Starting phenix.real_space_refine on Tue Sep 15 13:38:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bvp_30220/09_2026/7bvp_30220.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 24 5.49 5 S 180 5.16 5 C 25410 2.51 5 N 6834 2.21 5 O 7692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 122 residue(s): 0.23s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40146 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'NAD': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.52, per 1000 atoms: 0.21 Number of scatterers: 40146 At special positions: 0 Unit cell: (165.88, 255.112, 167.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 180 16.00 P 24 15.00 O 7692 8.00 N 6834 7.00 C 25410 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.65 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 903 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 723 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 737 " pdb="ZN ZN A 903 " - pdb=" NE2 HIS A 657 " pdb=" ZN B 903 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 723 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 737 " pdb="ZN ZN B 903 " - pdb=" NE2 HIS B 657 " pdb=" ZN C 903 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 723 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 737 " pdb="ZN ZN C 903 " - pdb=" NE2 HIS C 657 " pdb=" ZN D 903 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 723 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 737 " pdb="ZN ZN D 903 " - pdb=" NE2 HIS D 657 " pdb=" ZN E 903 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 723 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 737 " pdb="ZN ZN E 903 " - pdb=" NE2 HIS E 657 " pdb=" ZN F 903 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 723 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 737 " pdb="ZN ZN F 903 " - pdb=" NE2 HIS F 657 " 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9696 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 24 sheets defined 50.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.963A pdb=" N ILE A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.818A pdb=" N VAL A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 80 removed outlier: 3.635A pdb=" N SER A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.739A pdb=" N THR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 195 through 203 removed outlier: 3.607A pdb=" N LYS A 200 " --> pdb=" O PRO A 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.721A pdb=" N ALA A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.708A pdb=" N HIS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 287 removed outlier: 3.818A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL A 285 " --> pdb=" O ALA A 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU A 287 " --> pdb=" O GLN A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.650A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 3.578A pdb=" N HIS A 334 " --> pdb=" O PRO A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.753A pdb=" N GLU A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.613A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.996A pdb=" N ILE A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 425 removed outlier: 4.137A pdb=" N TRP A 424 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU A 438 " --> pdb=" O PRO A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.584A pdb=" N ASN A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 488 through 492' Processing helix chain 'A' and resid 496 through 506 removed outlier: 4.261A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 523 No H-bonds generated for 'chain 'A' and resid 521 through 523' Processing helix chain 'A' and resid 524 through 536 removed outlier: 3.769A pdb=" N GLY A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.562A pdb=" N ALA A 552 " --> pdb=" O PRO A 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 Processing helix chain 'A' and resid 625 through 628 removed outlier: 3.762A pdb=" N THR A 628 " --> pdb=" O TYR A 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 625 through 628' Processing helix chain 'A' and resid 643 through 664 removed outlier: 3.582A pdb=" N THR A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 662 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.705A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 696 through 717 removed outlier: 3.803A pdb=" N ARG A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR A 708 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 733 removed outlier: 3.825A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 removed outlier: 4.843A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASN A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS A 781 " --> pdb=" O GLU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 806 removed outlier: 3.539A pdb=" N LYS A 794 " --> pdb=" O ARG A 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 802 " --> pdb=" O LEU A 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 830 through 836 removed outlier: 3.502A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 839 No H-bonds generated for 'chain 'A' and resid 837 through 839' Processing helix chain 'A' and resid 841 through 845 removed outlier: 3.703A pdb=" N ALA A 844 " --> pdb=" O CYS A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.645A pdb=" N GLN A 856 " --> pdb=" O SER A 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 41 removed outlier: 3.963A pdb=" N ILE B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.819A pdb=" N VAL B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 80 removed outlier: 3.635A pdb=" N SER B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.739A pdb=" N THR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.606A pdb=" N LYS B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 239 removed outlier: 3.720A pdb=" N ALA B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 258 through 269 removed outlier: 3.709A pdb=" N HIS B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.818A pdb=" N LYS B 280 " --> pdb=" O GLY B 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 286 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LEU B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.651A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.579A pdb=" N HIS B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 363 removed outlier: 3.754A pdb=" N GLU B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 3.614A pdb=" N GLY B 386 " --> pdb=" O VAL B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 3.996A pdb=" N ILE B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.138A pdb=" N TRP B 424 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU B 438 " --> pdb=" O PRO B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.583A pdb=" N ASN B 492 " --> pdb=" O ARG B 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 488 through 492' Processing helix chain 'B' and resid 496 through 506 removed outlier: 4.261A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 523 No H-bonds generated for 'chain 'B' and resid 521 through 523' Processing helix chain 'B' and resid 524 through 536 removed outlier: 3.768A pdb=" N GLY B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.563A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 625 through 628 removed outlier: 3.762A pdb=" N THR B 628 " --> pdb=" O TYR B 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 625 through 628' Processing helix chain 'B' and resid 643 through 664 removed outlier: 3.582A pdb=" N THR B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 662 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.704A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 removed outlier: 3.542A pdb=" N GLU B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 717 removed outlier: 3.572A pdb=" N ARG B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR B 708 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN B 716 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 733 removed outlier: 3.825A pdb=" N SER B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 753 removed outlier: 4.843A pdb=" N CYS B 746 " --> pdb=" O ALA B 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN B 747 " --> pdb=" O LEU B 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA B 779 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS B 781 " --> pdb=" O GLU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 806 removed outlier: 3.539A pdb=" N LYS B 794 " --> pdb=" O ARG B 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 802 " --> pdb=" O LEU B 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 826 Processing helix chain 'B' and resid 830 through 836 removed outlier: 3.503A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 837 through 839 No H-bonds generated for 'chain 'B' and resid 837 through 839' Processing helix chain 'B' and resid 841 through 845 removed outlier: 3.702A pdb=" N ALA B 844 " --> pdb=" O CYS B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 863 removed outlier: 3.644A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 858 " --> pdb=" O LEU B 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN C 10 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 21 " --> pdb=" O LYS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 41 removed outlier: 3.964A pdb=" N ILE C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.818A pdb=" N VAL C 54 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 80 removed outlier: 3.635A pdb=" N SER C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR C 77 " --> pdb=" O SER C 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 142 through 159 removed outlier: 3.739A pdb=" N THR C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 195 through 203 removed outlier: 3.607A pdb=" N LYS C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 239 removed outlier: 3.720A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.709A pdb=" N HIS C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 287 removed outlier: 3.819A pdb=" N LYS C 280 " --> pdb=" O GLY C 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL C 285 " --> pdb=" O ALA C 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE C 286 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU C 287 " --> pdb=" O GLN C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.650A pdb=" N ALA C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.579A pdb=" N HIS C 334 " --> pdb=" O PRO C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 363 removed outlier: 3.753A pdb=" N GLU C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET C 362 " --> pdb=" O LYS C 358 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY C 363 " --> pdb=" O LEU C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.614A pdb=" N GLY C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.995A pdb=" N ILE C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 425 removed outlier: 4.137A pdb=" N TRP C 424 " --> pdb=" O