Starting phenix.real_space_refine on Wed Aug 27 03:15:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr8_34963/08_2025/8hr8_34963.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 216 5.16 5 C 29577 2.51 5 N 8023 2.21 5 O 8857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 46688 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6663 Classifications: {'peptide': 836} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Chain: "C" Number of atoms: 6655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6655 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "D" Number of atoms: 6654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6654 Classifications: {'peptide': 836} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 23, 'TRANS': 812} Chain breaks: 5 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 6633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6633 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 809} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 6658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6658 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 23, 'TRANS': 811} Chain breaks: 5 Chain: "G" Number of atoms: 6617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 830, 6617 Classifications: {'peptide': 830} Link IDs: {'PTRANS': 23, 'TRANS': 806} Chain breaks: 5 Chain: "H" Number of atoms: 6653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6653 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 23, 'TRANS': 810} Chain breaks: 5 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.52, per 1000 atoms: 0.25 Number of scatterers: 46688 At special positions: 0 Unit cell: (166.4, 179.92, 164.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 216 16.00 P 15 15.00 O 8857 8.00 N 8023 7.00 C 29577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11064 Finding SS restraints... Secondary structure from input PDB file: 290 helices and 22 sheets defined 62.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 34 through 51 removed outlier: 3.534A pdb=" N GLU A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 142 through 163 removed outlier: 3.896A pdb=" N TYR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 175 through 181 removed outlier: 3.878A pdb=" N ASP A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.941A pdb=" N GLU A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 241 removed outlier: 3.923A pdb=" N VAL A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.509A pdb=" N GLN A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 282 through 302 removed outlier: 3.593A pdb=" N GLY A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS A 292 " --> pdb=" O TYR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.578A pdb=" N ALA A 341 " --> pdb=" O ASP A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.630A pdb=" N GLU A 354 " --> pdb=" O ASP A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.577A pdb=" N MET A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 395 Processing helix chain 'A' and resid 412 through 425 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 437 through 441 Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.628A pdb=" N PHE A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 472 through 490 removed outlier: 4.159A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.953A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 519 Processing helix chain 'A' and resid 527 through 540 Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.565A pdb=" N SER A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 567 removed outlier: 3.810A pdb=" N LYS A 566 " --> pdb=" O ASN A 563 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A 567 " --> pdb=" O ASP A 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 563 through 567' Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.553A pdb=" N LYS A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.695A pdb=" N ILE A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 724 removed outlier: 3.574A pdb=" N ASN A 719 " --> pdb=" O GLN A 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 749 removed outlier: 3.565A pdb=" N ASN A 747 " --> pdb=" O PHE A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 793 Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.770A pdb=" N LYS A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 839 Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.558A pdb=" N LEU A 844 " --> pdb=" O PRO A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.725A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.988A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 Processing helix chain 'C' and resid 23 through 27 removed outlier: 4.229A pdb=" N THR C 27 " --> pdb=" O PRO C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 51 removed outlier: 3.731A pdb=" N ARG C 38 " --> pdb=" O GLN C 34 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 120 through 139 removed outlier: 3.932A pdb=" N LYS C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 163 removed outlier: 3.510A pdb=" N TYR C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 167 Processing helix chain 'C' and resid 173 through 175 No H-bonds generated for 'chain 'C' and resid 173 through 175' Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.615A pdb=" N GLU C 201 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 229 through 241 removed outlier: 3.947A pdb=" N VAL C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.527A pdb=" N ASN C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.788A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 312 through 318 Processing helix chain 'C' and resid 344 through 354 Processing helix chain 'C' and resid 361 through 374 removed outlier: 3.548A pdb=" N ASP C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET C 366 " --> pdb=" O SER C 362 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N TYR C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 370 " --> pdb=" O MET C 366 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU C 371 " --> pdb=" O TYR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 395 removed outlier: 3.773A pdb=" N LYS C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 425 removed outlier: 3.969A pdb=" N GLY C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 432 Processing helix chain 'C' and resid 442 through 458 removed outlier: 3.834A pdb=" N CYS C 447 " --> pdb=" O MET C 443 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 472 through 490 removed outlier: 3.706A pdb=" N SER C 487 " --> pdb=" O ALA C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 514 removed outlier: 3.825A pdb=" N CYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 509 " --> pdb=" O CYS C 505 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N PHE C 511 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C 512 " --> pdb=" O VAL C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.537A pdb=" N ALA C 519 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 539 removed outlier: 3.953A pdb=" N LEU C 531 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 532 " --> pdb=" O PHE C 528 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 533 " --> pdb=" O GLU C 529 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 536 " --> pdb=" O ILE C 532 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET C 539 " --> pdb=" O TYR C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 560 removed outlier: 3.891A pdb=" N TRP C 550 " --> pdb=" O SER C 546 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 557 " --> pdb=" O ARG C 553 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL C 558 " --> pdb=" O CYS C 554 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 559 " --> pdb=" O CYS C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'C' and resid 597 through 607 Processing helix chain 'C' and resid 622 through 633 removed outlier: 3.514A pdb=" N ASP C 631 " --> pdb=" O GLY C 627 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 650 removed outlier: 4.432A pdb=" N ASN C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 724 removed outlier: 3.576A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 715 " --> pdb=" O THR C 711 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP C 716 " --> pdb=" O LYS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 730 through 752 removed outlier: 4.060A pdb=" N ILE C 734 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 735 " --> pdb=" O ALA C 731 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 747 " --> pdb=" O PHE C 743 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 789 removed outlier: 3.873A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 832 removed outlier: 3.534A pdb=" N ILE C 823 " --> pdb=" O LYS C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 839 Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.739A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 4.019A pdb=" N LYS C 870 " --> pdb=" O LYS C 866 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 871 " --> pdb=" O ALA C 867 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 removed outlier: 3.504A pdb=" N ASP C 893 " --> pdb=" O ASP C 889 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR C 894 " --> pdb=" O GLU C 890 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU C 895 " --> pdb=" O GLU C 891 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR C 896 " --> pdb=" O TRP C 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 51 removed outlier: 3.551A pdb=" N SER D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR D 51 " --> pdb=" O ASN D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 96 removed outlier: 3.957A pdb=" N ASP D 96 " --> pdb=" O SER D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 138 removed outlier: 3.537A pdb=" N LYS D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 163 removed outlier: 3.875A pdb=" N ARG D 147 " --> pdb=" O SER D 143 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.145A pdb=" N ASP D 169 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 182 removed outlier: 4.055A pdb=" N ASP D 179 " --> pdb=" O GLU D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.824A pdb=" N VAL D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 268 Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 279 through 302 removed outlier: 3.505A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS D 292 " --> pdb=" O TYR D 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 