Starting phenix.real_space_refine on Thu Dec 26 17:14:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hr8_34963/12_2024/8hr8_34963.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hr8_34963/12_2024/8hr8_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_34963/12_2024/8hr8_34963.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hr8_34963/12_2024/8hr8_34963.map" model { file = "/net/cci-nas-00/data/ceres_data/8hr8_34963/12_2024/8hr8_34963.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hr8_34963/12_2024/8hr8_34963.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 25.39, per 1000 atoms: 0.54 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: 10.76 Conformation dependent library (CDL) restraints added in 5.8 seconds 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: 5.21 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: 17.99 Time building geometry restraints manager: 12.43 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: 2.480 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: 0.000 Extract box with map and model: 1.290 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 95.160 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.180 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:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.340 ------------------------------------------------------------------------------- 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= 0.149 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 : 9.71 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.001 TRP C 892 HIS 0.010 0.001 HIS F 292 PHE 0.032 0.001 PHE C 511 TYR 0.024 0.001 TYR C 538 ARG 0.009 0.000 ARG F 799 *********************** 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 : 5.565 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: 0.8086 (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: 0.6210 (pttm) REVERT: E 328 ILE cc_start: 0.7898 (mt) cc_final: 0.7631 (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: 0.6703 time to fit residues: 692.9271 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 : 5.260 ------------------------------------------------------------------------------- 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 490 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 297 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 chunk 455 optimal weight: 4.9990 chunk 176 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 338 optimal weight: 8.9990 chunk 527 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 575 GLN ** A 647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 ASN C 592 ASN C 647 ASN C 744 ASN C 762 HIS D 560 ASN D 583 HIS 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 549 HIS H 624 ASN ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 47503 Z= 0.518 Angle : 0.669 7.962 64116 Z= 0.354 Chirality : 0.046 0.214 7207 Planarity : 0.005 0.052 8202 Dihedral : 7.089 87.898 6452 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.15 % Allowed : 9.34 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 5755 helix: 0.17 (0.09), residues: 3223 sheet: -0.42 (0.32), residues: 270 loop : -0.98 (0.13), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 738 HIS 0.007 0.001 HIS E 549 PHE 0.032 0.002 PHE C 511 TYR 0.034 0.002 TYR C 588 ARG 0.007 0.001 ARG D 359 *********************** 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 565 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 506 time to evaluate : 5.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 370 GLU cc_start: 0.7699 (tp30) cc_final: 0.7427 (tp30) REVERT: A 751 GLN cc_start: 0.7706 (mp10) cc_final: 0.7442 (mp10) REVERT: A 832 ASN cc_start: 0.7494 (t0) cc_final: 0.7260 (t0) REVERT: D 161 GLN cc_start: 0.8670 (tm-30) cc_final: 0.8422 (tm-30) REVERT: D 366 MET cc_start: 0.8376 (ttt) cc_final: 0.7973 (ttm) REVERT: E 309 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.6909 (mp-120) REVERT: E 718 LYS cc_start: 0.7654 (pttm) cc_final: 0.7082 (ttpp) REVERT: G 381 GLN cc_start: 0.8805 (mt0) cc_final: 0.8602 (mt0) REVERT: G 793 TYR cc_start: 0.7986 (m-10) cc_final: 0.7746 (m-10) REVERT: H 590 LYS cc_start: 0.7123 (ptmm) cc_final: 0.6538 (ptpt) REVERT: H 710 ILE cc_start: 0.7867 (tp) cc_final: 0.7121 (mt) outliers start: 59 outliers final: 41 residues processed: 546 average time/residue: 0.6370 time to fit residues: 567.0080 Evaluate side-chains 498 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 455 time to evaluate : 5.736 ------------------------------------------------------------------------------- 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 309 GLN Chi-restraints excluded: chain E residue 649 VAL 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 609 SER 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 168 THR Chi-restraints excluded: chain G residue 312 THR 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 Chi-restraints excluded: chain H residue 747 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 