CYS C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU C 438 " --> pdb=" O PRO C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.583A pdb=" N ASN C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 492' Processing helix chain 'C' and resid 496 through 506 removed outlier: 4.262A pdb=" N VAL C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 523 No H-bonds generated for 'chain 'C' and resid 521 through 523' Processing helix chain 'C' and resid 524 through 536 removed outlier: 3.768A pdb=" N GLY C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.562A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 570 Processing helix chain 'C' and resid 625 through 628 removed outlier: 3.763A pdb=" N THR C 628 " --> pdb=" O TYR C 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 625 through 628' Processing helix chain 'C' and resid 643 through 664 removed outlier: 3.583A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYR C 662 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL C 663 " --> pdb=" O MET C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 685 removed outlier: 3.705A pdb=" N LEU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 685 through 692 Processing helix chain 'C' and resid 693 through 695 No H-bonds generated for 'chain 'C' and resid 693 through 695' Processing helix chain 'C' and resid 696 through 717 removed outlier: 3.802A pdb=" N ARG C 702 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR C 708 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 733 removed outlier: 3.826A pdb=" N SER C 724 " --> pdb=" O GLY C 720 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS C 728 " --> pdb=" O SER C 724 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 753 removed outlier: 4.844A pdb=" N CYS C 746 " --> pdb=" O ALA C 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN C 747 " --> pdb=" O LEU C 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP C 780 " --> pdb=" O ALA C 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 781 " --> pdb=" O GLU C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 806 removed outlier: 3.539A pdb=" N LYS C 794 " --> pdb=" O ARG C 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU C 796 " --> pdb=" O ALA C 792 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C 804 " --> pdb=" O ALA C 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS C 806 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 826 Processing helix chain 'C' and resid 830 through 836 removed outlier: 3.502A pdb=" N GLU C 834 " --> pdb=" O ASP C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 837 through 839 No H-bonds generated for 'chain 'C' and resid 837 through 839' Processing helix chain 'C' and resid 841 through 845 removed outlier: 3.702A pdb=" N ALA C 844 " --> pdb=" O CYS C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 863 removed outlier: 3.645A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN D 10 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA D 11 " --> pdb=" O ALA D 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG D 21 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 41 removed outlier: 3.963A pdb=" N ILE D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 57 removed outlier: 3.818A pdb=" N VAL D 54 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 80 removed outlier: 3.636A pdb=" N SER D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.739A pdb=" N THR D 146 " --> pdb=" O ALA D 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 195 through 203 removed outlier: 3.607A pdb=" N LYS D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 239 removed outlier: 3.721A pdb=" N ALA D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 Processing helix chain 'D' and resid 258 through 269 removed outlier: 3.709A pdb=" N HIS D 269 " --> pdb=" O ARG D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 287 removed outlier: 3.819A pdb=" N LYS D 280 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE D 286 " --> pdb=" O VAL D 282 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU D 287 " --> pdb=" O GLN D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.651A pdb=" N ALA D 305 " --> pdb=" O ALA D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.578A pdb=" N HIS D 334 " --> pdb=" O PRO D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 363 removed outlier: 3.753A pdb=" N GLU D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET D 362 " --> pdb=" O LYS D 358 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY D 363 " --> pdb=" O LEU D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 389 removed outlier: 3.613A pdb=" N GLY D 386 " --> pdb=" O VAL D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 405 removed outlier: 3.996A pdb=" N ILE D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 425 removed outlier: 4.137A pdb=" N TRP D 424 " --> pdb=" O CYS D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU D 438 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 488 through 492 removed outlier: 3.583A pdb=" N ASN D 492 " --> pdb=" O ARG D 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 488 through 492' Processing helix chain 'D' and resid 496 through 506 removed outlier: 4.261A pdb=" N VAL D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 523 No H-bonds generated for 'chain 'D' and resid 521 through 523' Processing helix chain 'D' and resid 524 through 536 removed outlier: 3.768A pdb=" N GLY D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.563A pdb=" N ALA D 552 " --> pdb=" O PRO D 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 625 through 628 removed outlier: 3.762A pdb=" N THR D 628 " --> pdb=" O TYR D 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 625 through 628' Processing helix chain 'D' and resid 643 through 664 removed outlier: 3.581A pdb=" N THR D 656 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR D 662 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D 663 " --> pdb=" O MET D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 685 removed outlier: 3.704A pdb=" N LEU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 692 Processing helix chain 'D' and resid 693 through 695 No H-bonds generated for 'chain 'D' and resid 693 through 695' Processing helix chain 'D' and resid 696 through 717 removed outlier: 3.803A pdb=" N ARG D 702 " --> pdb=" O VAL D 698 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR D 708 " --> pdb=" O HIS D 704 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN D 716 " --> pdb=" O ILE D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 733 removed outlier: 3.826A pdb=" N SER D 724 " --> pdb=" O GLY D 720 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 728 " --> pdb=" O SER D 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE D 733 " --> pdb=" O LEU D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 753 removed outlier: 4.843A pdb=" N CYS D 746 " --> pdb=" O ALA D 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN D 747 " --> pdb=" O LEU D 743 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG D 750 " --> pdb=" O CYS D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG D 774 " --> pdb=" O GLN D 770 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 779 " --> pdb=" O TYR D 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP D 780 " --> pdb=" O ALA D 776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS D 781 " --> pdb=" O GLU D 777 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 806 removed outlier: 3.538A pdb=" N LYS D 794 " --> pdb=" O ARG D 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 795 " --> pdb=" O THR D 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU D 796 " --> pdb=" O ALA D 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 802 " --> pdb=" O LEU D 798 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 804 " --> pdb=" O ALA D 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS D 806 " --> pdb=" O LEU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 826 Processing helix chain 'D' and resid 830 through 836 removed outlier: 3.502A pdb=" N GLU D 834 " --> pdb=" O ASP D 830 " (cutoff:3.500A) Processing helix chain 'D' and resid 837 through 839 No H-bonds generated for 'chain 'D' and resid 837 through 839' Processing helix chain 'D' and resid 841 through 845 removed outlier: 3.702A pdb=" N ALA D 844 " --> pdb=" O CYS D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 863 removed outlier: 3.645A pdb=" N GLN D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 858 " --> pdb=" O LEU D 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN E 10 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA E 11 " --> pdb=" O ALA E 7 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 21 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 41 removed outlier: 3.965A pdb=" N ILE E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 removed outlier: 3.818A pdb=" N VAL E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 80 removed outlier: 3.636A pdb=" N SER E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR E 77 " --> pdb=" O SER E 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 142 through 159 removed outlier: 3.739A pdb=" N THR E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 195 through 203 removed outlier: 3.607A pdb=" N LYS E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 239 removed outlier: 3.721A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 Processing helix chain 'E' and resid 258 through 269 removed outlier: 3.710A pdb=" N HIS E 269 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 287 removed outlier: 3.818A pdb=" N LYS E 280 " --> pdb=" O GLY E 276 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP E 284 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL E 285 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU E 287 " --> pdb=" O GLN E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.651A pdb=" N ALA E 305 " --> pdb=" O ALA E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.579A pdb=" N HIS E 334 " --> pdb=" O PRO E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 363 removed outlier: 3.753A pdb=" N GLU E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA E 361 " --> pdb=" O GLU E 357 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET E 362 " --> pdb=" O LYS E 358 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 389 removed outlier: 3.613A pdb=" N GLY E 386 " --> pdb=" O VAL E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 405 removed outlier: 3.996A pdb=" N ILE E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 425 removed outlier: 4.137A pdb=" N TRP E 424 " --> pdb=" O CYS E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU E 438 " --> pdb=" O PRO E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 488 through 492 removed outlier: 3.583A pdb=" N ASN E 492 " --> pdb=" O ARG E 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 488 through 492' Processing helix chain 'E' and resid 496 through 506 removed outlier: 4.262A pdb=" N VAL