296 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 307 Processing helix chain 'D' and resid 312 through 318 Processing helix chain 'D' and resid 344 through 356 removed outlier: 3.533A pdb=" N GLU D 354 " --> pdb=" O ASP D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.546A pdb=" N ASP D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 395 removed outlier: 4.360A pdb=" N LYS D 389 " --> pdb=" O ASP D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 433 removed outlier: 3.638A pdb=" N SER D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER D 427 " --> pdb=" O GLY D 423 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER D 428 " --> pdb=" O SER D 424 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 429 " --> pdb=" O MET D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 458 removed outlier: 3.546A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 removed outlier: 3.689A pdb=" N LEU D 466 " --> pdb=" O GLY D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 490 removed outlier: 4.200A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 503 Processing helix chain 'D' and resid 505 through 515 Processing helix chain 'D' and resid 516 through 519 Processing helix chain 'D' and resid 527 through 540 Processing helix chain 'D' and resid 546 through 559 removed outlier: 3.736A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 567 removed outlier: 4.319A pdb=" N ILE D 567 " --> pdb=" O ASP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 596 Processing helix chain 'D' and resid 600 through 607 Processing helix chain 'D' and resid 622 through 634 Processing helix chain 'D' and resid 638 through 649 removed outlier: 3.740A pdb=" N LYS D 648 " --> pdb=" O ASN D 644 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 652 No H-bonds generated for 'chain 'D' and resid 650 through 652' Processing helix chain 'D' and resid 706 through 724 removed outlier: 3.605A pdb=" N ASN D 719 " --> pdb=" O GLN D 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU D 722 " --> pdb=" O LYS D 718 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 730 through 752 Processing helix chain 'D' and resid 753 through 755 No H-bonds generated for 'chain 'D' and resid 753 through 755' Processing helix chain 'D' and resid 770 through 793 removed outlier: 3.798A pdb=" N VAL D 779 " --> pdb=" O MET D 775 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU D 790 " --> pdb=" O VAL D 786 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 831 removed outlier: 3.575A pdb=" N LYS D 820 " --> pdb=" O GLU D 816 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE D 821 " --> pdb=" O PHE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 839 through 847 Processing helix chain 'D' and resid 865 through 883 removed outlier: 3.636A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 897 removed outlier: 3.548A pdb=" N LEU D 895 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 51 removed outlier: 3.510A pdb=" N GLN E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 49 " --> pdb=" O ILE E 45 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR E 51 " --> pdb=" O ASN E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 95 removed outlier: 3.687A pdb=" N PHE E 85 " --> pdb=" O GLY E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 140 removed outlier: 3.513A pdb=" N GLY E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 163 removed outlier: 3.579A pdb=" N LYS E 150 " --> pdb=" O TYR E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.089A pdb=" N THR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.214A pdb=" N SER E 178 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP E 179 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 212 Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 229 through 240 removed outlier: 4.153A pdb=" N VAL E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 267 removed outlier: 3.554A pdb=" N GLN E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU E 267 " --> pdb=" O GLY E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 279 through 302 Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 312 through 318 Processing helix chain 'E' and resid 344 through 356 Processing helix chain 'E' and resid 361 through 373 removed outlier: 4.153A pdb=" N TYR E 367 " --> pdb=" O ASP E 363 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL E 368 " --> pdb=" O ALA E 364 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU E 370 " --> pdb=" O MET E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 395 removed outlier: 4.130A pdb=" N LYS E 389 " --> pdb=" O ASP E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 425 removed outlier: 3.533A pdb=" N SER E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 437 through 441 removed outlier: 3.772A pdb=" N PHE E 441 " --> pdb=" O GLN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 458 removed outlier: 3.588A pdb=" N LYS E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 472 through 490 removed outlier: 3.665A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 515 removed outlier: 3.885A pdb=" N CYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 507 " --> pdb=" O VAL E 503 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 540 removed outlier: 3.750A pdb=" N ILE E 532 " --> pdb=" O PHE E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 561 Processing helix chain 'E' and resid 563 through 567 removed outlier: 3.849A pdb=" N ILE E 567 " --> pdb=" O ASP E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 592 through 596 removed outlier: 3.793A pdb=" N GLU E 596 " --> pdb=" O ILE E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 606 Processing helix chain 'E' and resid 622 through 633 Processing helix chain 'E' and resid 638 through 649 removed outlier: 3.990A pdb=" N ASN E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS E 648 " --> pdb=" O ASN E 644 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL E 649 " --> pdb=" O ALA E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 724 removed outlier: 4.435A pdb=" N ILE E 710 " --> pdb=" O PHE E 706 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU E 722 " --> pdb=" O LYS E 718 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 727 No H-bonds generated for 'chain 'E' and resid 725 through 727' Processing helix chain 'E' and resid 730 through 752 Processing helix chain 'E' and resid 770 through 793 removed outlier: 3.595A pdb=" N ILE E 774 " --> pdb=" O ASN E 770 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU E 790 " --> pdb=" O VAL E 786 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR E 793 " --> pdb=" O GLU E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 831 removed outlier: 3.692A pdb=" N LYS E 820 " --> pdb=" O GLU E 816 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE E 821 " --> pdb=" O PHE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 834 through 839 Processing helix chain 'E' and resid 839 through 847 removed outlier: 3.703A pdb=" N LEU E 845 " --> pdb=" O LEU E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 851 through 856 removed outlier: 4.042A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 867 through 883 removed outlier: 3.632A pdb=" N GLU E 871 " --> pdb=" O ALA E 867 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS E 876 " --> pdb=" O THR E 872 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 896 removed outlier: 3.654A pdb=" N LEU E 895 " --> pdb=" O GLU E 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 51 removed outlier: 3.547A pdb=" N ILE F 49 " --> pdb=" O ILE F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 95 removed outlier: 3.581A pdb=" N SER F 95 " --> pdb=" O LYS F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 138 removed outlier: 3.516A pdb=" N MET F 132 " --> pdb=" O ARG F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 163 removed outlier: 3.783A pdb=" N GLN F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP F 153 " --> pdb=" O GLN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 167 Processing helix chain 'F' and resid 173 through 175 No H-bonds generated for 'chain 'F' and resid 173 through 175' Processing helix chain 'F' and resid 176 through 181 Processing helix chain 'F' and resid 195 through 212 Processing helix chain 'F' and resid 226 through 229 removed outlier: 3.667A pdb=" N ALA F 229 " --> pdb=" O GLN F 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.793A pdb=" N GLN F 259 " --> pdb=" O ARG F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 279 through 302 removed outlier: 3.605A pdb=" N GLU F 285 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN F 296 " --> pdb=" O HIS F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 312 through 318 Processing helix chain 'F' and resid 344 through 356 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.508A pdb=" N TYR F 367 " --> pdb=" O ASP F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 395 Processing helix chain 'F' and resid 412 through 425 removed outlier: 3.531A pdb=" N SER F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 433 Processing helix chain 'F' and resid 443 through 458 removed outlier: 3.710A pdb=" N LYS F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP F 449 " --> pdb=" O SER F 445 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN F 456 " --> pdb=" O THR F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 466 Processing helix chain 'F' and resid 472 through 490 removed outlier: 3.817A pdb=" N ILE F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 503 removed outlier: 3.606A pdb=" N PHE F 497 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 513 removed outlier: 4.382A pdb=" N VAL F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER F 509 " --> pdb=" O CYS F 505 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 519 Processing helix chain 'F' and resid 527 through 540 Processing helix chain 'F' and resid 546 through 560 Processing helix chain 'F' and resid 563 through 567 removed outlier: 4.098A pdb=" N ILE F 567 " --> pdb=" O ASP F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 596 removed outlier: 3.516A pdb=" N THR F 595 " --> pdb=" O ASN F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 607 Processing helix chain 'F' and resid 622 through 633 Processing helix chain 'F' and resid 638 through 647 removed outlier: 3.590A pdb=" N ILE F 642 " --> pdb=" O GLU F 638 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 645 " --> pdb=" O ALA F 641 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE F 646 " --> pdb=" O ILE F 642 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN F 647 " --> pdb=" O THR F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 705 through 724 removed outlier: 3.527A pdb=" N ALA F 709 " --> pdb=" O GLU F 705 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU F 722 " --> pdb=" O LYS F 718 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 727 No H-bonds generated for 'chain 'F' and resid 725 through 727' Processing helix chain 'F' and resid 730 through 752 Processing helix chain 'F' and resid 757 through 761 removed outlier: 4.394A pdb=" N GLU F 761 " --> pdb=" O ARG F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 794 removed outlier: 3.546A pdb=" N PHE F 782 " --> pdb=" O ASN F 778 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 789 " --> pdb=" O ALA F 785 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER F 791 " --> pdb=" O LEU F 787 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 792 " --> pdb=" O VAL F 788 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 832 removed outlier: 3.717A pdb=" N LYS F 820 " --> pdb=" O GLU F 816 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 825 " --> pdb=" O ILE F 821 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU F 826 " --> pdb=" O LYS F 822 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 829 " --> pdb=" O GLY F 825 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 847 Processing helix chain 'F' and resid 851 through 856 removed outlier: 4.038A pdb=" N PHE F 856 " --> pdb=" O HIS F 852 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 883 removed outlier: 4.264A pdb=" N LYS F 870 " --> pdb=" O LYS F 866 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 897 removed outlier: 3.510A pdb=" N TYR F 894 " --> pdb=" O GLU F 890 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 48 removed outlier: 3.553A pdb=" N ARG G 38 " --> pdb=" O GLN G 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP G 39 " --> pdb=" O LYS G 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU G 43 " --> pdb=" O ASP G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 120 through 138 Processing helix chain 'G' and resid 142 through 164 removed outlier: 3.535A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN G 152 " --> pdb=" O LYS G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 3.955A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 182 removed outlier: 4.075A pdb=" N ASP G 179 " --> pdb=" O GLU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 212 Processing helix chain 'G' and resid 228 through 241 removed outlier: 4.572A pdb=" N ASP G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 265 Processing helix chain 'G' and resid 270 through 277 removed outlier: 3.520A pdb=" N GLU G 275 " --> pdb=" O LYS G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 302 Processing helix chain 'G' and resid 312 through 318 Processing helix chain 'G' and resid 344 through 356 Processing helix chain 'G' and resid 361 through 374 removed outlier: 3.565A pdb=" N GLN G 374 " --> pdb=" O GLU G 370 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 395 removed outlier: 3.801A pdb=" N TYR G 391 " --> pdb=" O TYR G 387 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 425 Processing helix chain 'G' and resid 425 through 433 Processing helix chain 'G' and resid 443 through 458 removed outlier: 3.650A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE G 451 " --> pdb=" O CYS G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 466 removed outlier: 3.601A pdb=" N TYR G 465 " --> pdb=" O THR G 462 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 490 removed outlier: 3.649A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 503 Processing helix chain 'G' and resid 504 through 515 removed outlier: 4.032A pdb=" N VAL G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 540 removed outlier: 3.536A pdb=" N SER G 533 " --> pdb=" O GLU G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 561 removed outlier: 3.571A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL G 557 " --> pdb=" O ARG G 553 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER G 561 " --> pdb=" O VAL G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 563 through 567 removed outlier: 3.840A pdb=" N LYS G 566 " --> pdb=" O ASN G 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 592 through 596 removed outlier: 3.656A pdb=" N THR G 595 " --> pdb=" O ASN G 592 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 596 " --> pdb=" O ILE G 593 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 592 through 596' Processing helix chain 'G' and resid 600 through 608 Processing helix chain 'G' and resid 622 through 633 removed outlier: 3.870A pdb=" N SER G 633 " --> pdb=" O ILE G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 638 through 651 removed outlier: 3.555A pdb=" N LYS G 648 " --> pdb=" O ASN G 644 " (cutoff:3.500A) Processing helix chain 'G' and resid 707 through 724 removed outlier: 3.719A pdb=" N THR G 711 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL G 713 " --> pdb=" O ALA G 709 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN G 715 " --> pdb=" O THR G 711 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TRP G 716 " --> pdb=" O LYS G 712 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU G 722 " --> pdb=" O LYS G 718 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 727 No H-bonds generated for 'chain 'G' and resid 725 through 727' Processing helix chain 'G' and resid 730 through 752 removed outlier: 3.638A pdb=" N LEU G 745 " --> pdb=" O PHE G 741 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN G 746 " --> pdb=" O TYR G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 770 through 794 removed outlier: 3.653A pdb=" N MET G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 776 " --> pdb=" O ALA G 772 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER G 791 " --> pdb=" O LEU G 787 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU G 792 " --> pdb=" O VAL G 788 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR G 793 " --> pdb=" O GLU G 789 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 831 removed outlier: 3.670A pdb=" N GLU G 818 " --> pdb=" O VAL G 814 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS G 819 " --> pdb=" O ASP G 815 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS G 820 " --> pdb=" O GLU G 816 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE G 821 " --> pdb=" O PHE G 817 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE G 823 " --> pdb=" O LYS G 819 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS G 829 " --> pdb=" O GLY G 825 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA G 830 " --> pdb=" O GLU G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 834 through 839 Processing helix chain 'G' and resid 839 through 847 Processing helix chain 'G' and resid 848 through 850 No H-bonds generated for 'chain 'G' and resid 848 through 850' Processing helix chain 'G' and resid 851 through 856 removed outlier: 3.660A pdb=" N ILE G 855 " --> pdb=" O LEU G 851 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE G 856 " --> pdb=" O HIS G 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 851 through 856' Processing helix chain 'G' and resid 864 through 883 removed outlier: 4.619A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE G 874 " --> pdb=" O LYS G 870 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS G 876 " --> pdb=" O THR G 872 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE G 878 " --> pdb=" O PHE G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 897 Processing helix chain 'H' and resid 23 through 27 removed outlier: 4.052A pdb=" N THR H 27 " --> pdb=" O PRO H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 51 removed outlier: 3.506A pdb=" N ASP H 39 " --> pdb=" O LYS H 35 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE H 49 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR H 51 " --> pdb=" O ASN H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'H' and resid 120 through 139 Processing helix chain 'H' and resid 142 through 164 removed outlier: 3.738A pdb=" N LYS H 148 " --> pdb=" O ASN H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 175 through 180 removed outlier: 3.816A pdb=" N ASP H 179 " --> pdb=" O GLU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 212 removed outlier: 3.597A pdb=" N GLU H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'H' and resid 253 through 269 removed outlier: 3.517A pdb=" N ASN H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR H 269 " --> pdb=" O GLN H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 277 Processing helix chain 'H' and resid 279 through 302 Processing helix chain 'H' and resid 312 through 318 Processing helix chain 'H' and resid 344 through 354 Processing helix chain 'H' and resid 361 through 374 removed outlier: 3.571A pdb=" N ASP H 365 " --> pdb=" O GLY H 361 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU H 370 " --> pdb=" O MET H 366 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN H 374 " --> pdb=" O GLU H 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 393 removed outlier: 4.515A pdb=" N THR H 388 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS H 389 " --> pdb=" O ASP H 385 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 393 " --> pdb=" O LYS H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 425 removed outlier: 3.981A pdb=" N GLY H 423 " --> pdb=" O ASN H 419 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 433 removed outlier: 3.574A pdb=" N TYR H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG H 431 " --> pdb=" O SER H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 458 removed outlier: 3.875A pdb=" N LYS H 448 " --> pdb=" O ASP H 444 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP H 449 " --> pdb=" O SER H 445 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 466 Processing helix chain 'H' and resid 472 through 490 removed outlier: 3.589A pdb=" N ILE H 480 " --> pdb=" O ARG H 476 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN H 489 " --> pdb=" O GLN H 485 " (cutoff:3.500A) Processing helix chain 'H' and resid 494 through 503 Processing helix chain 'H' and resid 503 through 515 removed outlier: 3.687A pdb=" N SER H 507 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL H 508 " --> pdb=" O GLY H 504 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 509 " --> pdb=" O CYS H 505 