293 optimal weight: 7.9990 chunk 163 optimal weight: 9.9990 chunk 439 optimal weight: 0.8980 chunk 359 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 528 optimal weight: 8.9990 chunk 570 optimal weight: 10.0000 chunk 470 optimal weight: 5.9990 chunk 524 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 424 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS ** G 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 GLN H 384 GLN H 575 GLN H 652 GLN ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47503 Z= 0.287 Angle : 0.539 8.131 64116 Z= 0.288 Chirality : 0.041 0.154 7207 Planarity : 0.004 0.045 8202 Dihedral : 6.916 88.875 6452 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.44 % Allowed : 11.53 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5755 helix: 0.53 (0.09), residues: 3235 sheet: -0.59 (0.32), residues: 264 loop : -0.96 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 738 HIS 0.005 0.001 HIS F 292 PHE 0.023 0.002 PHE G 528 TYR 0.034 0.002 TYR C 535 ARG 0.004 0.000 ARG D 359 *********************** 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 586 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 512 time to evaluate : 5.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: A 370 GLU cc_start: 0.7629 (tp30) cc_final: 0.7391 (tp30) REVERT: A 473 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7801 (tp30) REVERT: A 751 GLN cc_start: 0.7665 (mp10) cc_final: 0.7398 (mp10) REVERT: C 254 LEU cc_start: 0.9326 (tp) cc_final: 0.9088 (tp) REVERT: D 161 GLN cc_start: 0.8644 (tm-30) cc_final: 0.8423 (tm-30) REVERT: D 366 MET cc_start: 0.8296 (ttt) cc_final: 0.7829 (ttm) REVERT: E 604 MET cc_start: 0.8190 (tpp) cc_final: 0.7882 (tpt) REVERT: E 608 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8096 (mm) REVERT: E 718 LYS cc_start: 0.7702 (pttm) cc_final: 0.7499 (ttpp) REVERT: G 381 GLN cc_start: 0.8707 (mt0) cc_final: 0.8430 (mt0) REVERT: G 436 TYR cc_start: 0.6081 (p90) cc_final: 0.5486 (p90) REVERT: G 534 GLU cc_start: 0.7710 (tp30) cc_final: 0.7461 (tp30) REVERT: G 793 TYR cc_start: 0.7835 (m-80) cc_final: 0.7615 (m-10) REVERT: H 224 ASP cc_start: 0.7251 (m-30) cc_final: 0.7047 (m-30) REVERT: H 590 LYS cc_start: 0.6987 (ptmm) cc_final: 0.6439 (ptpt) REVERT: H 710 ILE cc_start: 0.7786 (tp) cc_final: 0.7345 (mt) outliers start: 74 outliers final: 49 residues processed: 563 average time/residue: 0.6005 time to fit residues: 552.8734 Evaluate side-chains 518 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 467 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 573 MET Chi-restraints excluded: chain A residue 574 VAL 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 363 ASP 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 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 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 609 SER Chi-restraints excluded: chain F residue 611 VAL 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 765 MET Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 209 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 558 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 522 optimal weight: 5.9990 chunk 397 optimal weight: 3.9990 chunk 274 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 354 optimal weight: 2.9990 chunk 530 optimal weight: 10.0000 chunk 561 optimal weight: 0.0870 chunk 277 optimal weight: 5.9990 chunk 502 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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 ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 575 GLN C 624 ASN C 762 HIS ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS F 469 GLN G 615 ASN G 624 ASN H 165 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: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 47503 Z= 0.274 Angle : 0.521 8.368 64116 Z= 0.278 Chirality : 0.040 0.149 7207 Planarity : 0.004 0.044 8202 Dihedral : 6.733 88.692 6452 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.69 % Allowed : 13.14 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.11), residues: 5755 helix: 0.70 (0.09), residues: 3247 sheet: -0.56 (0.32), residues: 250 loop : -0.93 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 738 HIS 0.006 0.001 HIS H 762 PHE 0.023 0.001 PHE G 528 TYR 0.023 0.001 TYR C 538 ARG 0.006 0.000 ARG D 807 *********************** 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 596 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 509 time to evaluate : 5.506 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: A 370 GLU cc_start: 0.7589 (tp30) cc_final: 0.7366 (tp30) REVERT: A 473 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7752 (tp30) REVERT: A 751 GLN cc_start: 0.7646 (mp10) cc_final: 0.7385 (mp10) REVERT: C 254 LEU cc_start: 0.9319 (tp) cc_final: 0.9069 (tp) REVERT: C 464 PHE cc_start: 0.7617 (p90) cc_final: 0.7320 (p90) REVERT: D 366 MET cc_start: 0.8270 (ttt) cc_final: 0.7856 (ttm) REVERT: D 560 ASN cc_start: 0.8481 (OUTLIER) cc_final: 