cc_final: 0.8752 (pt) REVERT: D 730 SER cc_start: 0.9028 (p) cc_final: 0.8236 (t) REVERT: D 750 SER cc_start: 0.9346 (m) cc_final: 0.8879 (p) REVERT: D 774 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8115 (mm-40) REVERT: D 779 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8219 (tm-30) REVERT: D 820 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: D 894 LEU cc_start: 0.7508 (tt) cc_final: 0.6923 (mm) REVERT: D 902 MET cc_start: 0.8793 (tpp) cc_final: 0.8526 (tpp) REVERT: D 913 GLN cc_start: 0.8220 (pt0) cc_final: 0.8005 (pt0) REVERT: D 994 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8386 (t70) REVERT: C 62 MET cc_start: 0.4821 (OUTLIER) cc_final: 0.3735 (tpt) REVERT: C 117 ASN cc_start: 0.7473 (m-40) cc_final: 0.7190 (p0) REVERT: C 250 ASN cc_start: 0.5710 (m-40) cc_final: 0.5261 (p0) REVERT: C 305 GLN cc_start: 0.8362 (mt0) cc_final: 0.7730 (tm-30) REVERT: C 341 LYS cc_start: 0.3810 (OUTLIER) cc_final: 0.3087 (pttm) REVERT: C 366 MET cc_start: -0.1240 (tpt) cc_final: -0.1534 (tpt) REVERT: C 383 MET cc_start: 0.6162 (tpp) cc_final: 0.5927 (mpp) REVERT: A 515 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.6379 (p90) REVERT: A 708 SER cc_start: 0.8672 (t) cc_final: 0.8100 (m) REVERT: A 820 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8452 (m-30) REVERT: A 894 LEU cc_start: 0.8418 (mt) cc_final: 0.8136 (mp) REVERT: A 926 GLN cc_start: 0.8279 (mt0) cc_final: 0.7743 (mp10) REVERT: A 1017 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 1038 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8564 (mmmt) REVERT: B 37 ASN cc_start: 0.7309 (t0) cc_final: 0.7040 (t0) REVERT: B 40 THR cc_start: 0.7599 (p) cc_final: 0.7353 (p) REVERT: B 86 PHE cc_start: 0.8940 (t80) cc_final: 0.8546 (t80) REVERT: B 177 MET cc_start: 0.3758 (tmm) cc_final: 0.2427 (ptt) REVERT: B 196 ASN cc_start: 0.8502 (m-40) cc_final: 0.7967 (m-40) REVERT: B 212 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6824 (tp) REVERT: B 695 TYR cc_start: 0.9105 (p90) cc_final: 0.8478 (p90) REVERT: B 740 MET cc_start: 0.8653 (tmm) cc_final: 0.8230 (tmm) REVERT: B 803 SER cc_start: 0.8816 (t) cc_final: 0.8550 (p) REVERT: B 954 GLN cc_start: 0.8658 (mt0) cc_final: 0.8439 (mt0) REVERT: B 970 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.8087 (m-10) outliers start: 91 outliers final: 68 residues processed: 422 average time/residue: 0.1749 time to fit residues: 125.4027 Evaluate side-chains 404 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 327 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 617 CYS Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 734 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 994 ASP Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1121 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 183 optimal weight: 5.9990 chunk 299 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 368 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 340 optimal weight: 0.7980 chunk 355 optimal weight: 0.1980 chunk 30 optimal weight: 7.9990 chunk 371 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 957 GLN A 188 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 544 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.133737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.103012 restraints weight = 111206.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.104147 restraints weight = 65264.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.104156 restraints weight = 40074.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.104799 restraints weight = 37949.