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN H 513 " --> pdb=" O SER H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 519 removed outlier: 3.802A pdb=" N ALA H 519 " --> pdb=" O THR H 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 516 through 519' Processing helix chain 'H' and resid 527 through 540 Processing helix chain 'H' and resid 546 through 560 removed outlier: 3.581A pdb=" N TRP H 550 " --> pdb=" O SER H 546 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA H 556 " --> pdb=" O ASN H 552 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL H 557 " --> pdb=" O ARG H 553 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL H 558 " --> pdb=" O CYS H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 563 through 567 removed outlier: 3.732A pdb=" N LYS H 566 " --> pdb=" O ASN H 563 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE H 567 " --> pdb=" O ASP H 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 563 through 567' Processing helix chain 'H' and resid 597 through 607 Processing helix chain 'H' and resid 622 through 633 Processing helix chain 'H' and resid 638 through 651 removed outlier: 3.717A pdb=" N ILE H 642 " --> pdb=" O GLU H 638 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN H 644 " --> pdb=" O SER H 640 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA H 645 " --> pdb=" O ALA H 641 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS H 648 " --> pdb=" O ASN H 644 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 649 " --> pdb=" O ALA H 645 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA H 651 " --> pdb=" O ASN H 647 " (cutoff:3.500A) Processing helix chain 'H' and resid 705 through 724 removed outlier: 3.564A pdb=" N ALA H 709 " --> pdb=" O GLU H 705 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR H 711 " --> pdb=" O SER H 707 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN H 719 " --> pdb=" O GLN H 715 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU H 722 " --> pdb=" O LYS H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 725 through 727 No H-bonds generated for 'chain 'H' and resid 725 through 727' Processing helix chain 'H' and resid 730 through 752 removed outlier: 3.500A pdb=" N ASN H 746 " --> pdb=" O TYR H 742 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN H 747 " --> pdb=" O PHE H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 753 through 755 No H-bonds generated for 'chain 'H' and resid 753 through 755' Processing helix chain 'H' and resid 770 through 794 removed outlier: 3.723A pdb=" N PHE H 782 " --> pdb=" O ASN H 778 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER H 791 " --> pdb=" O LEU H 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 814 through 831 removed outlier: 3.519A pdb=" N LYS H 820 " --> pdb=" O GLU H 816 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE H 821 " --> pdb=" O PHE H 817 " (cutoff:3.500A) Processing helix chain 'H' and resid 839 through 848 Processing helix chain 'H' and resid 851 through 856 removed outlier: 3.885A pdb=" N PHE H 856 " --> pdb=" O HIS H 852 " (cutoff:3.500A) Processing helix chain 'H' and resid 864 through 883 removed outlier: 4.139A pdb=" N ASN H 869 " --> pdb=" O VAL H 865 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LYS H 870 " --> pdb=" O LYS H 866 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU H 880 " --> pdb=" O LYS H 876 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE H 881 " --> pdb=" O LEU H 877 " (cutoff:3.500A) Processing helix chain 'H' and resid 888 through 897 removed outlier: 4.378A pdb=" N TYR H 894 " --> pdb=" O GLU H 890 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 6.138A pdb=" N ILE A 14 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 331 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE A 16 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 106 removed outlier: 6.750A pdb=" N LYS A 105 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 219 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 252 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 569 through 570 removed outlier: 4.255A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A 655 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.200A pdb=" N ILE C 14 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LYS C 331 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE C 16 " --> pdb=" O LYS C 331 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.684A pdb=" N LYS C 105 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR C 219 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE C 220 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY C 252 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 569 through 570 removed outlier: 3.631A pdb=" N ASP C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 619 " --> pdb=" O SER C 609 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER C 609 " --> pdb=" O PHE C 619 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS C 655 " --> pdb=" O THR C 610 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 612 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 14 through 17 removed outlier: 5.707A pdb=" N ILE D 14 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LYS D 331 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE D 16 " --> pdb=" O LYS D 331 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 218 through 219 removed outlier: 7.477A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 569 through 570 Processing sheet with id=AB1, first strand: chain 'E' and resid 14 through 17 removed outlier: 6.250A pdb=" N ILE E 14 " --> pdb=" O LYS E 329 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LYS E 331 " --> pdb=" O ILE E 14 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ILE E 16 " --> pdb=" O LYS E 331 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE E 342 " --> pdb=" O VAL E 330 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 216 through 219 removed outlier: 6.484A pdb=" N ASN E 70 " --> pdb=" O VAL E 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA E 250 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N PHE E 72 " --> pdb=" O ALA E 250 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N GLY E 252 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL E 74 " --> pdb=" O GLY E 252 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 569 through 570 removed outlier: 3.627A pdb=" N MET E 573 " --> pdb=" O PHE E 570 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N CYS E 655 " --> pdb=" O LEU E 608 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 610 " --> pdb=" O CYS E 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AB5, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.789A pdb=" N LYS F 105 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N THR F 219 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N ILE F 308 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE F 73 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 573 through 575 removed outlier: 4.296A pdb=" N CYS F 655 " --> pdb=" O THR F 610 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 14 through 17 removed outlier: 6.057A pdb=" N ILE G 14 " --> pdb=" O LYS G 329 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LYS G 331 " --> pdb=" O ILE G 14 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE G 16 " --> pdb=" O LYS G 331 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 104 through 106 removed outlier: 3.650A pdb=" N THR G 251 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY G 252 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 569 through 570 Processing sheet with id=AC1, first strand: chain 'G' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'H' and resid 15 through 16 removed outlier: 4.549A pdb=" N ILE H 342 " --> pdb=" O VAL H 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 104 through 106 removed outlier: 6.742A pdb=" N LYS H 105 " --> pdb=" O LEU H 217 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR H 219 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR H 251 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY H 252 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE H 308 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N PHE H 73 " --> pdb=" O ILE H 308 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 569 through 570 removed outlier: 3.526A pdb=" N MET H 573 " --> pdb=" O PHE H 570 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP H 618 " --> pdb=" O LEU H 576 " (cutoff:3.500A) 2343 hydrogen bonds defined for protein. 6852 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: 11.65 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13957 1.34 - 1.46: 7499 1.46 - 1.58: 25694 1.58 - 1.70: 25 1.70 - 1.82: 328 Bond restraints: 47503 Sorted by residual: bond pdb=" N THR G 225 " pdb=" CA THR G 225 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.16e-02 7.43e+03 7.31e+00 bond pdb=" N ASP H 169 " pdb=" CA ASP H 169 " ideal model delta sigma weight residual 1.456 1.487 -0.032 1.22e-02 6.72e+03 6.70e+00 bond pdb=" N TYR G 172 " pdb=" CA TYR G 172 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.32e+00 bond pdb=" N ILE G 223 " pdb=" CA ILE G 223 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.20e+00 bond pdb=" N ASN A 144 " pdb=" CA ASN A 144 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.16e-02 7.43e+03 6.17e+00 ... (remaining 47498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 63032 1.47 - 2.93: 894 2.93 - 4.40: 164 4.40 - 5.87: 20 5.87 - 7.33: 6 Bond angle restraints: 64116 Sorted by residual: angle pdb=" N ILE D 223 " pdb=" CA ILE D 223 " pdb=" C ILE D 223 " ideal model delta sigma weight residual 111.91 108.15 3.76 8.90e-01 1.26e+00 1.78e+01 angle pdb=" N ILE F 510 " pdb=" CA ILE F 510 " pdb=" C ILE F 510 " ideal model delta sigma weight residual 112.98 108.54 4.44 1.25e+00 6.40e-01 1.26e+01 angle pdb=" C LYS C 173 " pdb=" CA LYS C 173 " pdb=" CB LYS C 173 " ideal model delta sigma weight residual 109.85 113.90 -4.05 1.14e+00 7.69e-01 1.26e+01 angle pdb=" N VAL F 515 " pdb=" CA VAL F 515 " pdb=" C VAL F 515 " ideal model delta sigma weight residual 113.71 110.45 3.26 9.50e-01 1.11e+00 1.18e+01 angle pdb=" N ILE H 339 " pdb=" CA ILE H 339 " pdb=" C ILE H 339 " ideal model delta sigma weight residual 113.20 109.93 3.27 9.60e-01 1.09e+00 1.16e+01 ... (remaining 64111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 25644 17.96 - 35.92: 2664 35.92 - 53.87: 528 53.87 - 71.83: 94 71.83 - 89.79: 53 Dihedral