E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 506 " --> pdb=" O VAL E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 523 No H-bonds generated for 'chain 'E' and resid 521 through 523' Processing helix chain 'E' and resid 524 through 536 removed outlier: 3.769A pdb=" N GLY E 528 " --> pdb=" O ILE E 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 561 removed outlier: 3.563A pdb=" N ALA E 552 " --> pdb=" O PRO E 548 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 625 through 628 removed outlier: 3.762A pdb=" N THR E 628 " --> pdb=" O TYR E 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 625 through 628' Processing helix chain 'E' and resid 643 through 664 removed outlier: 3.582A pdb=" N THR E 656 " --> pdb=" O LEU E 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR E 662 " --> pdb=" O ALA E 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL E 663 " --> pdb=" O MET E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 685 removed outlier: 3.705A pdb=" N LEU E 679 " --> pdb=" O ALA E 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU E 684 " --> pdb=" O LYS E 680 " (cutoff:3.500A) Processing helix chain 'E' and resid 685 through 692 Processing helix chain 'E' and resid 696 through 717 removed outlier: 3.802A pdb=" N ARG E 702 " --> pdb=" O VAL E 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR E 708 " --> pdb=" O HIS E 704 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN E 716 " --> pdb=" O ILE E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 733 removed outlier: 3.826A pdb=" N SER E 724 " --> pdb=" O GLY E 720 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS E 728 " --> pdb=" O SER E 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE E 733 " --> pdb=" O LEU E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 739 through 753 removed outlier: 4.843A pdb=" N CYS E 746 " --> pdb=" O ALA E 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN E 747 " --> pdb=" O LEU E 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG E 750 " --> pdb=" O CYS E 746 " (cutoff:3.500A) Processing helix chain 'E' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG E 774 " --> pdb=" O GLN E 770 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 779 " --> pdb=" O TYR E 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP E 780 " --> pdb=" O ALA E 776 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS E 781 " --> pdb=" O GLU E 777 " (cutoff:3.500A) Processing helix chain 'E' and resid 790 through 806 removed outlier: 3.539A pdb=" N LYS E 794 " --> pdb=" O ARG E 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 795 " --> pdb=" O THR E 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU E 796 " --> pdb=" O ALA E 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU E 802 " --> pdb=" O LEU E 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR E 804 " --> pdb=" O ALA E 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS E 806 " --> pdb=" O LEU E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 826 Processing helix chain 'E' and resid 830 through 836 removed outlier: 3.503A pdb=" N GLU E 834 " --> pdb=" O ASP E 830 " (cutoff:3.500A) Processing helix chain 'E' and resid 837 through 839 No H-bonds generated for 'chain 'E' and resid 837 through 839' Processing helix chain 'E' and resid 841 through 845 removed outlier: 3.701A pdb=" N ALA E 844 " --> pdb=" O CYS E 841 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 863 removed outlier: 3.645A pdb=" N GLN E 856 " --> pdb=" O SER E 852 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 858 " --> pdb=" O LEU E 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 21 removed outlier: 3.620A pdb=" N ASN F 10 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA F 11 " --> pdb=" O ALA F 7 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 41 removed outlier: 3.964A pdb=" N ILE F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 57 removed outlier: 3.818A pdb=" N VAL F 54 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER F 57 " --> pdb=" O ALA F 53 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 80 removed outlier: 3.634A pdb=" N SER F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR F 77 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR F 80 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.738A pdb=" N THR F 146 " --> pdb=" O ALA F 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 183 Processing helix chain 'F' and resid 195 through 203 removed outlier: 3.607A pdb=" N LYS F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 239 removed outlier: 3.721A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 Processing helix chain 'F' and resid 258 through 269 removed outlier: 3.709A pdb=" N HIS F 269 " --> pdb=" O ARG F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 287 removed outlier: 3.819A pdb=" N LYS F 280 " --> pdb=" O GLY F 276 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL F 285 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 286 " --> pdb=" O VAL F 282 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.650A pdb=" N ALA F 305 " --> pdb=" O ALA F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 3.578A pdb=" N HIS F 334 " --> pdb=" O PRO F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 363 removed outlier: 3.753A pdb=" N GLU F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA F 361 " --> pdb=" O GLU F 357 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N MET F 362 " --> pdb=" O LYS F 358 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY F 363 " --> pdb=" O LEU F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 389 removed outlier: 3.613A pdb=" N GLY F 386 " --> pdb=" O VAL F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 removed outlier: 3.996A pdb=" N ILE F 405 " --> pdb=" O SER F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 425 removed outlier: 4.137A pdb=" N TRP F 424 " --> pdb=" O CYS F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 removed outlier: 3.682A pdb=" N LEU F 438 " --> pdb=" O PRO F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 472 Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 488 through 492 removed outlier: 3.583A pdb=" N ASN F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 488 through 492' Processing helix chain 'F' and resid 496 through 506 removed outlier: 4.261A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 521 through 523 No H-bonds generated for 'chain 'F' and resid 521 through 523' Processing helix chain 'F' and resid 524 through 536 removed outlier: 3.769A pdb=" N GLY F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 561 removed outlier: 3.562A pdb=" N ALA F 552 " --> pdb=" O PRO F 548 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 625 through 628 removed outlier: 3.763A pdb=" N THR F 628 " --> pdb=" O TYR F 625 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 625 through 628' Processing helix chain 'F' and resid 643 through 664 removed outlier: 3.582A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 662 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL F 663 " --> pdb=" O MET F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 685 removed outlier: 3.704A pdb=" N LEU F 679 " --> pdb=" O ALA F 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU F 684 " --> pdb=" O LYS F 680 " (cutoff:3.500A) Processing helix chain 'F' and resid 685 through 692 removed outlier: 3.757A pdb=" N GLU F 692 " --> pdb=" O ALA F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 693 through 696 Processing helix chain 'F' and resid 698 through 717 removed outlier: 3.803A pdb=" N ARG F 702 " --> pdb=" O VAL F 698 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N THR F 708 " --> pdb=" O HIS F 704 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN F 716 " --> pdb=" O ILE F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 733 removed outlier: 3.826A pdb=" N SER F 724 " --> pdb=" O GLY F 720 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 728 " --> pdb=" O SER F 724 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE F 733 " --> pdb=" O LEU F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 739 through 753 removed outlier: 4.843A pdb=" N CYS F 746 " --> pdb=" O ALA F 742 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN F 747 " --> pdb=" O LEU F 743 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 782 removed outlier: 3.549A pdb=" N ARG F 774 " --> pdb=" O GLN F 770 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 779 " --> pdb=" O TYR F 775 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP F 780 " --> pdb=" O ALA F 776 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 781 " --> pdb=" O GLU F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 790 through 806 removed outlier: 3.538A pdb=" N LYS F 794 " --> pdb=" O ARG F 790 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 795 " --> pdb=" O THR F 791 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU F 802 " --> pdb=" O LEU F 798 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 804 " --> pdb=" O ALA F 800 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) Processing helix chain 'F' and resid 821 through 826 Processing helix chain 'F' and resid 830 through 836 removed outlier: 3.502A pdb=" N GLU F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 837 through 839 No H-bonds generated for 'chain 'F' and resid 837 through 839' Processing helix chain 'F' and resid 841 through 845 removed outlier: 3.702A pdb=" N ALA F 844 " --> pdb=" O CYS F 841 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 863 removed outlier: 3.645A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 88 through 92 removed outlier: 3.604A pdb=" N SER A 90 " --> pdb=" O THR A 99 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER B 369 " --> pdb=" O ARG B 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 395 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR B 372 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 220 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL B 219 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL B 255 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 221 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU B 322 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.151A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 274 removed outlier: 4.838A pdb=" N GLU A 322 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 219 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL A 255 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE A 221 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR A 372 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 220 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A 369 " --> pdb=" O ARG A 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 395 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 394 " --> pdb=" O ALA B 445 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER B 90 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR A 461 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 