0.8272 (t0) REVERT: E 247 VAL cc_start: 0.9566 (OUTLIER) cc_final: 0.9164 (t) REVERT: E 309 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.6827 (mp-120) REVERT: E 604 MET cc_start: 0.8200 (tpp) cc_final: 0.7920 (tpt) REVERT: E 608 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8128 (mm) REVERT: F 631 ASP cc_start: 0.7197 (m-30) cc_final: 0.6958 (m-30) REVERT: G 342 ILE cc_start: 0.7674 (mp) cc_final: 0.7174 (tp) REVERT: G 381 GLN cc_start: 0.8634 (mt0) cc_final: 0.8359 (mt0) REVERT: G 436 TYR cc_start: 0.6042 (p90) cc_final: 0.5367 (p90) REVERT: G 500 MET cc_start: 0.7704 (tpt) cc_final: 0.7117 (tpp) REVERT: G 534 GLU cc_start: 0.7716 (tp30) cc_final: 0.7471 (tp30) REVERT: G 793 TYR cc_start: 0.7827 (m-80) cc_final: 0.7596 (m-10) REVERT: H 224 ASP cc_start: 0.7212 (m-30) cc_final: 0.7004 (m-30) REVERT: H 313 MET cc_start: 0.7669 (tpt) cc_final: 0.7466 (tpt) REVERT: H 425 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.4137 (mmt) REVERT: H 590 LYS cc_start: 0.6952 (ptmm) cc_final: 0.6412 (ptpt) outliers start: 87 outliers final: 62 residues processed: 569 average time/residue: 0.5887 time to fit residues: 546.2830 Evaluate side-chains 534 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 466 time to evaluate : 5.021 ------------------------------------------------------------------------------- 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 291 GLU Chi-restraints excluded: chain A residue 530 GLN Chi-restraints excluded: chain A residue 573 MET 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 588 TYR 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 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 457 ASP 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 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 191 ILE 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 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 515 VAL 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 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 566 LYS Chi-restraints excluded: chain G residue 617 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 467 optimal weight: 10.0000 chunk 318 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 418 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 479 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 504 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 485 GLN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 624 ASN D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS H 575 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 47503 Z= 0.299 Angle : 0.526 10.145 64116 Z= 0.279 Chirality : 0.041 0.198 7207 Planarity : 0.004 0.043 8202 Dihedral : 6.638 89.317 6452 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.17 % Allowed : 14.13 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5755 helix: 0.77 (0.09), residues: 3257 sheet: -0.62 (0.32), residues: 250 loop : -0.92 (0.13), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 738 HIS 0.004 0.001 HIS H 762 PHE 0.023 0.002 PHE G 528 TYR 0.023 0.001 TYR C 538 ARG 0.009 0.000 ARG H 639 *********************** 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 609 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 497 time to evaluate : 4.186 Fit side-chains revert: symmetry clash REVERT: A 291 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: A 370 GLU cc_start: 0.7594 (tp30) cc_final: 0.7363 (tp30) REVERT: A 473 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7786 (tp30) REVERT: C 254 LEU cc_start: 0.9349 (tp) cc_final: 0.9065 (tp) REVERT: C 464 PHE cc_start: 0.7611 (p90) cc_final: 0.7284 (p90) REVERT: C 466 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8042 (mp) REVERT: C 553 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7990 (ttm110) REVERT: C 790 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: D 366 MET cc_start: 0.8274 (ttt) cc_final: 0.7830 (ttm) REVERT: D 560 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (t0) REVERT: E 247 VAL cc_start: 0.9567 (OUTLIER) cc_final: 0.9176 (t) REVERT: E 309 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.6848 (mp-120) REVERT: E 604 MET cc_start: 0.8222 (tpp) cc_final: 0.7937 (tpt) REVERT: E 608 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8117 (mm) REVERT: E 775 MET cc_start: 0.7657 (mmm) cc_final: 0.7428 (mmm) REVERT: G 342 ILE cc_start: 0.7772 (mp) cc_final: 0.7288 (tp) REVERT: G 381 GLN cc_start: 0.8655 (mt0) cc_final: 0.8326 (mt0) REVERT: G 436 TYR cc_start: 0.6184 (p90) cc_final: 0.5378 (p90) REVERT: G 500 MET cc_start: 0.7816 (tpt) cc_final: 0.7474 (tpt) REVERT: G 642 ILE cc_start: 0.6488 (mm) cc_final: 0.6273 (mm) REVERT: G 708 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6926 (t70) REVERT: G 802 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7921 (pt) REVERT: H 425 MET cc_start: 0.6108 (OUTLIER) cc_final: 0.4534 (mmt) REVERT: H 590 LYS cc_start: 0.6958 (ptmm) cc_final: 0.6424 (ptpt) outliers start: 112 outliers final: 76 residues processed: 