angle restraints: 28983 sinusoidal: 11919 harmonic: 17064 Sorted by residual: dihedral pdb=" C ASP G 224 " pdb=" N ASP G 224 " pdb=" CA ASP G 224 " pdb=" CB ASP G 224 " ideal model delta harmonic sigma weight residual -122.60 -133.43 10.83 0 2.50e+00 1.60e-01 1.88e+01 dihedral pdb=" CA PHE G 227 " pdb=" C PHE G 227 " pdb=" N ASP G 228 " pdb=" CA ASP G 228 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA THR D 225 " pdb=" C THR D 225 " pdb=" N GLN D 226 " pdb=" CA GLN D 226 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 28980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 6690 0.068 - 0.135: 504 0.135 - 0.203: 11 0.203 - 0.271: 1 0.271 - 0.338: 1 Chirality restraints: 7207 Sorted by residual: chirality pdb=" CA ASP G 224 " pdb=" N ASP G 224 " pdb=" C ASP G 224 " pdb=" CB ASP G 224 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CA ILE G 223 " pdb=" N ILE G 223 " pdb=" C ILE G 223 " pdb=" CB ILE G 223 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE H 104 " pdb=" CA ILE H 104 " pdb=" CG1 ILE H 104 " pdb=" CG2 ILE H 104 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 7204 not shown) Planarity restraints: 8202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 223 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ILE G 223 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE G 223 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP G 224 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 148 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.89e+00 pdb=" C LYS A 148 " 0.034 2.00e-02 2.50e+03 pdb=" O LYS A 148 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN A 149 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 511 " -0.012 2.00e-02 2.50e+03 1.43e-02 3.58e+00 pdb=" CG PHE C 511 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 511 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 511 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 511 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 511 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 511 " 0.003 2.00e-02 2.50e+03 ... (remaining 8199 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 726 2.67 - 3.23: 46205 3.23 - 3.79: 72301 3.79 - 4.34: 105141 4.34 - 4.90: 168940 Nonbonded interactions: 393313 Sorted by model distance: nonbonded pdb=" OG SER D 888 " pdb=" OE1 GLU D 891 " model vdw 2.116 3.040 nonbonded pdb=" OG1 THR G 83 " pdb=" O2G ATP G1001 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR F 83 " pdb=" O2G ATP F1001 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASN H 22 " pdb=" O2' ATP H1001 " model vdw 2.167 3.040 nonbonded pdb=" OH TYR H 140 " pdb=" O ILE H 210 " model vdw 2.174 3.040 ... (remaining 393308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'C' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'D' and (resid 13 through 51 or resid 69 through 394 or resid 412 through \ 517 or resid 527 through 663 or resid 706 through 897 or (resid 907 and (name N \ or name CA or name C or name O or name CB )) or resid 909 through 932)) selection = (chain 'E' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or resid 908 through 932)) selection = (chain 'F' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 517 or resid 527 through 634 or (resi \ d 635 and (name N or name CA or name C or name O or name CB )) or resid 636 thro \ ugh 663 or resid 706 through 897 or (resid 907 and (name N or name CA or name C \ or name O or name CB )) or resid 909 through 932)) selection = (chain 'G' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 51 or resid 69 through 94 or (resi \ d 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throug \ h 208 or (resid 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 through 394 or resid 412 through 634 or (resid 635 and (name N or name \ CA or name C or name O or name CB )) or resid 636 through 897 or (resid 907 and \ (name N or name CA or name C or name O or name CB )) or resid 909 through 932)) \ selection = (chain 'H' and (resid 13 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB )) or resid 96 through 208 or (resid 209 and \ (name N or name CA or name C or name O or name CB )) or resid 210 through 394 o \ r resid 412 through 517 or resid 527 through 634 or (resid 635 and (name N or na \ me CA or name C or name O or name CB )) or resid 636 through 663 or resid 706 th \ rough 897 or (resid 907 and (name N or name CA or name C or name O or name CB )) \ or resid 909 through 932)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 45.420 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.090 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 50.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.002 0.034 47503 Z= 0.115 Angle : 0.457 7.333 64116 Z= 0.253 Chirality : 0.038 0.338 7207 Planarity : 0.003 0.045 8202 Dihedral : 15.293 89.790 17919 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.02 % Allowed : 0.49 % Favored : 99.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.11), residues: 5755 helix: -0.09 (0.09), residues: 3090 sheet: 0.32 (0.34), residues: 270 loop : -0.69 (0.13), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 799 TYR 0.024 0.001 TYR C 538 PHE 0.032 0.001 PHE C 511 TRP 0.028 0.001 TRP C 892 HIS 0.010 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00232 (47503) covalent geometry : angle 0.45727 (64116) hydrogen bonds : bond 0.26108 ( 2343) hydrogen bonds : angle 8.32638 ( 6852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 635 time to evaluate : 1.919 Fit side-chains revert: symmetry clash REVERT: C 498 LEU cc_start: 0.8527 (mt) cc_final: 0.8257 (mt) REVERT: C 500 MET cc_start: 0.8572 (tpt) cc_final: 0.8087 (tpt) REVERT: D 161 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7834 (tm-30) REVERT: D 336 MET cc_start: 0.7584 (mtp) cc_final: 0.7271 (mtp) REVERT: D 527 LYS cc_start: 0.6498 (pttm) cc_final: 0.6211 (pttm) REVERT: E 328 ILE cc_start: 0.7898 (mt) cc_final: 0.7632 (mt) REVERT: F 161 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7555 (tp-100) REVERT: G 604 MET cc_start: 0.7597 (tpp) cc_final: 0.7091 (tpp) outliers start: 1 outliers final: 1 residues processed: 636 average time/residue: 0.3152 time to fit residues: 324.3395 Evaluate side-chains 506 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 505 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 394 optimal weight: 7.9990 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 523 optimal weight: 6.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 0.0070 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 592 ASN C 647 ASN C 744 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN D 560 ASN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS E 346 GLN E 357 ASN E 491 GLN E 577 ASN E 898 ASN F 22 ASN G 94 ASN G 97 GLN G 381 GLN ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 837 ASN H 154 GLN H 295 GLN H 384 GLN H 549 HIS H 624 ASN ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.142528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116103 restraints weight = 71197.189| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.08 r_work: 0.3151 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 47503 Z= 0.267 Angle : 0.610 7.185 64116 Z= 0.327 Chirality : 0.043 0.198 7207 Planarity : 0.005 0.049 8202 Dihedral : 7.003 89.079 6452 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.99 % Allowed : 8.46 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.11), residues: 5755 helix: 0.32 (0.09), residues: 3218 sheet: -0.29 (0.32), residues: 270 loop : -0.89 (0.13), residues: 2267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 359 TYR 0.030 0.002 TYR C 588 PHE 0.029 0.002 PHE C 511 TRP 0.020 0.002 TRP E 738 HIS 0.006 0.001 HIS E 549 Details of bonding type rmsd covalent geometry : bond 0.00636 (47503) covalent geometry : angle 0.61022 (64116) hydrogen bonds : bond 0.05983 ( 2343) hydrogen bonds : angle 5.24707 ( 6852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 517 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 370 GLU cc_start: 0.8119 (tp30) cc_final: 0.7871 (tp30) REVERT: A 751 GLN cc_start: 0.7907 (mp10) cc_final: 0.7624 (mp10) REVERT: A 832 ASN cc_start: 0.7912 (t0) cc_final: 0.7677 (t0) REVERT: C 710 ILE cc_start: 0.7401 (mt) cc_final: 0.6455 (pt) REVERT: D 161 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8666 (tm-30) REVERT: D 366 MET cc_start: 0.8697 (ttt) cc_final: 0.8338 (ttm) REVERT: E 473 GLU cc_start: 0.8086 (tp30) cc_final: 0.7855 (tp30) REVERT: E 652 GLN cc_start: 0.7219 (mp10) cc_final: 0.6913 (tp-100) REVERT: E 718 LYS cc_start: 0.7766 (pttm) cc_final: 0.7241 (ttpp) REVERT: F 411 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7543 (tp) REVERT: G 366 MET cc_start: 0.8472 (ttt) cc_final: 0.8210 (ttm) REVERT: G 381 GLN cc_start: 0.8777 (mt0) cc_final: 0.8571 (mt0) REVERT: G 793 TYR cc_start: 0.8245 (m-10) cc_final: 0.7908 (m-10) REVERT: H 500 MET cc_start: 0.8412 (tpp) cc_final: 0.8197 (tpp) outliers start: 51 outliers final: 36 residues processed: 549 average time/residue: 0.3140 time to fit residues: 280.1822 Evaluate side-chains 499 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 461 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 815 ASP Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 610 THR Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 438 optimal weight: 0.9980 chunk 570 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 527 optimal weight: 10.0000 chunk 367 optimal weight: 0.7980 chunk 213 optimal weight: 4.9990 chunk 335 optimal weight: 1.9990 chunk 491 optimal weight: 3.9990 chunk 308 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 260 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 875 ASN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS G 615 ASN H 165 HIS H 575 GLN ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118437 restraints weight = 70777.153| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.95 r_work: 0.3202 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 47503 Z= 0.147 Angle : 0.504 8.269 64116 Z= 0.271 Chirality : 0.040 0.143 7207 Planarity : 0.004 0.043 8202 Dihedral : 6.748 88.550 6452 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.18 % Allowed : 10.95 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.11), residues: 5755 helix: 0.68 (0.09), residues: 3243 sheet: -0.25 (0.33), residues: 252 loop : -0.86 (0.13), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 799 TYR 0.022 0.001 TYR C 535 PHE 0.018 0.001 PHE C 646 TRP 0.021 0.002 TRP E 738 HIS 0.005 