595 " --> pdb=" O ALA A 542 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ARG A 481 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 541 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU A 483 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 482 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE A 513 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 484 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU A 515 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR A 486 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 608 through 612 Processing sheet with id=AA6, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.151A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR B 461 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 595 " --> pdb=" O ALA B 542 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG B 481 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE B 541 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 483 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA B 482 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE B 513 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 484 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU B 515 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR B 486 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 612 Processing sheet with id=AA9, first strand: chain 'C' and resid 88 through 92 removed outlier: 3.603A pdb=" N SER C 90 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 369 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 395 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR D 372 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL D 220 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL D 219 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL D 255 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE D 221 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU D 319 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET D 343 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY D 321 " --> pdb=" O MET D 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG D 345 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU D 322 " --> pdb=" O LEU D 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 167 through 169 removed outlier: 6.150A pdb=" N ILE C 190 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL C 212 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA C 192 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 271 through 274 removed outlier: 4.838A pdb=" N GLU C 322 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 319 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET C 343 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY C 321 " --> pdb=" O MET C 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG C 345 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 219 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL C 255 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE C 221 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR C 372 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL C 220 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 369 " --> pdb=" O ARG C 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 395 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ILE C 394 " --> pdb=" O ALA D 445 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER D 90 " --> pdb=" O THR D 99 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR C 461 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 595 " --> pdb=" O ALA C 542 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG C 481 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE C 541 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C 483 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA C 482 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE C 513 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 484 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 515 " --> pdb=" O ILE C 484 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR C 486 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 608 through 612 Processing sheet with id=AB5, first strand: chain 'D' and resid 167 through 169 removed outlier: 6.151A pdb=" N ILE D 190 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL D 212 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA D 192 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR D 461 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL D 595 " --> pdb=" O ALA D 542 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG D 481 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE D 541 " --> pdb=" O ARG D 481 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU D 483 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA D 482 " --> pdb=" O GLU D 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE D 513 " --> pdb=" O ALA D 482 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE D 484 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 515 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR D 486 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 608 through 612 Processing sheet with id=AB8, first strand: chain 'E' and resid 88 through 92 removed outlier: 3.603A pdb=" N SER E 90 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER F 369 " --> pdb=" O ARG F 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU F 395 " --> pdb=" O SER F 369 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR F 372 " --> pdb=" O PRO F 218 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL F 220 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL F 219 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL F 255 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE F 221 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU F 319 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET F 343 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY F 321 " --> pdb=" O MET F 343 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ARG F 345 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLU F 322 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 167 through 169 removed outlier: 6.151A pdb=" N ILE E 190 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL E 212 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA E 192 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 271 through 274 removed outlier: 4.839A pdb=" N GLU E 322 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 319 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N MET E 343 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY E 321 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG E 345 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 219 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL E 255 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE E 221 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR E 372 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 220 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER E 369 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU E 395 " --> pdb=" O SER E 369 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE E 394 " --> pdb=" O ALA F 445 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER F 90 " --> pdb=" O THR F 99 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR E 461 " --> pdb=" O VAL E 634 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL E 595 " --> pdb=" O ALA E 542 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG E 481 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE E 541 " --> pdb=" O ARG E 481 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU E 483 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA E 482 " --> pdb=" O GLU E 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE E 513 " --> pdb=" O ALA E 482 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE E 484 " --> pdb=" O PHE E 513 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU E 515 " --> pdb=" O ILE E 484 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR E 486 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 608 through 612 Processing sheet with id=AC4, first strand: chain 'F' and resid 167 through 169 removed outlier: 6.151A pdb=" N ILE F 190 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL F 212 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA F 192 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 460 through 463 removed outlier: 6.662A pdb=" N TYR F 461 " --> pdb=" O VAL F 634 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL F 595 " --> pdb=" O ALA F 542 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ARG F 481 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE F 541 " --> pdb=" O ARG F 481 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU F 483 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA F 482 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N PHE F 513 " --> pdb=" O ALA F 482 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE F 484 " --> pdb=" O PHE F 513 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLU F 515 " --> pdb=" O ILE F 484 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR F 486 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 608 through 612 1468 hydrogen bonds defined for protein. 4239 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: 10.10 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12913 1.34 - 1.46: 5429 1.46 - 1.57: 22260 1.57 - 1.69: 48 1.69 - 1.81: 306 Bond restraints: 40956 Sorted by residual: bond pdb=" C4A NAD E 901 " pdb=" C5A NAD E 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAD F 902 " pdb=" C5A NAD F 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" C4A NAD A 902 " pdb=" C5A NAD A 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD E 902 " pdb=" C5A NAD E 902 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C4A NAD F 901 " pdb=" C5A NAD F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.80e+01 ... (remaining 40951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 54153 1.85 - 3.70: 1172 3.70 - 5.54: 230 5.54 - 7.39: 59 7.39 - 9.24: 42 Bond angle restraints: 55656 Sorted by residual: angle pdb=" C ASN D 696 " pdb=" N PRO D 697 " pdb=" CA PRO D 697 " ideal model delta sigma weight residual 119.28 125.15 -5.87 1.10e+00 8.26e-01 2.85e+01 angle pdb=" C ASN B 696 " pdb=" N PRO B 697 " pdb=" CA PRO B 697 " ideal model delta sigma weight residual 119.64 124.71 -5.07 1.01e+00 9.80e-01 2.52e+01 angle pdb=" C ASN E 696 " pdb=" N PRO E 697 " pdb=" CA PRO E 697 " ideal model delta sigma weight residual 119.84 125.52 -5.68 1.25e+00 6.40e-01 2.06e+01 angle pdb=" N VAL A 360 " pdb=" CA VAL A 360 " pdb=" C VAL A 360 " ideal model delta sigma weight residual 112.29 108.76 3.53 9.40e-01 1.13e+00 1.41e+01 angle pdb=" N VAL F 360 " pdb=" CA VAL F 360 " pdb=" C VAL F 360 " ideal model delta sigma weight residual 112.29 108.77 3.52 9.40e-01 1.13e+00 1.41e+01 ... (remaining 55651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 