576 average time/residue: 0.5600 time to fit residues: 526.8996 Evaluate side-chains 547 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 461 time to evaluate : 4.093 ------------------------------------------------------------------------------- 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 573 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain C residue 272 THR 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 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 790 GLU 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 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 457 ASP 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 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 191 ILE 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 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 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 366 MET Chi-restraints excluded: chain G residue 573 MET Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 765 MET Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 272 THR 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 609 SER Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS 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 188 optimal weight: 5.9990 chunk 505 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 329 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 562 optimal weight: 9.9990 chunk 466 optimal weight: 5.9990 chunk 260 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 185 optimal weight: 0.9990 chunk 295 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN A 513 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN 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 439 HIS H 489 ASN H 575 GLN ** H 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 47503 Z= 0.343 Angle : 0.546 11.950 64116 Z= 0.288 Chirality : 0.042 0.165 7207 Planarity : 0.004 0.044 8202 Dihedral : 6.636 89.631 6452 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.37 % Allowed : 14.91 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.11), residues: 5755 helix: 0.76 (0.09), residues: 3259 sheet: -0.69 (0.32), residues: 250 loop : -0.95 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 892 HIS 0.007 0.001 HIS H 762 PHE 0.033 0.002 PHE G 528 TYR 0.026 0.002 TYR H 927 ARG 0.012 0.000 ARG H 639 *********************** 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 615 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 493 time to evaluate : 4.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8478 (OUTLIER) cc_final: 0.8133 (t0) REVERT: A 171 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6882 (pp20) REVERT: A 291 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: A 370 GLU cc_start: 0.7610 (tp30) cc_final: 0.7385 (tp30) REVERT: C 254 LEU cc_start: 0.9343 (tp) cc_final: 0.9062 (tp) REVERT: C 464 PHE cc_start: 0.7609 (p90) cc_final: 0.7273 (p90) REVERT: C 466 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8052 (mp) REVERT: C 553 ARG cc_start: 0.8260 (ttm110) cc_final: 0.7986 (ttm110) REVERT: C 790 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7614 (tt0) REVERT: D 366 MET cc_start: 0.8283 (ttt) cc_final: 0.7840 (ttm) REVERT: D 560 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.8337 (t0) REVERT: E 247 VAL cc_start: 0.9569 (OUTLIER) cc_final: 0.9180 (t) REVERT: E 309 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6887 (mp-120) REVERT: E 604 MET cc_start: 0.8259 (tpp) cc_final: 0.7987 (tpt) REVERT: E 608 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8095 (mm) REVERT: G 342 ILE cc_start: 0.7778 (mp) cc_final: 0.7291 (tp) REVERT: G 436 TYR cc_start: 0.6029 (p90) cc_final: 0.5128 (p90) REVERT: G 642 ILE cc_start: 0.6533 (mm) cc_final: 0.6316 (mm) REVERT: G 708 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6913 (t70) REVERT: G 802 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7922 (pt) REVERT: H 370 GLU cc_start: 0.6799 (tp30) cc_final: 0.6356 (tp30) REVERT: H 425 MET cc_start: 0.6049 (OUTLIER) cc_final: 0.4387 (mmt) REVERT: H 500 MET cc_start: 0.7701 (tpp) cc_final: 0.7379 (tpp) REVERT: H 590 LYS cc_start: 0.7016 (ptmm) cc_final: 0.6460 (ptpt) outliers start: 122 outliers final: 87 residues processed: 581 average time/residue: 0.5545 time to fit residues: 530.6038 Evaluate side-chains 572 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 473 time to evaluate : 4.994 ------------------------------------------------------------------------------- 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 171 GLU 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 516 THR 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 795 SER Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain C residue 272 THR 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 588 TYR Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 790 GLU 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 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 532 