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00337 (47503) covalent geometry : angle 0.50364 (64116) hydrogen bonds : bond 0.04624 ( 2343) hydrogen bonds : angle 4.75749 ( 6852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 542 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7509 (mp0) REVERT: A 370 GLU cc_start: 0.8292 (tp30) cc_final: 0.8055 (tp30) REVERT: A 473 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8131 (tp30) REVERT: A 618 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8201 (m-30) REVERT: C 254 LEU cc_start: 0.9360 (tp) cc_final: 0.9148 (tp) REVERT: D 161 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8841 (tm-30) REVERT: D 366 MET cc_start: 0.8819 (ttt) cc_final: 0.8448 (ttm) REVERT: D 604 MET cc_start: 0.7888 (mmt) cc_final: 0.7686 (mmm) REVERT: E 309 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.6959 (mp-120) REVERT: E 458 ARG cc_start: 0.7652 (mmm160) cc_final: 0.7369 (mmm160) REVERT: E 473 GLU cc_start: 0.8296 (tp30) cc_final: 0.8071 (tp30) REVERT: E 604 MET cc_start: 0.8240 (tpp) cc_final: 0.7986 (tpt) REVERT: E 608 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8175 (mm) REVERT: E 652 GLN cc_start: 0.7252 (mp10) cc_final: 0.6915 (tp-100) REVERT: G 289 MET cc_start: 0.7975 (tpp) cc_final: 0.7450 (tpt) REVERT: G 366 MET cc_start: 0.8601 (ttt) cc_final: 0.8330 (ttm) REVERT: G 381 GLN cc_start: 0.8666 (mt0) cc_final: 0.8394 (mt0) REVERT: G 793 TYR cc_start: 0.8284 (m-80) cc_final: 0.7984 (m-10) REVERT: G 879 ASP cc_start: 0.7106 (m-30) cc_final: 0.6699 (t0) REVERT: H 224 ASP cc_start: 0.7906 (m-30) cc_final: 0.7688 (m-30) REVERT: H 370 GLU cc_start: 0.7218 (tp30) cc_final: 0.6771 (tp30) REVERT: H 710 ILE cc_start: 0.7662 (tp) cc_final: 0.7258 (mt) outliers start: 61 outliers final: 40 residues processed: 584 average time/residue: 0.3024 time to fit residues: 287.8232 Evaluate side-chains 531 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 487 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 898 ASN Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain F residue 913 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 447 optimal weight: 6.9990 chunk 147 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 407 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 0.0980 chunk 531 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 474 optimal weight: 5.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 GLN C 485 GLN C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS F 469 GLN G 624 ASN H 154 GLN H 295 GLN H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.143303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115899 restraints weight = 70543.749| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.03 r_work: 0.3169 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 47503 Z= 0.145 Angle : 0.493 9.742 64116 Z= 0.263 Chirality : 0.039 0.147 7207 Planarity : 0.004 0.045 8202 Dihedral : 6.562 87.602 6452 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.48 % Allowed : 12.42 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.20 (0.11), residues: 5755 helix: 0.86 (0.09), residues: 3253 sheet: -0.31 (0.33), residues: 246 loop : -0.82 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 639 TYR 0.023 0.001 TYR C 538 PHE 0.026 0.001 PHE D 646 TRP 0.020 0.001 TRP E 738 HIS 0.006 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00338 (47503) covalent geometry : angle 0.49257 (64116) hydrogen bonds : bond 0.04146 ( 2343) hydrogen bonds : angle 4.54648 ( 6852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 528 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8707 (p) cc_final: 0.8466 (p) REVERT: A 291 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 473 GLU cc_start: 0.8289 (tm-30) cc_final: 0.8040 (tp30) REVERT: A 618 ASP cc_start: 0.8247 (m-30) cc_final: 0.8027 (m-30) REVERT: C 254 LEU cc_start: 0.9334 (tp) cc_final: 0.9083 (tp) REVERT: C 464 PHE cc_start: 0.7710 (p90) cc_final: 0.7426 (p90) REVERT: C 850 ILE cc_start: 0.7865 (mp) cc_final: 0.7663 (mt) REVERT: D 161 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8705 (tm-30) REVERT: D 366 MET cc_start: 0.8665 (ttt) cc_final: 0.8270 (ttm) REVERT: E 309 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.6936 (mp-120) REVERT: E 604 MET cc_start: 0.8208 (tpp) cc_final: 0.7929 (tpt) REVERT: E 608 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8135 (mm) REVERT: E 652 GLN cc_start: 0.7152 (mp10) cc_final: 0.6895 (tp-100) REVERT: G 342 ILE cc_start: 0.7755 (mp) cc_final: 0.7210 (tp) REVERT: G 366 MET cc_start: 0.8297 (ttt) cc_final: 0.8018 (ttm) REVERT: G 381 GLN cc_start: 0.8516 (mt0) cc_final: 0.8206 (mt0) REVERT: G 436 TYR cc_start: 0.6209 (p90) cc_final: 0.5571 (p90) REVERT: G 500 MET cc_start: 0.8240 (tpt) cc_final: 0.7532 (tpp) REVERT: G 534 GLU cc_start: 0.7926 (tp30) cc_final: 0.7422 (tp30) REVERT: G 642 ILE cc_start: 0.6281 (mm) cc_final: 0.6046 (mm) REVERT: G 793 TYR cc_start: 0.8160 (m-80) cc_final: 0.7828 (m-10) REVERT: G 879 ASP cc_start: 0.6998 (m-30) cc_final: 0.6719 (t0) REVERT: H 224 ASP cc_start: 0.7738 (m-30) cc_final: 0.7528 (m-30) REVERT: H 370 GLU cc_start: 0.6995 (tp30) cc_final: 0.6667 (tp30) REVERT: H 425 MET cc_start: 0.5956 (OUTLIER) cc_final: 0.4359 (mmt) REVERT: H 710 ILE cc_start: 0.7747 (tp) cc_final: 0.7295 (mt) outliers start: 76 outliers final: 54 residues processed: 578 average time/residue: 0.2234 time to fit residues: 212.4593 Evaluate side-chains 549 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 491 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 609 SER Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 487 optimal weight: 10.0000 chunk 389 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 580 optimal weight: 10.0000 chunk 467 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 475 optimal weight: 8.9990 chunk 414 optimal weight: 0.1980 chunk 210 optimal weight: 10.0000 chunk 489 optimal weight: 5.9990 chunk 373 optimal weight: 4.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 GLN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS H 549 HIS H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114473 restraints weight = 70389.488| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.04 r_work: 0.3144 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 47503 Z= 0.195 Angle : 0.525 10.598 64116 Z= 0.278 Chirality : 0.041 0.179 7207 Planarity : 0.004 0.043 8202 Dihedral : 6.546 88.898 6452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.02 % Allowed : 13.40 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.11), residues: 5755 helix: 0.86 (0.09), residues: 3263 sheet: -0.48 (0.33), residues: 240 loop : -0.85 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 639 TYR 0.025 0.001 TYR H 927 PHE 0.022 0.002 PHE C 777 TRP 0.019 0.002 TRP C 892 HIS 0.004 0.001 HIS F 839 Details of bonding type rmsd covalent geometry : bond 0.00467 (47503) covalent geometry : angle 0.52494 (64116) hydrogen bonds : bond 0.04204 ( 2343) hydrogen bonds : angle 4.51694 ( 6852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 507 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8773 (p) cc_final: 0.8569 (p) REVERT: A 291 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 618 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.7962 (m-30) REVERT: C 254 LEU cc_start: 0.9372 (tp) cc_final: 0.9096 (tp) REVERT: C 376 VAL cc_start: 0.4823 (t) cc_final: 0.4562 (p) REVERT: C 464 PHE cc_start: 0.7718 (p90) cc_final: 0.7334 (p90) REVERT: C 466 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8079 (mp) REVERT: D 161 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8700 (tm-30) REVERT: D 366 MET cc_start: 0.8686 (ttt) cc_final: 0.8253 (ttm) REVERT: D 560 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8455 (t0) REVERT: E 247 VAL cc_start: 0.9582 (OUTLIER) cc_final: 0.9202 (t) REVERT: E 309 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7017 (mp-120) REVERT: E 604 MET cc_start: 0.8230 (tpp) cc_final: 0.7989 (tpt) REVERT: E 608 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8131 (mm) REVERT: E 652 GLN cc_start: 0.7203 (mp10) cc_final: 0.6927 (tp-100) REVERT: E 775 MET cc_start: 0.7852 (mmm) cc_final: 0.7534 (mmm) REVERT: F 765 MET cc_start: 0.6204 (mmt) cc_final: 0.5918 (mmm) REVERT: G 342 ILE cc_start: 0.7780 (mp) cc_final: 0.7242 (tp) REVERT: G 381 GLN cc_start: 0.8599 (mt0) cc_final: 0.8276 (mt0) REVERT: G 436 TYR cc_start: 0.6253 (p90) cc_final: 0.5467 (p90) REVERT: G 500 MET cc_start: 0.8310 (tpt) cc_final: 0.7960 (tpt) REVERT: G 534 GLU cc_start: 0.7964 (tp30) cc_final: 0.7515 (tp30) REVERT: G 642 ILE cc_start: 0.6480 (mm) cc_final: 0.6230 (mm) REVERT: H 370 GLU cc_start: 0.7054 (tp30) cc_final: 0.6718 (tp30) REVERT: H 425 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.4439 (mmt) REVERT: H 500 MET cc_start: 0.8483 (tpp) cc_final: 0.8146 (tpp) outliers start: 104 outliers final: 68 residues processed: 581 average time/residue: 0.2172 time to fit residues: 207.6454 Evaluate side-chains 552 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 476 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 609 SER Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 489 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 11 optimal weight: 0.0470 chunk 419 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 334 optimal weight: 0.8980 chunk 523 optimal weight: 10.0000 chunk 390 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 overall best weight: 2.