22836 17.98 - 35.97: 1356 35.97 - 53.95: 262 53.95 - 71.93: 40 71.93 - 89.91: 28 Dihedral angle restraints: 24522 sinusoidal: 9450 harmonic: 15072 Sorted by residual: dihedral pdb=" CA PHE D 462 " pdb=" C PHE D 462 " pdb=" N ARG D 463 " pdb=" CA ARG D 463 " ideal model delta harmonic sigma weight residual 180.00 155.67 24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PHE A 462 " pdb=" C PHE A 462 " pdb=" N ARG A 463 " pdb=" CA ARG A 463 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA PHE C 462 " pdb=" C PHE C 462 " pdb=" N ARG C 463 " pdb=" CA ARG C 463 " ideal model delta harmonic sigma weight residual 180.00 155.70 24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 24519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 4128 0.038 - 0.076: 1576 0.076 - 0.114: 521 0.114 - 0.152: 140 0.152 - 0.190: 37 Chirality restraints: 6402 Sorted by residual: chirality pdb=" C3D NAD A 902 " pdb=" C2D NAD A 902 " pdb=" C4D NAD A 902 " pdb=" O3D NAD A 902 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" C3D NAD C 901 " pdb=" C2D NAD C 901 " pdb=" C4D NAD C 901 " pdb=" O3D NAD C 901 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.88e-01 chirality pdb=" C3D NAD F 902 " pdb=" C2D NAD F 902 " pdb=" C4D NAD F 902 " pdb=" O3D NAD F 902 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.76e-01 ... (remaining 6399 not shown) Planarity restraints: 7134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 102 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.96e+00 pdb=" N PRO A 103 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 102 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO B 103 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 103 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 103 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 102 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO F 103 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO F 103 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 103 " -0.036 5.00e-02 4.00e+02 ... (remaining 7131 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 547 2.66 - 3.22: 34474 3.22 - 3.78: 60175 3.78 - 4.34: 89269 4.34 - 4.90: 144198 Nonbonded interactions: 328663 Sorted by model distance: nonbonded pdb=" O ASN B 696 " pdb=" ND2 ASN B 696 " model vdw 2.094 3.120 nonbonded pdb=" OE2 GLU E 335 " pdb=" O2D NAD E 901 " model vdw 2.113 3.040 nonbonded pdb=" OD1 ASP A 519 " pdb=" O3D NAD A 902 " model vdw 2.195 3.040 nonbonded pdb=" ND2 ASN A 696 " pdb=" CB ALA A 699 " model vdw 2.248 3.540 nonbonded pdb=" ND2 ASN B 696 " pdb=" CB ALA B 699 " model vdw 2.248 3.540 ... (remaining 328658 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 44.220 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.007 0.798 40976 Z= 0.564 Angle : 0.720 9.238 55656 Z= 0.371 Chirality : 0.047 0.190 6402 Planarity : 0.006 0.066 7134 Dihedral : 12.390 89.914 14826 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.34 % Allowed : 8.19 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.97 (0.08), residues: 5202 helix: -4.88 (0.03), residues: 2454 sheet: -2.81 (0.15), residues: 882 loop : -2.76 (0.12), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 463 TYR 0.009 0.001 TYR E 409 PHE 0.022 0.002 PHE C 714 TRP 0.007 0.001 TRP A 424 HIS 0.004 0.001 HIS F 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.22 (40956) covalent geometry : angle 0.72031 / 0.37 (55656) hydrogen bonds : bond 0.33964 / 22.73 ( 1468) hydrogen bonds : angle 9.94810 / 6.86 ( 4239) metal coordination : bond 0.04170 / 2.78 ( 18) Misc. bond : bond 0.74327 / 37.59 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1183 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 1044 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8676 (t70) REVERT: A 427 ASN cc_start: 0.8329 (m-40) cc_final: 0.8126 (m-40) REVERT: A 463 ARG cc_start: 0.1589 (OUTLIER) cc_final: 0.0473 (mtm180) REVERT: A 760 GLN cc_start: 0.7523 (pp30) cc_final: 0.7082 (pm20) REVERT: A 839 ASP cc_start: 0.4770 (t70) cc_final: 0.4169 (t70) REVERT: B 558 MET cc_start: 0.7480 (mtt) cc_final: 0.7274 (mtt) REVERT: B 774 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7813 (mtp180) REVERT: C 1 MET cc_start: 0.6502 (tpt) cc_final: 0.6237 (tpt) REVERT: C 241 ASP cc_start: 0.8534 (t70) cc_final: 0.8286 (t0) REVERT: C 341 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 416 SER cc_start: 0.9377 (p) cc_final: 0.8970 (m) REVERT: C 576 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.7658 (mt) REVERT: C 604 GLU cc_start: 0.8586 (pm20) cc_final: 0.8188 (pm20) REVERT: C 839 ASP cc_start: 0.7760 (t70) cc_final: 0.7507 (t70) REVERT: D 186 ASP cc_start: 0.8574 (p0) cc_final: 0.8347 (p0) REVERT: D 200 LYS cc_start: 0.8584 (tppt) cc_final: 0.8215 (tmtt) REVERT: D 286 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8213 (mt) REVERT: D 576 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8150 (mt) REVERT: E 95 PHE cc_start: 0.8947 (m-80) cc_final: 0.7996 (m-80) REVERT: E 384 TYR cc_start: 0.6624 (t80) cc_final: 0.6383 (t80) REVERT: E 463 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7688 (tpt170) REVERT: E 576 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.7868 (mt) REVERT: E 631 MET cc_start: 0.8813 (ttm) cc_final: 0.8599 (ttp) REVERT: E 692 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (mm-30) REVERT: E 866 ASP cc_start: 0.7214 (p0) cc_final: 0.6750 (p0) REVERT: F 69 ASN cc_start: 0.8037 (m110) cc_final: 0.7826 (m110) REVERT: F 217 THR cc_start: 0.8902 (m) cc_final: 0.8562 (p) REVERT: F 286 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7373 (mt) REVERT: F 332 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: F 554 ILE cc_start: 0.8189 (mm) cc_final: 0.7645 (mt) REVERT: F 568 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7062 (mt-10) REVERT: F 682 LEU cc_start: 0.6971 (mt) cc_final: 0.6704 (mt) REVERT: F 721 VAL cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (t) outliers start: 139 outliers final: 33 residues processed: 1155 average time/residue: 0.2772 time to fit residues: 515.4257 Evaluate side-chains 562 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 517 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 802 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 695 LYS Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 721 VAL Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 694 SER Chi-restraints excluded: chain E residue 695 LYS Chi-restraints excluded: chain E residue 721 VAL Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 721 VAL Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 9.9990 chunk 41 optimal weight: 0.0670 chunk 265 optimal weight: 1.9990 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 0.0770 chunk 223 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN A 132 ASN A 147 ASN A 188 ASN A 427 ASN A 437 HIS ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 70 HIS B 132 ASN B 147 ASN B 269 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 437 HIS B 440 ASN B 618 GLN ** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 GLN B 756 ASN B 765 GLN C 30 GLN C 132 ASN C 147 ASN C 377 ASN C 427 ASN C 437 HIS C 440 ASN C 565 HIS C 618 GLN C 691 HIS D 30 GLN D 132 ASN D 147 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS D 618 GLN E 30 GLN E 132 ASN E 147 ASN E 269 HIS E 275 GLN ** E 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 GLN E 756 ASN F 132 ASN F 147 ASN F 427 ASN F 437 HIS F 440 ASN F 618 GLN F 765 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.107001 restraints weight = 60776.977| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.80 r_work: 0.3023 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40976 Z= 0.126 Angle : 0.594 9.098 55656 Z= 0.307 Chirality : 0.044 0.174 6402 Planarity : 0.005 0.057 7134 Dihedral : 7.148 86.948 5725 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.07 % Allowed : 13.40 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.09), residues: 5202 helix: -2.85 (0.08), residues: 2508 sheet: -2.48 (0.15), residues: 864 loop : -2.48 (0.12), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 865 TYR 0.024 0.001 TYR A 690 PHE 0.021 0.001 PHE A 566 TRP 0.009 0.001 TRP C 424 HIS 0.005 0.001 HIS F 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (40956) covalent geometry : angle 0.59439 / 0.31 (55656) hydrogen bonds : bond 0.05093 / 3.33 ( 1468) hydrogen bonds : angle 4.54896 / 3.13 ( 4239) metal coordination : bond 0.00525 / 0.33 ( 18) Misc. bond : bond 0.00103 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 607 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9156 (OUTLIER) cc_final: 0.8784 (t70) REVERT: A 165 ASP cc_start: 0.7018 (p0) cc_final: 0.6762 (p0) REVERT: A 412 LYS cc_start: 0.9017 (tptt) cc_final: 0.8783 (tptt) REVERT: A 463 ARG cc_start: 0.2348 (OUTLIER) cc_final: 0.0698 (mtm180) REVERT: A 526 ARG cc_start: 0.7383 (mtt180) cc_final: 0.7135 (mtm110) REVERT: A 591 LYS cc_start: 0.7732 (mmtp) cc_final: 0.7340 (mptt) REVERT: A 619 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8104 (ttpt) REVERT: A 831 LYS cc_start: 0.6177 (ptpt) cc_final: 0.5951 (ptpt) REVERT: A 839 ASP cc_start: 0.6046 (t70) cc_final: 0.5185 (t70) REVERT: A 853 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6648 (mm-30) REVERT: B 15 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7996 (mtp-110) REVERT: B 59 MET cc_start: 0.6403 (mmm) cc_final: 0.5994 (ppp) REVERT: B 198 MET cc_start: 0.8399 (ttp) cc_final: 0.8053 (ttp) REVERT: B 241 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.7169 (t0) REVERT: B 412 LYS cc_start: 0.8574 (tppp) cc_final: 0.8232 (tppp) REVERT: B 431 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7356 (mm-30) REVERT: B 558 MET cc_start: 0.8638 (mtt) cc_final: 0.8339 (mtt) REVERT: B 574 MET cc_start: 0.8408 (ttt) cc_final: 0.8101 (ttt) REVERT: B 576 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8466 (mt) REVERT: B 692 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7537 (mm-30) REVERT: C 1 MET cc_start: 0.6670 (tpt) cc_final: 0.6394 (tpt) REVERT: C 86 CYS cc_start: 0.9053 (m) cc_final: 0.8694 (m) REVERT: C 341 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8977 (mp) REVERT: C 358 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8547 (mttm) REVERT: C 416 SER cc_start: 0.9515 (p) cc_final: 0.9124 (m) REVERT: C 604 GLU cc_start: 0.8778 (pm20) cc_final: 0.8565 (pm20) REVERT: D 148 LYS cc_start: 0.8578 (tptt) cc_final: 0.8375 (tptt) REVERT: D 182 MET cc_start: 0.8881 (mtm) cc_final: 0.8657 (mtm) REVERT: D 200 LYS cc_start: 0.8986 (tppt) cc_final: 0.8533 (tmtt) REVERT: D 286 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8384 (mt) REVERT: D 555 MET cc_start: 0.8743 (ptm) cc_final: 0.8499 (mtp) REVERT: E 189 LEU cc_start: 0.9247 (tp) cc_final: 0.9039 (tp) REVERT: E 241 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7674 (t0) REVERT: E 371 LEU cc_start: 0.8802 (tp) cc_final: 0.8415 (tp) REVERT: E 463 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8088 (tpt170) REVERT: E 618 GLN cc_start: 