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 593 ILE Chi-restraints excluded: chain D residue 610 THR Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 886 LEU Chi-restraints excluded: chain D residue 921 THR 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 301 LEU Chi-restraints excluded: chain E residue 309 GLN Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 458 ARG 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 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 720 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 366 MET Chi-restraints excluded: chain G residue 450 ILE Chi-restraints excluded: chain G residue 573 MET Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 272 THR 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 339 ILE 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 648 LYS 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 541 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 320 optimal weight: 10.0000 chunk 410 optimal weight: 6.9990 chunk 318 optimal weight: 4.9990 chunk 473 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 chunk 559 optimal weight: 9.9990 chunk 350 optimal weight: 0.7980 chunk 341 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN 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 652 GLN H 762 HIS ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47503 Z= 0.161 Angle : 0.477 13.709 64116 Z= 0.255 Chirality : 0.039 0.145 7207 Planarity : 0.003 0.045 8202 Dihedral : 6.411 88.745 6452 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.57 % Allowed : 16.33 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 5755 helix: 1.08 (0.09), residues: 3256 sheet: -0.45 (0.32), residues: 252 loop : -0.79 (0.13), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 892 HIS 0.008 0.001 HIS H 762 PHE 0.031 0.001 PHE G 528 TYR 0.021 0.001 TYR C 538 ARG 0.009 0.000 ARG G 78 *********************** 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 625 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 544 time to evaluate : 4.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.8157 (t0) REVERT: A 291 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: C 86 ILE cc_start: 0.8658 (tt) cc_final: 0.8395 (tt) REVERT: C 254 LEU cc_start: 0.9279 (tp) cc_final: 0.8995 (tp) REVERT: C 553 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7828 (ttm110) REVERT: D 105 LYS cc_start: 0.8347 (mmpt) cc_final: 0.8138 (mmpt) REVERT: D 366 MET cc_start: 0.8183 (ttt) cc_final: 0.7779 (ttm) REVERT: D 560 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8249 (t0) REVERT: E 247 VAL cc_start: 0.9565 (OUTLIER) cc_final: 0.9182 (t) REVERT: E 309 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.6813 (mp-120) REVERT: E 346 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7799 (tt0) REVERT: E 604 MET cc_start: 0.8264 (tpp) cc_final: 0.7925 (tpt) REVERT: E 608 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (mm) REVERT: E 643 THR cc_start: 0.7689 (p) cc_final: 0.7292 (t) REVERT: F 512 ASN cc_start: 0.7912 (t0) cc_final: 0.7471 (t0) REVERT: G 342 ILE cc_start: 0.7721 (mp) cc_final: 0.7294 (tp) REVERT: G 436 TYR cc_start: 0.5883 (p90) cc_final: 0.4987 (p90) REVERT: G 708 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6850 (t70) REVERT: G 802 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7936 (pt) REVERT: H 425 MET cc_start: 0.5803 (OUTLIER) cc_final: 0.4203 (mmt) outliers start: 81 outliers final: 52 residues processed: 598 average time/residue: 0.5404 time to fit residues: 526.3306 Evaluate side-chains 550 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 488 time to evaluate : 4.313 ------------------------------------------------------------------------------- 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 516 THR 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 917 LEU 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 C residue 815 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU 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 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 294 GLU 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 212 ASP Chi-restraints excluded: chain F residue 219 THR 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 573 MET Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 312 THR Chi-restraints excluded: chain G residue 566 LYS Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 802 ILE Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 129 LEU 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 549 HIS Chi-restraints excluded: chain H residue 609 SER Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 581 random chunks: chunk 346 optimal weight: 10.0000 chunk 223 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 110 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 356 optimal weight: 5.9990 chunk 381 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 440 optimal weight: 0.2980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 