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS H 489 ASN H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114535 restraints weight = 70239.561| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.01 r_work: 0.3135 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47503 Z= 0.183 Angle : 0.514 12.540 64116 Z= 0.272 Chirality : 0.040 0.154 7207 Planarity : 0.004 0.043 8202 Dihedral : 6.512 89.632 6452 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.94 % Allowed : 14.17 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.11), residues: 5755 helix: 0.91 (0.09), residues: 3267 sheet: -0.50 (0.33), residues: 240 loop : -0.85 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 639 TYR 0.021 0.001 TYR C 538 PHE 0.025 0.001 PHE D 646 TRP 0.021 0.002 TRP C 892 HIS 0.007 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00439 (47503) covalent geometry : angle 0.51446 (64116) hydrogen bonds : bond 0.04041 ( 2343) hydrogen bonds : angle 4.46031 ( 6852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 495 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8816 (p) cc_final: 0.8616 (p) REVERT: A 291 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 618 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7998 (m-30) REVERT: C 254 LEU cc_start: 0.9372 (tp) cc_final: 0.9075 (tp) REVERT: C 464 PHE cc_start: 0.7689 (p90) cc_final: 0.7316 (p90) REVERT: C 466 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 553 ARG cc_start: 0.8314 (ttm110) cc_final: 0.8093 (ttm110) REVERT: D 161 GLN cc_start: 0.8945 (tm-30) cc_final: 0.8685 (tm-30) REVERT: D 313 MET cc_start: 0.8120 (ttp) cc_final: 0.7910 (ttp) REVERT: D 366 MET cc_start: 0.8686 (ttt) cc_final: 0.8258 (ttm) REVERT: D 560 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8461 (t0) REVERT: E 247 VAL cc_start: 0.9581 (OUTLIER) cc_final: 0.9206 (t) REVERT: E 309 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7041 (mp-120) REVERT: E 346 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: E 604 MET cc_start: 0.8239 (tpp) cc_final: 0.8004 (tpt) REVERT: E 608 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8133 (mm) REVERT: E 652 GLN cc_start: 0.7215 (mp10) cc_final: 0.6922 (tp-100) REVERT: F 437 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: F 765 MET cc_start: 0.6248 (mmt) cc_final: 0.5955 (mmm) REVERT: G 342 ILE cc_start: 0.7865 (mp) cc_final: 0.7344 (tp) REVERT: G 381 GLN cc_start: 0.8605 (mt0) cc_final: 0.8245 (mt0) REVERT: G 436 TYR cc_start: 0.6343 (p90) cc_final: 0.5455 (p90) REVERT: G 534 GLU cc_start: 0.7974 (tp30) cc_final: 0.7528 (tp30) REVERT: G 642 ILE cc_start: 0.6535 (mm) cc_final: 0.6289 (mm) REVERT: G 802 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8088 (pt) REVERT: G 879 ASP cc_start: 0.6905 (m-30) cc_final: 0.6584 (t0) REVERT: H 370 GLU cc_start: 0.7043 (tp30) cc_final: 0.6720 (tp30) REVERT: H 425 MET cc_start: 0.6056 (OUTLIER) cc_final: 0.4432 (mmt) REVERT: H 500 MET cc_start: 0.8393 (tpp) cc_final: 0.8009 (tpp) outliers start: 100 outliers final: 69 residues processed: 566 average time/residue: 0.1983 time to fit residues: 185.6133 Evaluate side-chains 558 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 478 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 466 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 532 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 655 CYS Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain E residue 756 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 750 ASP Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 609 SER Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 37 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 323 optimal weight: 0.0270 chunk 303 optimal weight: 5.9990 chunk 573 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 549 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN H 762 HIS ** H 794 HIS ** 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 = 0.3746 r_free = 0.3746 target = 0.145417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117705 restraints weight = 70388.544| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.05 r_work: 0.3199 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 47503 Z= 0.109 Angle : 0.470 13.556 64116 Z= 0.251 Chirality : 0.039 0.218 7207 Planarity : 0.003 0.045 8202 Dihedral : 6.309 89.177 6452 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.57 % Allowed : 15.01 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.11), residues: 5755 helix: 1.16 (0.09), residues: 3262 sheet: -0.34 (0.33), residues: 252 loop : -0.76 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 639 TYR 0.020 0.001 TYR C 538 PHE 0.017 0.001 PHE C 227 TRP 0.026 0.002 TRP C 892 HIS 0.008 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00244 (47503) covalent geometry : angle 0.47042 (64116) hydrogen bonds : bond 0.03521 ( 2343) hydrogen bonds : angle 4.28659 ( 6852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 550 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8719 (p) cc_final: 0.8468 (p) REVERT: A 291 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: A 618 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: C 254 LEU cc_start: 0.9287 (tp) cc_final: 0.9005 (tp) REVERT: C 553 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7948 (ttm110) REVERT: C 895 LEU cc_start: 0.7815 (mm) cc_final: 0.7539 (mm) REVERT: D 161 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8658 (tm-30) REVERT: D 366 MET cc_start: 0.8610 (ttt) cc_final: 0.8218 (ttm) REVERT: D 465 TYR cc_start: 0.8825 (m-80) cc_final: 0.8605 (m-80) REVERT: D 560 ASN cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (t0) REVERT: D 604 MET cc_start: 0.7694 (mmt) cc_final: 0.7458 (mmm) REVERT: E 247 VAL cc_start: 0.9574 (OUTLIER) cc_final: 0.9209 (t) REVERT: E 309 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.6969 (mp-120) REVERT: E 346 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: E 604 MET cc_start: 0.8233 (tpp) cc_final: 0.7969 (tpt) REVERT: E 608 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8168 (mm) REVERT: E 643 THR cc_start: 0.8058 (p) cc_final: 0.7642 (t) REVERT: E 652 GLN cc_start: 0.7159 (mp10) cc_final: 0.6847 (tp-100) REVERT: F 255 ARG cc_start: 0.8856 (tpt90) cc_final: 0.8654 (tpt90) REVERT: F 437 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: F 512 ASN cc_start: 0.8361 (t0) cc_final: 0.7902 (t0) REVERT: F 790 GLU cc_start: 0.8113 (tp30) cc_final: 0.7891 (tp30) REVERT: G 342 ILE cc_start: 0.7832 (mp) cc_final: 0.7335 (tp) REVERT: G 366 MET cc_start: 0.8267 (ttt) cc_final: 0.7993 (ttm) REVERT: G 436 TYR cc_start: 0.6078 (p90) cc_final: 0.5205 (p90) REVERT: G 500 MET cc_start: 0.8333 (tpt) cc_final: 0.7906 (tpt) REVERT: G 534 GLU cc_start: 0.7962 (tp30) cc_final: 0.7544 (tp30) REVERT: G 642 ILE cc_start: 0.6504 (mm) cc_final: 0.6252 (mm) REVERT: G 708 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.7000 (t70) REVERT: G 879 ASP cc_start: 0.6997 (m-30) cc_final: 0.6526 (t0) REVERT: H 224 ASP cc_start: 0.7689 (m-30) cc_final: 0.7467 (m-30) REVERT: H 370 GLU cc_start: 0.6942 (tp30) cc_final: 0.6652 (tp30) REVERT: H 425 MET cc_start: 0.5899 (OUTLIER) cc_final: 0.4320 (mmt) REVERT: H 500 MET cc_start: 0.8440 (tpp) cc_final: 0.7976 (tpp) outliers start: 81 outliers final: 47 residues processed: 607 average time/residue: 0.1878 time to fit residues: 187.6314 Evaluate side-chains 563 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 506 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 608 LEU Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 244 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 309 optimal weight: 20.0000 chunk 200 optimal weight: 7.9990 chunk 575 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 113 optimal weight: 0.0070 chunk 242 optimal weight: 0.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN C 647 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118443 restraints weight = 70462.279| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.07 r_work: 0.3186 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 47503 Z= 0.109 Angle : 0.473 13.824 64116 Z= 0.251 Chirality : 0.038 0.170 7207 Planarity : 0.003 0.042 8202 Dihedral : 6.191 88.588 6452 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.48 % Allowed : 15.45 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.11), residues: 5755 helix: 1.29 (0.09), residues: 3261 sheet: -0.24 (0.33), residues: 250 loop : -0.70 (0.13), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 639 TYR 0.019 0.001 TYR C 538 PHE 0.026 0.001 PHE D 646 TRP 0.030 0.001 TRP C 892 HIS 0.010 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00246 (47503) covalent geometry : angle 0.47313 (64116) hydrogen bonds : bond 0.03436 ( 2343) hydrogen bonds : angle 4.19567 ( 6852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 535 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8725 (p) cc_final: 0.8453 (p) REVERT: A 291 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: A 604 MET cc_start: 0.8326 (tpt) cc_final: 0.8118 (tpt) REVERT: A 618 ASP cc_start: 0.8225 (m-30) cc_final: 0.7998 (m-30) REVERT: C 181 LEU cc_start: 0.8296 (mt) cc_final: 0.7960 (mp) REVERT: C 254 LEU cc_start: 0.9271 (tp) cc_final: 0.8984 (tp) REVERT: C 895 LEU cc_start: 0.7755 (mm) cc_final: 0.7495 (mm) REVERT: D 105 LYS cc_start: 0.8621 (mmpt) cc_final: 0.8088 (mmtt) REVERT: D 161 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8667 (tm-30) REVERT: D 313 MET cc_start: 0.7799 (ttp) cc_final: 0.7561 (ttp) REVERT: D 332 THR cc_start: 0.8535 (m) cc_final: 0.8320 (p) REVERT: D 465 TYR cc_start: 0.8818 (m-80) cc_final: 0.8559 (m-80) REVERT: D 560 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8375 (t0) REVERT: D 604 MET cc_start: 0.7681 (mmt) cc_final: 0.7455 (mmm) REVERT: E 247 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9215 (t) REVERT: E 309 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6973 (mp-120) REVERT: E 346 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: E 604 MET cc_start: 0.8242 (tpp) cc_final: 0.8010 (tpt) REVERT: E 643 THR cc_start: 0.8071 (p) cc_final: 0.7655 (t) REVERT: E 652 GLN cc_start: 0.7083 (mp10) cc_final: 0.6785 (tp-100) REVERT: F 437 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: F 512 ASN cc_start: 0.8469 (t0) cc_final: 0.8046 (t0) REVERT: F 876 LYS cc_start: 0.8729 (tptt) cc_final: 0.8439 (mmtm) REVERT: G 342 ILE cc_start: 0.7803 (mp) cc_final: 0.7333 (tp) REVERT: G 366 MET cc_start: 0.8334 (ttt) cc_final: 0.8094 (ttm) REVERT: G 436 TYR cc_start: 0.6109 (p90) cc_final: 0.5226 (p90) REVERT: G 500 MET cc_start: 0.8392 (tpt) cc_final: 0.7919 (tpt) REVERT: G 534 GLU cc_start: 0.7995 (tp30) cc_final: 0.7570 (tp30) REVERT: G 642 ILE cc_start: 0.6470 (mm) cc_final: 0.6223 (mm) REVERT: G 646 PHE cc_start: 0.7612 (t80) cc_final: 0.7290 (t80) REVERT: G 708 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.6979 (t70) REVERT: G 780 LEU cc_start: 0.8825 (mt) cc_final: 0.8604 (mt) REVERT: G 879 ASP cc_start: 0.7035 (m-30) cc_final: 0.6561 (t0) REVERT: H 224 ASP cc_start: 0.7714 (m-30) cc_final: 0.7504 (m-30) REVERT: H 258 SER cc_start: 0.8892 (p) cc_final: 0.8664 (p) REVERT: H 425 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.4325 (mmt) REVERT: H 500 MET cc_start: 0.8405 (tpp) cc_final: 0.7912 (tpp) REVERT: H 502 LEU cc_start: 0.8486 (mp) cc_final: 0.8140 (mp) REVERT: H 775 MET cc_start: 0.8099 (mmm) cc_final: 0.7844 (mmm) outliers start: 76 outliers final: 53 residues processed: 586 average time/residue: 0.1817 time to fit residues: 175.8578 Evaluate side-chains 558 