0.6723 (mm-40) cc_final: 0.6487 (mm110) REVERT: E 652 LEU cc_start: 0.8763 (mt) cc_final: 0.8470 (mt) REVERT: E 692 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8586 (mm-30) REVERT: E 866 ASP cc_start: 0.7560 (p0) cc_final: 0.7044 (p0) REVERT: F 52 MET cc_start: 0.7470 (mtp) cc_final: 0.7256 (mtp) REVERT: F 69 ASN cc_start: 0.8624 (m110) cc_final: 0.8239 (m110) REVERT: F 332 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7975 (m-80) REVERT: F 547 SER cc_start: 0.8355 (OUTLIER) cc_final: 0.8047 (m) REVERT: F 554 ILE cc_start: 0.7638 (mm) cc_final: 0.7206 (mt) REVERT: F 568 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7480 (mt-10) REVERT: F 582 LYS cc_start: 0.7523 (ttmm) cc_final: 0.7260 (tppt) REVERT: F 592 MET cc_start: 0.7190 (tpp) cc_final: 0.6511 (tpp) REVERT: F 682 LEU cc_start: 0.7977 (mt) cc_final: 0.7738 (mt) REVERT: F 847 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7235 (mtp85) outliers start: 128 outliers final: 65 residues processed: 706 average time/residue: 0.2471 time to fit residues: 288.9457 Evaluate side-chains 557 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 479 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 619 LYS Chi-restraints excluded: chain A residue 694 SER Chi-restraints excluded: chain A residue 695 LYS Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 576 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 696 ASN Chi-restraints excluded: chain B residue 766 TYR Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 480 LYS Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 756 ASN Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 423 SER Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 404 optimal weight: 0.0670 chunk 333 optimal weight: 0.0870 chunk 94 optimal weight: 6.9990 chunk 129 optimal weight: 0.4980 chunk 59 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 291 optimal weight: 0.6980 chunk 431 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS A 828 ASN B 410 ASN B 756 ASN C 69 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS F 132 ASN F 188 ASN F 440 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107330 restraints weight = 60440.442| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.98 r_work: 0.2992 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 40976 Z= 0.099 Angle : 0.534 13.287 55656 Z= 0.270 Chirality : 0.043 0.162 6402 Planarity : 0.004 0.051 7134 Dihedral : 6.616 81.374 5692 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.45 % Allowed : 14.51 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.10), residues: 5202 helix: -1.64 (0.09), residues: 2508 sheet: -2.25 (0.16), residues: 828 loop : -2.07 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 141 TYR 0.018 0.001 TYR C 302 PHE 0.020 0.001 PHE A 714 TRP 0.013 0.001 TRP C 424 HIS 0.004 0.001 HIS F 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (40956) covalent geometry : angle 0.53422 / 0.27 (55656) hydrogen bonds : bond 0.03602 / 2.38 ( 1468) hydrogen bonds : angle 3.98151 / 2.74 ( 4239) metal coordination : bond 0.00389 / 0.24 ( 18) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 540 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9092 (OUTLIER) cc_final: 0.8592 (t70) REVERT: A 412 LYS cc_start: 0.8976 (tptt) cc_final: 0.8739 (tptt) REVERT: A 463 ARG cc_start: 0.3315 (OUTLIER) cc_final: 0.1307 (mtm180) REVERT: A 526 ARG cc_start: 0.7465 (mtt180) cc_final: 0.7212 (mtm180) REVERT: A 558 MET cc_start: 0.7398 (mmt) cc_final: 0.7141 (mmt) REVERT: A 591 LYS cc_start: 0.7821 (mmtp) cc_final: 0.7464 (mptt) REVERT: A 839 ASP cc_start: 0.5793 (t70) cc_final: 0.4842 (t70) REVERT: B 84 LYS cc_start: 0.8608 (mtmm) cc_final: 0.7855 (mmmt) REVERT: B 198 MET cc_start: 0.8355 (ttp) cc_final: 0.8034 (ttp) REVERT: B 241 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7283 (t0) REVERT: B 431 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 574 MET cc_start: 0.8417 (ttt) cc_final: 0.8081 (ttt) REVERT: B 692 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: B 834 GLU cc_start: 0.7974 (tt0) cc_final: 0.7570 (tm-30) REVERT: C 1 MET cc_start: 0.6788 (tpt) cc_final: 0.6557 (tpt) REVERT: C 86 CYS cc_start: 0.8967 (m) cc_final: 0.8673 (m) REVERT: C 341 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.9000 (mp) REVERT: C 362 MET cc_start: 0.8426 (mpp) cc_final: 0.7734 (mpp) REVERT: C 416 SER cc_start: 0.9476 (p) cc_final: 0.9120 (m) REVERT: C 604 GLU cc_start: 0.8777 (pm20) cc_final: 0.8553 (pm20) REVERT: C 759 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8706 (mmmm) REVERT: D 17 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8696 (ttmt) REVERT: D 128 LEU cc_start: 0.8712 (pp) cc_final: 0.8496 (pt) REVERT: D 182 MET cc_start: 0.8956 (mtm) cc_final: 0.8709 (mtm) REVERT: D 200 LYS cc_start: 0.8882 (tppt) cc_final: 0.8430 (tmtt) REVERT: D 241 ASP cc_start: 0.8258 (t0) cc_final: 0.7961 (t0) REVERT: D 286 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8343 (mt) REVERT: E 74 GLU cc_start: 0.8325 (tt0) cc_final: 0.8065 (tt0) REVERT: E 141 ARG cc_start: 0.8323 (ttt180) cc_final: 0.8110 (mtp-110) REVERT: E 179 ASN cc_start: 0.7836 (t0) cc_final: 0.7394 (m-40) REVERT: E 189 LEU cc_start: 0.9279 (tp) cc_final: 0.9011 (tp) REVERT: E 198 MET cc_start: 0.7252 (tmm) cc_final: 0.6460 (tmm) REVERT: E 241 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7714 (t0) REVERT: E 259 TYR cc_start: 0.6090 (t80) cc_final: 0.5710 (t80) REVERT: E 343 MET cc_start: 0.7259 (mmt) cc_final: 0.6746 (mmt) REVERT: E 371 LEU cc_start: 0.8740 (tp) cc_final: 0.8395 (tp) REVERT: E 395 LEU cc_start: 0.8687 (mm) cc_final: 0.8418 (mt) REVERT: E 576 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.7952 (mt) REVERT: E 618 GLN cc_start: 0.6461 (mm-40) cc_final: 0.6172 (mm-40) REVERT: E 652 LEU cc_start: 0.8630 (mt) cc_final: 0.8202 (mt) REVERT: E 866 ASP cc_start: 0.7594 (p0) cc_final: 0.7326 (p0) REVERT: F 52 MET cc_start: 0.7439 (mtp) cc_final: 0.7189 (mtp) REVERT: F 98 ILE cc_start: 0.8397 (mt) cc_final: 0.7926 (tt) REVERT: F 158 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8009 (mp) REVERT: F 332 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7958 (m-80) REVERT: F 449 GLU cc_start: 0.7766 (mp0) cc_final: 0.7123 (tt0) REVERT: F 455 LYS cc_start: 0.7259 (mttt) cc_final: 0.6246 (mmtt) REVERT: F 547 SER cc_start: 0.8285 (OUTLIER) cc_final: 0.8054 (m) REVERT: F 554 ILE cc_start: 0.7414 (mm) cc_final: 0.6929 (mt) REVERT: F 568 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7284 (mp0) REVERT: F 582 LYS cc_start: 0.7504 (ttmm) cc_final: 0.7286 (tppt) REVERT: F 682 LEU cc_start: 0.7963 (mt) cc_final: 0.7743 (mt) outliers start: 102 outliers final: 58 residues processed: 621 average time/residue: 0.2381 time to fit residues: 247.0419 Evaluate side-chains 537 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 468 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 766 TYR Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 576 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 118 optimal weight: 0.8980 chunk 280 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 474 optimal weight: 1.9990 chunk 360 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 422 optimal weight: 3.9990 chunk 358 optimal weight: 6.9990 chunk 296 optimal weight: 0.6980 chunk 337 optimal weight: 0.0060 chunk 200 optimal weight: 0.8980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 ASN B 765 GLN B 840 GLN C 387 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 440 ASN F 747 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109778 restraints weight = 59990.251| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.78 r_work: 0.3052 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40976 Z= 0.104 Angle : 0.519 7.823 55656 Z= 0.261 Chirality : 0.043 0.167 6402 Planarity : 0.004 0.048 7134 Dihedral : 6.202 77.320 5672 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.83 % Allowed : 14.65 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.11), residues: 5202 helix: -1.02 (0.10), residues: 2508 sheet: -2.00 (0.16), residues: 828 loop : -1.85 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 847 TYR 0.022 0.001 TYR B 259 PHE 0.019 0.001 PHE A 714 TRP 0.008 0.001 TRP A 801 HIS 0.006 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (40956) covalent geometry : angle 0.51901 / 0.26 (55656) hydrogen bonds : bond 0.03172 / 2.09 ( 1468) hydrogen bonds : angle 3.74451 / 2.57 ( 4239) metal coordination : bond 0.00530 / 0.33 ( 18) Misc. bond : bond 0.00022 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 508 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9145 (OUTLIER) cc_final: 0.8704 (t70) REVERT: A 362 MET cc_start: 0.7946 (mtt) cc_final: 0.7668 (mtt) REVERT: A 412 LYS cc_start: 0.8940 (tptt) cc_final: 0.8733 (tptt) REVERT: A 463 ARG cc_start: 0.3039 (OUTLIER) cc_final: 0.1205 (mtm180) REVERT: A 526 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7177 (mtm180) REVERT: A 558 MET cc_start: 0.7360 (mmt) cc_final: 0.7119 (mmt) REVERT: A 591 LYS cc_start: 0.7958 (mmtp) cc_final: 0.7594 (mmtm) REVERT: A 839 ASP cc_start: 0.6011 (t70) cc_final: 0.5289 (t0) REVERT: B 15 ARG cc_start: 0.8424 (mtm-85) cc_final: 0.7842 (mtp-110) REVERT: B 84 LYS cc_start: 0.8580 (mtmm) cc_final: 0.7859 (mmmt) REVERT: B 198 MET cc_start: 0.8442 (ttp) cc_final: 0.8127 (ttp) REVERT: B 241 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7180 (t0) REVERT: B 431 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7415 (mm-30) REVERT: B 574 MET cc_start: 0.8385 (ttt) cc_final: 0.8023 (ttt) REVERT: B 624 ASP cc_start: 0.7883 (t70) cc_final: 0.7664 (t0) REVERT: B 692 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7777 (mm-30) REVERT: B 834 GLU cc_start: 0.7973 (tt0) cc_final: 0.7600 (tm-30) REVERT: C 1 MET cc_start: 0.6923 (tpt) cc_final: 0.6670 (tpt) REVERT: C 86 CYS cc_start: 0.8951 (m) cc_final: 0.8648 (m) REVERT: C 416 SER cc_start: 0.9423 (p) cc_final: 0.9075 (m) REVERT: C 759 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8672 (mmmm) REVERT: C 760 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8961 (pp30) REVERT: D 128 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8430 (pt) REVERT: D 182 MET cc_start: 0.8996 (mtm) cc_final: 0.8793 (mtm) REVERT: D 200 LYS cc_start: 0.8751 (tppt) cc_final: 0.8344 (tmtt) REVERT: D 241 ASP cc_start: 0.8280 (t0) cc_final: 0.7914 (t0) REVERT: D 286 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8285 (mt) REVERT: E 52 MET cc_start: 0.7410 (mtp) cc_final: 0.6552 (tpp) REVERT: E 198 MET cc_start: 0.7351 (tmm) cc_final: 0.6509 (tmm) REVERT: E 241 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7598 (t0) REVERT: E 343 MET cc_start: 0.7109 (mmt) cc_final: 0.6690 (mmt) REVERT: E 371 LEU cc_start: 0.8642 (tp) cc_final: 0.8287 (tp) REVERT: E 395 LEU cc_start: 0.8672 (mm) cc_final: 0.8409 (mt) REVERT: E 549 MET cc_start: 0.8530 (mtm) cc_final: 0.8310 (mtp) REVERT: E 576 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8019 (mt) REVERT: E 618 GLN cc_start: 0.6641 (mm-40) cc_final: 0.6428 (mm110) REVERT: E 652 LEU cc_start: 0.8581 (mt) cc_final: 0.8178 (mt) REVERT: E 866 ASP cc_start: 0.7553 (p0) cc_final: 0.7197 (p0) REVERT: F 52 MET cc_start: 0.7632 (mtp) cc_final: 0.7405 (mtp) REVERT: F 98 ILE cc_start: 0.8416 (mt) cc_final: 0.7973 (tt) REVERT: F 158 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.8065 (mp) REVERT: F 332 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: F 449 GLU cc_start: 0.7839 (mp0) cc_final: 0.7240 (tt0) REVERT: F 455 LYS cc_start: 0.7232 (mttt) cc_final: 0.6296 (mmtt) REVERT: F 554 ILE cc_start: 0.7452 (mm) cc_final: 0.7005 (mt) REVERT: F 555 MET cc_start: 0.8479 (mtp) cc_final: 0.8227 (mtm) REVERT: F 582 LYS cc_start: 0.7532 (ttmm) cc_final: 0.7300 (tppt) REVERT: F 682 LEU cc_start: 0.7981 (mt) cc_final: 0.7746 (mt) REVERT: F 847 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7098 (mtp180) outliers start: 118 outliers final: 78 residues processed: 600 average time/residue: 0.2487 time to fit residues: 248.5836 Evaluate side-chains 553 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 463 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 440 ASN Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 332 optimal weight: 0.8980 chunk 496 optimal weight: 0.8980 chunk 391 optimal weight: 0.7980 chunk 413 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 364 optimal weight: 0.5980 chunk 296 optimal weight: 0.7980 chunk 311 optimal weight: 0.2980 chunk 325 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110888 restraints weight = 59658.798| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.09 r_work: 0.3034 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 40976 Z= 0.100 Angle : 0.505 9.573 55656 Z= 0.254 Chirality : 0.043 0.168 6402 Planarity : 0.004 0.047 7134 Dihedral : 5.982 72.665 5666 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.91 % Allowed : 15.18 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.11), residues: 5202 helix: -0.62 (0.10), residues: 2538 sheet: -1.81 (0.17), residues: 822 loop : -1.70 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.017 0.001 TYR C 302 PHE 0.019 0.001 PHE A 714 TRP 0.010 0.001 TRP A 801 HIS 0.008 0.001 HIS E 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (40956) covalent geometry : angle 0.50515 / 0.25 (55656) hydrogen bonds : bond 0.02945 / 1.94 ( 1468) hydrogen bonds : angle 3.61002 / 2.48 ( 4239) metal coordination : bond 0.00467 / 0.28 ( 18) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 488 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.7901 (mtt) cc_final: 0.7638 (mtt) REVERT: A 412 LYS cc_start: 0.8951 (tptt) cc_final: 0.8743 (tptt) REVERT: A 463 ARG cc_start: 0.2939 (OUTLIER) cc_final: 0.1239 (mtm180) REVERT: A 526 ARG cc_start: 0.7396 (mtt180) cc_final: 0.7080 (mtm180) REVERT: A 591 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7598 (mmtm) REVERT: A 718 PHE cc_start: 0.8168 (m-80) cc_final: 0.7917 (m-80) REVERT: A 809 LEU cc_start: 0.6896 (OUTLIER) cc_final: 0.6661 (mt) REVERT: A 831 LYS cc_start: 0.6441 (ttpt) cc_final: 0.6084 (pttt) REVERT: A 839 ASP cc_start: 0.6170 (t70) cc_final: 0.5495 (t0) REVERT: A 867 TYR cc_start: 0.5877 (t80) cc_final: 0.5543 (t80) REVERT: B 15 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8057 (ttp-110) REVERT: B 59 MET cc_start: 0.6446 (mtp) cc_final: 0.6119 (mtm) REVERT: B 84 LYS cc_start: 0.8570 (mtmm) cc_final: 0.7863 (mmmt) REVERT: B 198 MET cc_start: 0.8444 (ttp) cc_final: 0.8122 (ttp) REVERT: B 241 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7454 (t0) REVERT: B 431 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7499 (mm-30) REVERT: B 624 ASP cc_start: 0.8029 (t70) cc_final: 0.7773 (t0) REVERT: B 834 GLU cc_start: 0.7987 (tt0) cc_final: 0.7594 (tm-30) REVERT: C 1 MET cc_start: 0.6950 (tpt) cc_final: 0.6649 (tpt) REVERT: C 86 CYS cc_start: 0.8985 (m) cc_final: 0.8672 (m) REVERT: C 416 SER cc_start: 0.9435 (p) cc_final: 0.9083 (m) REVERT: C 647 CYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8774 (p) REVERT: C 759 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8735 (mmmm) REVERT: C 760 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8923 (pp30) REVERT: D 128 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8405 (pt) REVERT: D 200 LYS cc_start: 0.8675 (tppt) cc_final: 0.8276 (tmtt) REVERT: D 241 ASP cc_start: 0.8384 (t0) cc_final: 0.8158 (t0) REVERT: D 286 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8251 (mt) REVERT: E 52 MET cc_start: 0.7331 (mtp) cc_final: 0.6475 (tpp) REVERT: E 179 ASN cc_start: 0.7738 (t0) cc_final: 0.7252 (m-40) REVERT: E 198 MET cc_start: 0.7308 (tmm) cc_final: 0.6416 (tmm) REVERT: E 241 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7646 (t0) REVERT: E 341 LEU cc_start: 0.7152 (mt) cc_final: 0.6846 (mt) REVERT: E 343 MET cc_start: 0.7043 (mmt) cc_final: 0.6660 (mmt) REVERT: E 371 LEU cc_start: 0.8794 (tp) cc_final: 0.8453 (tp) REVERT: E 576 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8021 (mt) REVERT: E 618 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6486 (mm110) REVERT: E 652 LEU cc_start: 0.8562 (mt) cc_final: 0.8214 (mt) REVERT: E 866 ASP cc_start: 0.7591 (p0) cc_final: 0.7155 (p0) REVERT: F 98 ILE cc_start: 0.8421 (mt) cc_final: 0.7968 (tt) REVERT: F 332 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: F 455 LYS cc_start: 0.7335 (mttt) cc_final: 0.6384 (mmtt) REVERT: F 547 SER cc_start: 0.8346 (OUTLIER) cc_final: 0.8126 (m) REVERT: F 554 ILE cc_start: 0.7295 (mm) cc_final: 0.6845 (mt) REVERT: F 555 MET cc_start: 0.8644 (mtp) cc_final: 0.8389 (mtm) REVERT: F 582 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7347 (tppt) REVERT: F 682 LEU cc_start: 0.7985 (mt) cc_final: 0.7752 (mt) REVERT: F 808 GLU cc_start: 0.7494 (pt0) cc_final: 0.6970 (mp0) outliers start: 121 outliers final: 83 residues processed: 585 average time/residue: 0.2400 time to fit residues: 236.0358 Evaluate side-chains 546 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 452 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 241 ASP Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 314 optimal weight: 0.2980 chunk 377 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 375 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 316 optimal weight: 0.8980 chunk 308 optimal weight: 0.8980 chunk 168 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 333 optimal weight: 0.6980 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN E 727 HIS E 840 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107489 restraints weight = 60174.902| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.99 r_work: 0.2959 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40976 Z= 0.162 Angle : 0.556 11.248 55656 Z= 0.279 Chirality : 0.045 0.173 6402 Planarity : 0.004 0.050 7134 Dihedral : 6.019 74.223 5659 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.31 % Allowed : 15.15 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.11), residues: 5202 helix: -0.48 (0.10), residues: 2568 sheet: -1.68 (0.17), residues: 786 loop : -1.71 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 847 TYR 0.018 0.001 TYR C 302 PHE 0.015 0.001 PHE A 714 TRP 0.016 0.001 TRP A 801 HIS 0.005 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (40956) covalent geometry : angle 0.55638 / 0.28 (55656) hydrogen bonds : bond 0.03418 / 2.26 ( 1468) hydrogen bonds : angle 3.70851 / 2.55 ( 4239) metal coordination : bond 0.00938 / 0.59 ( 18) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 457 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9205 (OUTLIER) cc_final: 0.8724 (t70) REVERT: A 362 MET cc_start: 0.8138 (mtt) cc_final: 0.7912 (mtt) REVERT: A 463 ARG cc_start: 0.3118 (OUTLIER) cc_final: 0.1341 (mtm180) REVERT: A 526 ARG cc_start: 0.7366 (mtt180) cc_final: 0.7089 (mtm180) REVERT: A 539 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7504 (t) REVERT: A 591 LYS cc_start: 0.7891 (mmtp) cc_final: 0.7526 (mmtm) REVERT: A 799 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6093 (tt) REVERT: A 801 TRP cc_start: 0.7475 (t60) cc_final: 0.7211 (t60) REVERT: A 809 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6644 (mt) REVERT: A 831 LYS cc_start: 0.6472 (ttpt) cc_final: 0.6162 (pttt) REVERT: A 839 ASP cc_start: 0.6271 (t70) cc_final: 0.5662 (t0) REVERT: A 867 TYR cc_start: 0.5902 (t80) cc_final: 0.5624 (t80) REVERT: B 15 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8102 (ttp-110) REVERT: B 84 LYS cc_start: 0.8610 (mtmm) cc_final: 0.7773 (mmmt) REVERT: B 198 MET cc_start: 0.8512 (ttp) cc_final: 0.8116 (ttp) REVERT: B 431 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 834 GLU cc_start: 0.8053 (tt0) cc_final: 0.7638 (tm-30) REVERT: C 86 CYS cc_start: 0.9004 (m) cc_final: 0.8683 (m) REVERT: C 416 SER cc_start: 0.9447 (p) cc_final: 0.9093 (m) REVERT: C 443 THR cc_start: 0.9337 (t) cc_final: 0.8969 (m) REVERT: C 759 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8748 (mmmm) REVERT: C 760 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.9011 (pp30) REVERT: D 172 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 200 LYS cc_start: 0.8800 (tppt) cc_final: 0.8387 (tmtt) REVERT: D 283 GLN cc_start: 0.8848 (mt0) cc_final: 0.8470 (mt0) REVERT: E 52 MET cc_start: 0.7506 (mtp) cc_final: 0.6636 (tpp) REVERT: E 59 MET cc_start: 0.7692 (ptp) cc_final: 0.6595 (ptp) REVERT: E 198 MET cc_start: 0.7287 (tmm) cc_final: 0.6394 (tmm) REVERT: E 341 LEU cc_start: 0.6790 (mt) cc_final: 0.6538 (mt) REVERT: E 343 MET cc_start: 0.6889 (mmt) cc_final: 0.6536 (mmt) REVERT: E 371 LEU cc_start: 0.8704 (tp) cc_final: 0.8310 (tp) REVERT: E 395 LEU cc_start: 0.8633 (mm) cc_final: 0.8287 (mt) REVERT: E 576 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8221 (mt) REVERT: F 98 ILE cc_start: 0.8510 (mt) cc_final: 0.8009 (tt) REVERT: F 332 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: F 455 LYS cc_start: 0.7454 (mttt) cc_final: 0.6398 (mmtt) REVERT: F 547 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.8181 (m) REVERT: F 549 MET cc_start: 0.7638 (ttm) cc_final: 0.7220 (ttp) REVERT: F 554 ILE cc_start: 0.7408 (mm) cc_final: 0.6970 (mt) REVERT: F 555 MET cc_start: 0.8707 (mtp) cc_final: 0.8466 (mtm) REVERT: F 582 LYS cc_start: 0.7655 (ttmm) cc_final: 0.7399 (tppt) REVERT: F 682 LEU cc_start: 0.7949 (mt) cc_final: 0.7699 (mt) REVERT: F 808 GLU cc_start: 0.7511 (pt0) cc_final: 0.7104 (mp0) REVERT: F 834 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6976 (mt-10) REVERT: F 847 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7247 (mtp180) outliers start: 138 outliers final: 105 residues processed: 569 average time/residue: 0.2445 time to fit residues: 232.8992 Evaluate side-chains 538 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 422 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 337 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 477 optimal weight: 8.9990 chunk 461 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 ASN B 188 ASN B 377 ASN C 410 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 GLN E 840 GLN F 299 GLN F 377 ASN F 440 