226 GLN ** A 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS E 560 ASN ** E 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 47503 Z= 0.231 Angle : 0.506 13.510 64116 Z= 0.267 Chirality : 0.040 0.202 7207 Planarity : 0.004 0.042 8202 Dihedral : 6.364 88.786 6452 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.82 % Allowed : 16.81 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.11), residues: 5755 helix: 1.09 (0.09), residues: 3262 sheet: -0.50 (0.33), residues: 240 loop : -0.79 (0.13), residues: 2253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 892 HIS 0.008 0.001 HIS H 762 PHE 0.028 0.001 PHE D 646 TYR 0.020 0.001 TYR C 538 ARG 0.010 0.000 ARG F 255 *********************** 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 603 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 509 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8127 (t0) REVERT: A 171 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6766 (pp20) REVERT: A 291 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: C 86 ILE cc_start: 0.8695 (tt) cc_final: 0.8421 (tt) REVERT: C 181 LEU cc_start: 0.8087 (mt) cc_final: 0.7861 (mp) REVERT: C 254 LEU cc_start: 0.9274 (tp) cc_final: 0.8981 (tp) REVERT: D 105 LYS cc_start: 0.8347 (mmpt) cc_final: 0.8131 (mmpt) REVERT: D 159 GLN cc_start: 0.8250 (tt0) cc_final: 0.8019 (tt0) REVERT: D 560 ASN cc_start: 0.8524 (OUTLIER) cc_final: 0.8266 (t0) REVERT: E 247 VAL cc_start: 0.9572 (OUTLIER) cc_final: 0.9182 (t) REVERT: E 309 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6808 (mp-120) REVERT: E 346 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7748 (tt0) REVERT: E 604 MET cc_start: 0.8274 (tpp) cc_final: 0.7963 (tpt) REVERT: E 608 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8153 (mm) REVERT: F 512 ASN cc_start: 0.8042 (t0) cc_final: 0.7637 (t0) REVERT: G 342 ILE cc_start: 0.7742 (mp) cc_final: 0.7301 (tp) REVERT: G 381 GLN cc_start: 0.8512 (mt0) cc_final: 0.8138 (mt0) REVERT: G 436 TYR cc_start: 0.6007 (p90) cc_final: 0.5011 (p90) REVERT: G 500 MET cc_start: 0.7635 (tpt) cc_final: 0.7405 (tpt) REVERT: G 708 ASP cc_start: 0.7247 (OUTLIER) cc_final: 0.6857 (t70) REVERT: G 780 LEU cc_start: 0.8777 (mt) cc_final: 0.8565 (mt) REVERT: H 370 GLU cc_start: 0.6715 (tp30) cc_final: 0.6345 (tp30) REVERT: H 425 MET cc_start: 0.5961 (OUTLIER) cc_final: 0.4395 (mmt) REVERT: H 775 MET cc_start: 0.7838 (mmm) cc_final: 0.7485 (mmm) outliers start: 94 outliers final: 61 residues processed: 574 average time/residue: 0.4981 time to fit residues: 466.9115 Evaluate side-chains 556 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 485 time to evaluate : 3.971 ------------------------------------------------------------------------------- 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 171 GLU 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 516 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 818 GLU 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 543 ARG Chi-restraints excluded: chain C residue 558 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 C residue 815 ASP Chi-restraints excluded: chain C residue 865 VAL Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 285 GLU 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 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 425 MET 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 F residue 32 LEU Chi-restraints excluded: chain F residue 83 THR 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 471 GLU Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 86 ILE 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 708 ASP Chi-restraints excluded: chain G residue 750 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 129 LEU 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 425 MET 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 648 LYS 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 509 optimal weight: 6.9990 chunk 536 optimal weight: 10.0000 chunk 489 optimal weight: 2.9990 chunk 521 optimal weight: 3.9990 chunk 314 optimal weight: 6.9990 chunk 227 optimal weight: 9.9990 chunk 409 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 471 optimal weight: 10.0000 chunk 493 optimal weight: 6.9990 chunk 520 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 456 GLN C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 HIS E 560 ASN G 552 ASN H 575 GLN H 647 ASN ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 47503 Z= 0.421 Angle : 0.598 12.890 64116 Z= 0.313 Chirality : 0.044 0.205 7207 Planarity : 0.004 0.049 8202 Dihedral : 6.622 89.073 6452 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.92 % Allowed : 16.93 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.11), residues: 5755 helix: 0.82 (0.09), residues: 3262 sheet: -0.78 (0.32), residues: 250 loop : -0.95 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 892 HIS 0.009 0.001 HIS F 292 PHE 0.025 0.002 PHE C 777 TYR 0.025 0.002 TYR C 538 ARG 0.011 0.001 ARG H 639 *********************** 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 595 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 496 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8342 (t0) REVERT: A 171 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6845 (pp20) REVERT: A 291 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: C 181 LEU cc_start: 0.8052 (mt) cc_final: 0.7834 (mp) REVERT: C 254 LEU cc_start: 0.9378 (tp) cc_final: 0.9096 (tp) REVERT: C 443 MET cc_start: 0.7195 (mmm) cc_final: 0.6801 (mmm) REVERT: C 464 PHE cc_start: 0.7431 (p90) cc_final: 0.7195 (p90) REVERT: C 790 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: D 105 LYS cc_start: 0.8400 (mmpt) cc_final: 0.8135 (mmpt) REVERT: D 159 GLN cc_start: 0.8302 (tt0) cc_final: 0.8097 (tt0) REVERT: D 560 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8412 (t0) REVERT: E 309 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.6953 (mp-120) REVERT: E 346 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7765 (tt0) REVERT: E 608 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8131 (mm) REVERT: G 342 ILE cc_start: 0.7749 (mp) cc_final: 0.7285 (tp) REVERT: G 381 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8404 (mt0) REVERT: G 436 TYR cc_start: 0.5830 (p90) cc_final: 0.4713 (p90) REVERT: G 499 GLN cc_start: 0.7937 (mt0) cc_final: 0.7709 (mt0) REVERT: G 708 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6968 (t70) REVERT: H 370 GLU cc_start: 0.6838 (tp30) cc_final: 0.6398 (tp30) REVERT: H 425 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.4507 (mmt) REVERT: H 590 LYS cc_start: 0.7100 (ptmm) cc_final: 0.6737 (mttp) outliers start: 99 outliers final: 73 residues processed: 568 average time/residue: 0.5022 time to fit residues: 464.6676 Evaluate side-chains 564 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 480 time to evaluate : 3.929 ------------------------------------------------------------------------------- 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 171 GLU 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 516 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain A residue 909 ILE 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 543 ARG 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 790 GLU Chi-restraints excluded: chain C residue 815 ASP 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 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 532 ILE 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 D residue 921 THR 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 F residue 32 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 212 ASP Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 308 ILE 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 541 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 720 VAL Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 86 ILE 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 381 GLN Chi-restraints excluded: chain G residue 573 MET Chi-restraints excluded: chain G residue 617 MET Chi-restraints excluded: chain G residue 653 THR Chi-restraints excluded: chain G residue 708 ASP Chi-restraints excluded: chain G residue 850 ILE Chi-restraints excluded: chain H residue 129 LEU 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 332 THR Chi-restraints excluded: chain H residue 339 ILE 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 549 HIS Chi-restraints excluded: chain H residue 558 VAL Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS 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 342 optimal weight: 3.9990 chunk 551 optimal weight: 2.9990 chunk 336 optimal weight: 0.6980 chunk 261 optimal weight: 3.9990 chunk 383 optimal weight: 0.0770 chunk 578 optimal weight: 3.9990 chunk 532 optimal weight: 10.0000 chunk 460 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 282 optimal weight: 4.9990 overall best weight: 1.7142 ------------------------------------------------------------------------------- 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 456 GLN ** C 575 GLN ** 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 560 ASN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 575 GLN H 647 ASN ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2226 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= 0.210 Angle : 0.515 13.576 64116 Z= 0.272 Chirality : 0.040 0.186 7207 Planarity : 0.004 0.049 8202 Dihedral : 6.448 88.223 6452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.59 % Allowed : 17.32 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.11), residues: 5755 helix: 1.04 (0.09), residues: 3258 sheet: -0.68 (0.32), residues: 240 loop : -0.84 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 892 HIS 0.009 0.001 HIS H 762 PHE 0.018 0.001 PHE C 646 TYR 0.023 0.001 TYR C 538 ARG 0.008 0.000 ARG H 639 ********************** 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 583 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 501 time to evaluate : 4.