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 497 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 554 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 276 optimal weight: 0.9980 chunk 469 optimal weight: 20.0000 chunk 222 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 374 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 431 optimal weight: 7.9990 chunk 351 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.144969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117334 restraints weight = 70277.110| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.09 r_work: 0.3176 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 47503 Z= 0.140 Angle : 0.493 13.513 64116 Z= 0.260 Chirality : 0.039 0.166 7207 Planarity : 0.003 0.042 8202 Dihedral : 6.203 88.572 6452 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.59 % Allowed : 15.78 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.11), residues: 5755 helix: 1.29 (0.09), residues: 3261 sheet: -0.29 (0.33), residues: 252 loop : -0.71 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 639 TYR 0.037 0.001 TYR D 538 PHE 0.019 0.001 PHE A 874 TRP 0.031 0.001 TRP C 892 HIS 0.009 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00332 (47503) covalent geometry : angle 0.49327 (64116) hydrogen bonds : bond 0.03572 ( 2343) hydrogen bonds : angle 4.21112 ( 6852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 505 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 168 THR cc_start: 0.8751 (p) cc_final: 0.8481 (p) REVERT: A 169 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8498 (t0) REVERT: A 291 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: A 431 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.7844 (ttm170) REVERT: A 618 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: C 254 LEU cc_start: 0.9274 (tp) cc_final: 0.8988 (tp) REVERT: D 105 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8090 (mmtt) REVERT: D 161 GLN cc_start: 0.8912 (tm-30) cc_final: 0.8660 (tm-30) REVERT: D 313 MET cc_start: 0.7953 (ttp) cc_final: 0.7722 (ttp) REVERT: D 332 THR cc_start: 0.8591 (m) cc_final: 0.8374 (p) REVERT: D 465 TYR cc_start: 0.8836 (m-80) cc_final: 0.8569 (m-80) REVERT: D 560 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8390 (t0) REVERT: D 604 MET cc_start: 0.7723 (mmt) cc_final: 0.7483 (mmm) REVERT: E 247 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9218 (t) REVERT: E 309 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6987 (mp-120) REVERT: E 346 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: E 604 MET cc_start: 0.8239 (tpp) cc_final: 0.8011 (tpt) REVERT: E 652 GLN cc_start: 0.7106 (mp10) cc_final: 0.6785 (tp40) REVERT: F 437 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: F 876 LYS cc_start: 0.8719 (tptt) cc_final: 0.8461 (mmtm) REVERT: G 342 ILE cc_start: 0.7816 (mp) cc_final: 0.7335 (tp) REVERT: G 366 MET cc_start: 0.8354 (ttt) cc_final: 0.8109 (ttm) REVERT: G 436 TYR cc_start: 0.5985 (p90) cc_final: 0.5043 (p90) REVERT: G 500 MET cc_start: 0.8388 (tpt) cc_final: 0.7887 (tpt) REVERT: G 534 GLU cc_start: 0.7993 (tp30) cc_final: 0.7560 (tp30) REVERT: G 642 ILE cc_start: 0.6474 (mm) cc_final: 0.6223 (mm) REVERT: G 646 PHE cc_start: 0.7632 (t80) cc_final: 0.7302 (t80) REVERT: G 708 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7025 (t70) REVERT: G 780 LEU cc_start: 0.8803 (mt) cc_final: 0.8585 (mt) REVERT: G 879 ASP cc_start: 0.6993 (m-30) cc_final: 0.6668 (t0) REVERT: H 224 ASP cc_start: 0.7692 (m-30) cc_final: 0.7476 (m-30) REVERT: H 370 GLU cc_start: 0.6969 (tp30) cc_final: 0.6714 (tp30) REVERT: H 425 MET cc_start: 0.5967 (OUTLIER) cc_final: 0.4402 (mmt) REVERT: H 500 MET cc_start: 0.8415 (tpp) cc_final: 0.7963 (tpp) REVERT: H 502 LEU cc_start: 0.8492 (mp) cc_final: 0.8158 (mp) REVERT: H 775 MET cc_start: 0.8257 (mmm) cc_final: 0.7922 (mmm) outliers start: 82 outliers final: 58 residues processed: 561 average time/residue: 0.1846 time to fit residues: 171.3169 Evaluate side-chains 559 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 491 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 549 HIS Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 535 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 167 optimal weight: 0.1980 chunk 197 optimal weight: 10.0000 chunk 544 optimal weight: 0.9990 chunk 530 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 417 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 GLN C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119318 restraints weight = 70979.455| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.05 r_work: 0.3199 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 47503 Z= 0.103 Angle : 0.472 13.924 64116 Z= 0.250 Chirality : 0.038 0.154 7207 Planarity : 0.003 0.056 8202 Dihedral : 6.100 88.560 6452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.40 % Allowed : 16.07 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.11), residues: 5755 helix: 1.41 (0.09), residues: 3260 sheet: -0.20 (0.33), residues: 248 loop : -0.67 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 799 TYR 0.023 0.001 TYR H 146 PHE 0.023 0.001 PHE C 646 TRP 0.035 0.002 TRP C 892 HIS 0.010 0.001 HIS H 762 Details of bonding type rmsd covalent geometry : bond 0.00229 (47503) covalent geometry : angle 0.47164 (64116) hydrogen bonds : bond 0.03302 ( 2343) hydrogen bonds : angle 4.12520 ( 6852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11510 Ramachandran restraints generated. 5755 Oldfield, 0 Emsley, 5755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 523 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 168 THR cc_start: 0.8716 (p) cc_final: 0.8430 (p) REVERT: A 291 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 431 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7839 (ttm170) REVERT: A 618 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: C 254 LEU cc_start: 0.9224 (tp) cc_final: 0.8965 (tp) REVERT: C 895 LEU cc_start: 0.7694 (mm) cc_final: 0.7444 (mm) REVERT: D 105 LYS cc_start: 0.8609 (mmpt) cc_final: 0.8080 (mmtt) REVERT: D 161 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8658 (tm-30) REVERT: D 332 THR cc_start: 0.8518 (m) cc_final: 0.8308 (p) REVERT: D 465 TYR cc_start: 0.8813 (m-80) cc_final: 0.8546 (m-80) REVERT: D 560 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8330 (t0) REVERT: D 604 MET cc_start: 0.7646 (mmt) cc_final: 0.7424 (mmm) REVERT: E 247 VAL cc_start: 0.9543 (OUTLIER) cc_final: 0.9198 (t) REVERT: E 309 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.6915 (mp-120) REVERT: E 346 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: E 458 ARG cc_start: 0.7226 (mmm160) cc_final: 0.6883 (mmm-85) REVERT: E 604 MET cc_start: 0.8284 (tpp) cc_final: 0.7886 (tpt) REVERT: E 652 GLN cc_start: 0.7049 (mp10) cc_final: 0.6731 (tp-100) REVERT: F 255 ARG cc_start: 0.8873 (tpt90) cc_final: 0.8654 (tpt90) REVERT: F 437 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8194 (pm20) REVERT: G 342 ILE cc_start: 0.7846 (mp) cc_final: 0.7368 (tp) REVERT: G 366 MET cc_start: 0.8347 (ttt) cc_final: 0.8108 (ttm) REVERT: G 436 TYR cc_start: 0.5934 (p90) cc_final: 0.4991 (p90) REVERT: G 500 MET cc_start: 0.8431 (tpt) cc_final: 0.7931 (tpt) REVERT: G 534 GLU cc_start: 0.7960 (tp30) cc_final: 0.7494 (tp30) REVERT: G 604 MET cc_start: 0.7739 (tpp) cc_final: 0.7316 (tpp) REVERT: G 642 ILE cc_start: 0.6501 (mm) cc_final: 0.6290 (mm) REVERT: G 646 PHE cc_start: 0.7578 (t80) cc_final: 0.7247 (t80) REVERT: G 708 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7010 (t70) REVERT: G 780 LEU cc_start: 0.8810 (mt) cc_final: 0.8593 (mt) REVERT: G 879 ASP cc_start: 0.6985 (m-30) cc_final: 0.6667 (t0) REVERT: H 224 ASP cc_start: 0.7660 (m-30) cc_final: 0.7447 (m-30) REVERT: H 258 SER cc_start: 0.8904 (p) cc_final: 0.8644 (p) REVERT: H 425 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.4226 (mmt) REVERT: H 500 MET cc_start: 0.8346 (tpp) cc_final: 0.7830 (tpp) REVERT: H 502 LEU cc_start: 0.8464 (mp) cc_final: 0.8176 (mp) REVERT: H 775 MET cc_start: 0.8268 (mmm) cc_final: 0.7993 (mmm) outliers start: 72 outliers final: 55 residues processed: 570 average time/residue: 0.1754 time to fit residues: 166.0182 Evaluate side-chains 561 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 497 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 516 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 815 ASP Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain E residue 140 TYR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain E residue 649 VAL Chi-restraints excluded: chain E residue 717 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 222 ASP Chi-restraints excluded: chain F residue 437 GLU Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 532 ILE Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 171 GLU Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain H residue 426 LEU Chi-restraints excluded: chain H residue 488 GLU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 733 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 68 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 418 optimal weight: 8.9990 chunk 232 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 chunk 134 optimal weight: 0.0010 chunk 18 optimal weight: 4.9990 chunk 482 optimal weight: 0.2980 chunk 122 optimal weight: 8.9990 chunk 516 optimal weight: 4.9990 overall best weight: 2.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS E 439 HIS F 22 ASN H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115882 restraints weight = 70614.479| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.12 r_work: 0.3156 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47503 Z= 0.179 Angle : 0.525 13.634 64116 Z= 0.276 Chirality : 0.041 0.181 7207 Planarity : 0.004 0.057 8202 Dihedral : 6.212 87.923 6452 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.46 % Allowed : 16.31 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.11), residues: 5755 helix: 1.27 (0.09), residues: 3262 sheet: -0.29 (0.33), residues: 252 loop : -0.70 (0.13), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 639 TYR 0.027 0.001 TYR D 538 PHE 0.021 0.002 PHE G 227 TRP 0.031 0.002 TRP C 892 HIS 0.008 0.001 HIS F 292 Details of bonding type rmsd covalent geometry : bond 0.00433 (47503) covalent geometry : angle 0.52510 (64116) hydrogen bonds : bond 0.03743 ( 2343) hydrogen bonds : angle 4.23646 ( 6852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8116.18 seconds wall clock time: 140 minutes 45.95 seconds (8445.95 seconds total)