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.104838 restraints weight = 31430.893| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.7846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30643 Z= 0.116 Angle : 0.600 13.452 41702 Z= 0.304 Chirality : 0.045 0.361 4647 Planarity : 0.004 0.043 5403 Dihedral : 4.363 25.107 4071 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 2.29 % Allowed : 18.67 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.13), residues: 3757 helix: 0.96 (0.16), residues: 1056 sheet: 0.14 (0.18), residues: 692 loop : -0.77 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 457 TYR 0.026 0.001 TYR D 365 PHE 0.030 0.001 PHE D 541 TRP 0.051 0.002 TRP D 258 HIS 0.005 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00258 (30601) covalent geometry : angle 0.59756 (41618) SS BOND : bond 0.00329 ( 42) SS BOND : angle 1.35073 ( 84) hydrogen bonds : bond 0.03955 ( 1165) hydrogen bonds : angle 5.24686 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 374 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 386 LYS cc_start: 0.8617 (pttt) cc_final: 0.8236 (tttm) REVERT: D 582 LEU cc_start: 0.9059 (tp) cc_final: 0.8676 (pt) REVERT: D 730 SER cc_start: 0.9003 (p) cc_final: 0.8102 (t) REVERT: D 750 SER cc_start: 0.9136 (m) cc_final: 0.8652 (p) REVERT: D 774 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8265 (mm-40) REVERT: D 779 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8256 (tm-30) REVERT: D 820 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8772 (m-30) REVERT: D 823 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7876 (m-10) REVERT: D 894 LEU cc_start: 0.7545 (tt) cc_final: 0.6982 (mm) REVERT: D 994 ASP cc_start: 0.8846 (m-30) cc_final: 0.8343 (t70) REVERT: C 62 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.3589 (tpt) REVERT: C 117 ASN cc_start: 0.7664 (m-40) cc_final: 0.7325 (p0) REVERT: C 250 ASN cc_start: 0.5692 (m-40) cc_final: 0.5248 (p0) REVERT: C 305 GLN cc_start: 0.8363 (mt0) cc_final: 0.7742 (tm-30) REVERT: C 341 LYS cc_start: 0.3879 (OUTLIER) cc_final: 0.3123 (pttm) REVERT: C 366 MET cc_start: -0.1281 (tpt) cc_final: -0.1552 (tpt) REVERT: C 383 MET cc_start: 0.6417 (tpp) cc_final: 0.6164 (mpp) REVERT: C 577 LYS cc_start: 0.3608 (tppt) cc_final: 0.3340 (ptpp) REVERT: A 104 TRP cc_start: 0.7839 (m-90) cc_final: 0.7635 (m-90) REVERT: A 128 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 515 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.6382 (p90) REVERT: A 611 LEU cc_start: 0.8943 (tt) cc_final: 0.8697 (tt) REVERT: A 708 SER cc_start: 0.8699 (t) cc_final: 0.8135 (m) REVERT: A 740 MET cc_start: 0.7235 (mmm) cc_final: 0.6808 (mmm) REVERT: A 820 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: A 894 LEU cc_start: 0.8536 (mt) cc_final: 0.8258 (mp) REVERT: A 902 MET cc_start: 0.8839 (tpp) cc_final: 0.8541 (tpt) REVERT: A 926 GLN cc_start: 0.8155 (mt0) cc_final: 0.7701 (mp10) REVERT: A 1017 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8035 (tm-30) REVERT: B 40 THR cc_start: 0.7684 (p) cc_final: 0.7430 (p) REVERT: B 86 PHE cc_start: 0.8945 (t80) cc_final: 0.8563 (t80) REVERT: B 177 MET cc_start: 0.3962 (tmm) cc_final: 0.2870 (ptt) REVERT: B 196 ASN cc_start: 0.8488 (m-40) cc_final: 0.7999 (m-40) REVERT: B 212 LEU cc_start: 0.7284 (pp) cc_final: 0.6801 (tp) REVERT: B 242 LEU cc_start: 0.7637 (mt) cc_final: 0.7268 (mm) REVERT: B 695 TYR cc_start: 0.9075 (p90) cc_final: 0.8695 (p90) REVERT: B 764 ASN cc_start: 0.8288 (t0) cc_final: 0.7943 (t0) REVERT: B 777 ASN cc_start: 0.9284 (t0) cc_final: 0.9056 (t0) REVERT: B 954 GLN cc_start: 0.8529 (mt0) cc_final: 0.8240 (mt0) REVERT: B 970 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8068 (m-10) REVERT: B 1041 ASP cc_start: 0.7855 (t70) cc_final: 0.7605 (t70) outliers start: 76 outliers final: 53 residues processed: 430 average time/residue: 0.1734 time to fit residues: 126.6108 Evaluate side-chains 397 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 336 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 865 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1049 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 357 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 264 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 319 optimal weight: 10.0000 chunk 296 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 751 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1083 HIS A 317 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.131788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.101122 restraints weight = 113154.