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8150 (t0) REVERT: A 171 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6791 (pp20) REVERT: A 291 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: C 181 LEU cc_start: 0.8013 (mt) cc_final: 0.7799 (mp) REVERT: C 254 LEU cc_start: 0.9287 (tp) cc_final: 0.8996 (tp) REVERT: C 443 MET cc_start: 0.7159 (mmm) cc_final: 0.6782 (mmm) REVERT: D 159 GLN cc_start: 0.8261 (tt0) cc_final: 0.8026 (tt0) REVERT: D 560 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8345 (t0) REVERT: E 247 VAL cc_start: 0.9560 (OUTLIER) cc_final: 0.9191 (t) REVERT: E 309 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.6857 (mp-120) REVERT: E 346 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: E 604 MET cc_start: 0.8236 (tpp) cc_final: 0.7937 (tpt) REVERT: E 608 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (mm) REVERT: G 342 ILE cc_start: 0.7747 (mp) cc_final: 0.7314 (tp) REVERT: G 381 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: G 436 TYR cc_start: 0.5741 (p90) cc_final: 0.4693 (p90) REVERT: G 534 GLU cc_start: 0.7585 (tp30) cc_final: 0.7359 (tp30) REVERT: G 646 PHE cc_start: 0.7432 (t80) cc_final: 0.7225 (t80) REVERT: G 708 ASP cc_start: 0.7264 (OUTLIER) cc_final: 0.6860 (t70) REVERT: H 224 ASP cc_start: 0.7217 (m-30) cc_final: 0.7016 (m-30) REVERT: H 370 GLU cc_start: 0.6734 (tp30) cc_final: 0.6352 (tp30) REVERT: H 425 MET cc_start: 0.5950 (OUTLIER) cc_final: 0.4339 (mmt) REVERT: H 590 LYS cc_start: 0.7000 (ptmm) cc_final: 0.6635 (mttp) outliers start: 82 outliers final: 65 residues processed: 558 average time/residue: 0.4914 time to fit residues: 448.3156 Evaluate side-chains 563 residues out of total 5156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 487 time to evaluate : 3.923 ------------------------------------------------------------------------------- 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 171 GLU 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 516 THR 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 909 ILE Chi-restraints excluded: chain C residue 259 GLN Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 543 ARG 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 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 283 LEU Chi-restraints excluded: chain D residue 285 GLU Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 516 THR Chi-restraints excluded: chain D residue 532 ILE 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 301 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 560 ASN 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 F residue 32 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 508 VAL Chi-restraints excluded: chain F residue 541 VAL Chi-restraints excluded: chain F residue 573 MET Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 624 ASN Chi-restraints excluded: chain F residue 851 LEU Chi-restraints excluded: chain G residue 86 ILE 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 381 GLN Chi-restraints excluded: chain G residue 573 MET 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 129 LEU 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 549 HIS Chi-restraints excluded: chain H residue 610 THR Chi-restraints excluded: chain H residue 648 LYS 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 366 optimal weight: 0.0770 chunk 490 optimal weight: 0.2980 chunk 141 optimal weight: 9.9990 chunk 424 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 0.0050 chunk 461 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 474 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.8756 ------------------------------------------------------------------------------- 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 456 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 624 ASN ** C 794 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 ASN ** 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 469 GLN H 575 GLN ** H 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 778 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3716 r_free = 0.3716 target = 0.143013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.115598 restraints weight = 70244.153| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.01 r_work: 0.3161 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.306 47503 Z= 0.261 Angle : 0.619 59.168 64116 Z= 0.343 Chirality : 0.039 0.194 7207 Planarity : 0.004 0.050 8202 Dihedral : 6.447 88.202 6452 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.61 % Allowed : 17.41 % Favored : 80.97 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 5755 helix: 1.06 (0.09), residues: 3258 sheet: -0.68 (0.32), residues: 240 loop : -0.83 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 892 HIS 0.015 0.001 HIS A 439 PHE 0.017 0.001 PHE C 227 TYR 0.072 0.001 TYR H 535 ARG 0.007 0.000 ARG C 758 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9327.92 seconds wall clock time: 168 minutes 6.17 seconds (10086.17 seconds total)