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.101721 restraints weight = 73485.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.102423 restraints weight = 51122.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.103058 restraints weight = 36681.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.103232 restraints weight = 31885.882| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30643 Z= 0.141 Angle : 0.614 14.629 41702 Z= 0.310 Chirality : 0.045 0.371 4647 Planarity : 0.004 0.048 5403 Dihedral : 4.406 35.676 4071 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.49 % Favored : 96.43 % Rotamer: Outliers : 2.20 % Allowed : 18.94 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.13), residues: 3757 helix: 0.93 (0.16), residues: 1065 sheet: 0.15 (0.18), residues: 710 loop : -0.81 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1039 TYR 0.024 0.002 TYR D 904 PHE 0.027 0.001 PHE B 62 TRP 0.077 0.002 TRP D 258 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00322 (30601) covalent geometry : angle 0.60918 (41618) SS BOND : bond 0.00327 ( 42) SS BOND : angle 1.75857 ( 84) hydrogen bonds : bond 0.03986 ( 1165) hydrogen bonds : angle 5.23652 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7514 Ramachandran restraints generated. 3757 Oldfield, 0 Emsley, 3757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 335 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 223 LEU cc_start: 0.8109 (mm) cc_final: 0.7116 (mm) REVERT: D 386 LYS cc_start: 0.8599 (pttt) cc_final: 0.8098 (ttmt) REVERT: D 582 LEU cc_start: 0.9018 (tp) cc_final: 0.8657 (pt) REVERT: D 779 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8308 (tm-30) REVERT: D 820 ASP cc_start: 0.9012 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: D 823 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7850 (m-10) REVERT: D 894 LEU cc_start: 0.7530 (tt) cc_final: 0.6949 (mm) REVERT: D 994 ASP cc_start: 0.8840 (m-30) cc_final: 0.8344 (t70) REVERT: C 62 MET cc_start: 0.4742 (OUTLIER) cc_final: 0.3526 (tpp) REVERT: C 82 MET cc_start: 0.2230 (pmm) cc_final: 0.1642 (pmm) REVERT: C 117 ASN cc_start: 0.7591 (m-40) cc_final: 0.7270 (p0) REVERT: C 250 ASN cc_start: 0.5713 (m-40) cc_final: 0.5276 (p0) REVERT: C 305 GLN cc_start: 0.8360 (mt0) cc_final: 0.7720 (tm-30) REVERT: C 341 LYS cc_start: 0.3927 (OUTLIER) cc_final: 0.3094 (pttm) REVERT: C 366 MET cc_start: -0.1651 (tpt) cc_final: -0.1899 (tpt) REVERT: C 383 MET cc_start: 0.6439 (tpp) cc_final: 0.6133 (mpp) REVERT: C 462 MET cc_start: 0.4361 (mmp) cc_final: 0.2994 (mtp) REVERT: C 577 LYS cc_start: 0.3458 (tppt) cc_final: 0.3114 (ptpp) REVERT: A 128 ILE cc_start: 0.8636 (mt) cc_final: 0.8423 (mm) REVERT: A 515 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.6414 (p90) REVERT: A 708 SER cc_start: 0.8652 (t) cc_final: 0.8062 (m) REVERT: A 740 MET cc_start: 0.7596 (mmm) cc_final: 0.7290 (mmm) REVERT: A 808 ASP cc_start: 0.7517 (t0) cc_final: 0.7265 (t0) REVERT: A 820 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: A 894 LEU cc_start: 0.8531 (mt) cc_final: 0.8266 (mp) REVERT: A 900 MET cc_start: 0.7809 (mtt) cc_final: 0.7560 (mtm) REVERT: A 902 MET cc_start: 0.8848 (tpp) cc_final: 0.8511 (tpt) REVERT: A 926 GLN cc_start: 0.8124 (mt0) cc_final: 0.7719 (mp10) REVERT: A 1003 SER cc_start: 0.9498 (OUTLIER) cc_final: 0.9169 (p) REVERT: A 1017 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8040 (tm-30) REVERT: B 86 PHE cc_start: 0.8885 (t80) cc_final: 0.8524 (t80) REVERT: B 177 MET cc_start: 0.3810 (tmm) cc_final: 0.3161 (ptt) REVERT: B 196 ASN cc_start: 0.8449 (m-40) cc_final: 0.8129 (m-40) REVERT: B 212 LEU cc_start: 0.7028 (pp) cc_final: 0.6542 (tp) REVERT: B 242 LEU cc_start: 0.7462 (mt) cc_final: 0.7121 (mm) REVERT: B 695 TYR cc_start: 0.9110 (p90) cc_final: 0.8709 (p90) REVERT: B 764 ASN cc_start: 0.8352 (t0) cc_final: 0.8007 (t0) REVERT: B 777 ASN cc_start: 0.9296 (t0) cc_final: 0.9061 (t0) REVERT: B 954 GLN cc_start: 0.8546 (mt0) cc_final: 0.8263 (mt0) REVERT: B 970 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8156 (m-10) outliers start: 73 outliers final: 58 residues processed: 394 average time/residue: 0.1597 time to fit residues: 107.7616 Evaluate side-chains 391 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 325 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 238 PHE Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain D residue 284 THR Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 719 THR Chi-restraints excluded: chain D residue 736 VAL Chi-restraints excluded: chain D residue 751 ASN Chi-restraints excluded: chain D residue 759 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 820 ASP Chi-restraints excluded: chain D residue 823 PHE Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 922 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 996 LEU Chi-restraints excluded: chain D residue 1001 LEU Chi-restraints excluded: chain D residue 1012 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1062 PHE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 341 LYS Chi-restraints excluded: chain C residue 445 THR Chi-restraints excluded: chain C residue 542 CYS Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 92 PHE Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 970 PHE Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1049 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 95 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 354 optimal weight: 0.1980 chunk 159 optimal weight: 0.0070 chunk 295 optimal weight: 0.8980 chunk 376 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 253 optimal weight: 0.3980 chunk 35 optimal weight: 10.0000 chunk 282 optimal weight: 2.9990 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 165 ASN D 751 ASN ** D 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 ASN ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.133717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.102234 restraints weight = 113597.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.103884 restraints weight = 66798.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.104597 restraints weight = 40925.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.105587 restraints weight = 29101.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.105479 restraints weight = 25253.032| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.7996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30643 Z= 0.109 Angle : 0.601 15.403 41702 Z= 0.300 Chirality : 0.045 0.378 4647 Planarity : 0.004 0.042 5403 Dihedral : 4.209 25.867 4071 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.98 % Favored : 96.89 % Rotamer: Outliers : 2.02 % Allowed : 19.21 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 3757 helix: 1.05 (0.16), residues: 1057 sheet: 0.16 (0.18), residues: 718 loop : -0.72 (0.14), residues: 1982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1039 TYR 0.024 0.001 TYR B 904 PHE 0.030 0.001 PHE D 541 TRP 0.090 0.002 TRP D 258 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00234 (30601) covalent geometry : angle 0.59907 (41618) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.30769 ( 84) hydrogen bonds : bond 0.03762 ( 1165) hydrogen bonds : angle 5.09854 ( 3276) =============================================================================== Job complete usr+sys time: 6189.48 seconds wall clock time: 107 minutes 31.66 seconds (6451.66 seconds total)