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105147 restraints weight = 60076.676| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.90 r_work: 0.2966 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 40976 Z= 0.190 Angle : 0.589 12.214 55656 Z= 0.297 Chirality : 0.046 0.173 6402 Planarity : 0.004 0.054 7134 Dihedral : 6.157 74.233 5659 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.55 % Allowed : 15.49 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.11), residues: 5202 helix: -0.42 (0.10), residues: 2568 sheet: -1.60 (0.17), residues: 816 loop : -1.65 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 488 TYR 0.018 0.001 TYR C 302 PHE 0.014 0.001 PHE C 714 TRP 0.013 0.002 TRP A 801 HIS 0.008 0.001 HIS B 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (40956) covalent geometry : angle 0.58921 / 0.30 (55656) hydrogen bonds : bond 0.03635 / 2.41 ( 1468) hydrogen bonds : angle 3.80060 / 2.62 ( 4239) metal coordination : bond 0.00978 / 0.61 ( 18) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 444 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ARG cc_start: 0.2895 (OUTLIER) cc_final: 0.1372 (mtm180) REVERT: A 526 ARG cc_start: 0.7473 (mtt180) cc_final: 0.7161 (mtm180) REVERT: A 591 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7568 (mmtm) REVERT: A 799 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5864 (tt) REVERT: A 801 TRP cc_start: 0.7532 (t60) cc_final: 0.7285 (t60) REVERT: A 809 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6630 (mt) REVERT: A 831 LYS cc_start: 0.6568 (ttpt) cc_final: 0.6114 (ptpt) REVERT: A 839 ASP cc_start: 0.6290 (t70) cc_final: 0.5695 (t0) REVERT: A 867 TYR cc_start: 0.5891 (t80) cc_final: 0.5643 (t80) REVERT: B 15 ARG cc_start: 0.8410 (mtm-85) cc_final: 0.8193 (ttp-110) REVERT: B 198 MET cc_start: 0.8584 (ttp) cc_final: 0.8245 (ttp) REVERT: B 265 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.6906 (tpt170) REVERT: B 412 LYS cc_start: 0.8702 (tppp) cc_final: 0.8272 (tppp) REVERT: B 431 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7420 (mm-30) REVERT: B 604 GLU cc_start: 0.7874 (pm20) cc_final: 0.7563 (pm20) REVERT: B 803 GLU cc_start: 0.8330 (tp30) cc_final: 0.8119 (tp30) REVERT: B 834 GLU cc_start: 0.8011 (tt0) cc_final: 0.7580 (tm-30) REVERT: C 86 CYS cc_start: 0.9023 (m) cc_final: 0.8703 (m) REVERT: C 416 SER cc_start: 0.9455 (p) cc_final: 0.9106 (m) REVERT: C 443 THR cc_start: 0.9356 (t) cc_final: 0.9004 (m) REVERT: C 760 GLN cc_start: 0.9263 (OUTLIER) cc_final: 0.9022 (pp30) REVERT: D 172 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8149 (tm-30) REVERT: D 200 LYS cc_start: 0.8806 (tppt) cc_final: 0.8368 (tmtt) REVERT: D 283 GLN cc_start: 0.8832 (mt0) cc_final: 0.8467 (mt0) REVERT: D 789 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7421 (m-30) REVERT: D 840 GLN cc_start: 0.9180 (tp40) cc_final: 0.8977 (tp40) REVERT: E 52 MET cc_start: 0.7543 (mtp) cc_final: 0.6652 (tpp) REVERT: E 59 MET cc_start: 0.7843 (ptp) cc_final: 0.6702 (ptp) REVERT: E 198 MET cc_start: 0.7294 (tmm) cc_final: 0.6429 (tmm) REVERT: E 207 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8162 (mtmm) REVERT: E 341 LEU cc_start: 0.6959 (mt) cc_final: 0.6700 (mt) REVERT: E 371 LEU cc_start: 0.8732 (tp) cc_final: 0.8364 (tp) REVERT: E 389 MET cc_start: 0.8774 (mtp) cc_final: 0.8568 (mtp) REVERT: E 395 LEU cc_start: 0.8608 (mm) cc_final: 0.8268 (mt) REVERT: E 576 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8174 (mt) REVERT: F 69 ASN cc_start: 0.8704 (m110) cc_final: 0.8487 (m110) REVERT: F 98 ILE cc_start: 0.8449 (mt) cc_final: 0.7931 (tt) REVERT: F 332 PHE cc_start: 0.8369 (OUTLIER) cc_final: 0.7462 (m-10) REVERT: F 455 LYS cc_start: 0.7301 (mttt) cc_final: 0.6341 (mmtt) REVERT: F 547 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7973 (m) REVERT: F 549 MET cc_start: 0.7719 (ttm) cc_final: 0.7303 (ttp) REVERT: F 554 ILE cc_start: 0.7465 (mm) cc_final: 0.7044 (mt) REVERT: F 555 MET cc_start: 0.8713 (mtp) cc_final: 0.8486 (mtm) REVERT: F 582 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7441 (tppt) REVERT: F 682 LEU cc_start: 0.7944 (mt) cc_final: 0.7686 (mt) REVERT: F 834 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.6959 (mt-10) outliers start: 148 outliers final: 113 residues processed: 561 average time/residue: 0.2579 time to fit residues: 241.6099 Evaluate side-chains 536 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 413 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 411 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 694 SER Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 472 ASP Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 451 MET Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 521 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 8 optimal weight: 0.0170 chunk 152 optimal weight: 2.9990 chunk 314 optimal weight: 6.9990 chunk 459 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 411 optimal weight: 1.9990 chunk 45 optimal weight: 10.0000 chunk 289 optimal weight: 0.6980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN D 188 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 ASN F 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.143077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.104934 restraints weight = 60271.706| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.95 r_work: 0.2975 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 40976 Z= 0.099 Angle : 0.524 12.306 55656 Z= 0.263 Chirality : 0.043 0.170 6402 Planarity : 0.004 0.053 7134 Dihedral : 5.855 65.371 5659 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.76 % Allowed : 16.43 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.12), residues: 5202 helix: -0.13 (0.11), residues: 2544 sheet: -1.58 (0.18), residues: 804 loop : -1.50 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 21 TYR 0.020 0.001 TYR E 75 PHE 0.017 0.001 PHE A 714 TRP 0.012 0.001 TRP A 801 HIS 0.002 0.001 HIS A 737 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (40956) covalent geometry : angle 0.52425 / 0.26 (55656) hydrogen bonds : bond 0.02862 / 1.90 ( 1468) hydrogen bonds : angle 3.58350 / 2.46 ( 4239) metal coordination : bond 0.00453 / 0.32 ( 18) Misc. bond : bond 0.00017 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 462 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9148 (OUTLIER) cc_final: 0.8611 (t70) REVERT: A 166 LEU cc_start: 0.8576 (tp) cc_final: 0.8297 (tt) REVERT: A 463 ARG cc_start: 0.2688 (OUTLIER) cc_final: 0.1127 (mtm180) REVERT: A 526 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7177 (mtm180) REVERT: A 591 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7423 (mmtm) REVERT: A 780 ASP cc_start: 0.6361 (p0) cc_final: 0.5416 (t0) REVERT: A 801 TRP cc_start: 0.7583 (t60) cc_final: 0.7224 (t60) REVERT: A 809 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6560 (mt) REVERT: A 831 LYS cc_start: 0.6500 (ttpt) cc_final: 0.6059 (ptpt) REVERT: A 839 ASP cc_start: 0.6421 (t70) cc_final: 0.5748 (t0) REVERT: A 867 TYR cc_start: 0.5878 (t80) cc_final: 0.5668 (t80) REVERT: B 15 ARG cc_start: 0.8357 (mtm-85) cc_final: 0.8140 (ttp-110) REVERT: B 70 HIS cc_start: 0.9147 (t-170) cc_final: 0.8583 (t-170) REVERT: B 84 LYS cc_start: 0.8592 (mtmm) cc_final: 0.7776 (mmmt) REVERT: B 198 MET cc_start: 0.8511 (ttp) cc_final: 0.8154 (ttp) REVERT: B 265 ARG cc_start: 0.7544 (mmm-85) cc_final: 0.6883 (tpt170) REVERT: B 431 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7470 (mm-30) REVERT: B 624 ASP cc_start: 0.8077 (t70) cc_final: 0.7824 (t0) REVERT: B 834 GLU cc_start: 0.7926 (tt0) cc_final: 0.7582 (tm-30) REVERT: C 86 CYS cc_start: 0.8861 (m) cc_final: 0.8558 (m) REVERT: C 416 SER cc_start: 0.9466 (p) cc_final: 0.9133 (m) REVERT: C 443 THR cc_start: 0.9309 (t) cc_final: 0.8955 (m) REVERT: C 574 MET cc_start: 0.8973 (ttm) cc_final: 0.8691 (mtp) REVERT: C 647 CYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8754 (p) REVERT: C 760 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.9060 (pp30) REVERT: C 840 GLN cc_start: 0.9155 (tp40) cc_final: 0.8877 (tp-100) REVERT: D 172 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8194 (tm-30) REVERT: D 200 LYS cc_start: 0.8703 (tppt) cc_final: 0.8241 (tmtt) REVERT: D 286 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (mt) REVERT: D 719 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9026 (mp) REVERT: D 789 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7003 (m-30) REVERT: D 840 GLN cc_start: 0.9126 (tp40) cc_final: 0.8891 (tp40) REVERT: E 52 MET cc_start: 0.7479 (mtp) cc_final: 0.6557 (tpp) REVERT: E 75 TYR cc_start: 0.8920 (m-80) cc_final: 0.8684 (m-80) REVERT: E 102 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7773 (mm-30) REVERT: E 198 MET cc_start: 0.7298 (tmm) cc_final: 0.6399 (tmm) REVERT: E 241 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7617 (t0) REVERT: E 341 LEU cc_start: 0.6796 (mt) cc_final: 0.6569 (mt) REVERT: E 371 LEU cc_start: 0.8693 (tp) cc_final: 0.8364 (tp) REVERT: E 395 LEU cc_start: 0.8510 (mm) cc_final: 0.8159 (mt) REVERT: E 576 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8032 (mt) REVERT: E 869 GLU cc_start: 0.6144 (mt-10) cc_final: 0.5934 (mt-10) REVERT: F 98 ILE cc_start: 0.8321 (mt) cc_final: 0.7813 (tt) REVERT: F 198 MET cc_start: 0.7444 (tmm) cc_final: 0.7201 (tmm) REVERT: F 332 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7479 (m-10) REVERT: F 455 LYS cc_start: 0.7324 (mttt) cc_final: 0.6322 (mmtt) REVERT: F 547 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7961 (m) REVERT: F 549 MET cc_start: 0.7582 (ttm) cc_final: 0.7145 (ttp) REVERT: F 554 ILE cc_start: 0.7243 (mm) cc_final: 0.6838 (mt) REVERT: F 555 MET cc_start: 0.8638 (mtp) cc_final: 0.8403 (mtm) REVERT: F 582 LYS cc_start: 0.7597 (ttmm) cc_final: 0.7355 (tppt) REVERT: F 682 LEU cc_start: 0.7912 (mt) cc_final: 0.7687 (mt) REVERT: F 808 GLU cc_start: 0.7054 (pt0) cc_final: 0.6144 (mp0) REVERT: F 834 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: F 847 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7030 (mtp180) outliers start: 115 outliers final: 72 residues processed: 556 average time/residue: 0.2577 time to fit residues: 238.7501 Evaluate side-chains 511 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 425 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 82 optimal weight: 6.9990 chunk 378 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 498 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 349 optimal weight: 0.3980 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 490 optimal weight: 7.9990 chunk 376 optimal weight: 3.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 GLN C 387 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 840 GLN F 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104296 restraints weight = 60112.074| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.80 r_work: 0.2953 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40976 Z= 0.184 Angle : 0.594 12.282 55656 Z= 0.299 Chirality : 0.046 0.200 6402 Planarity : 0.004 0.055 7134 Dihedral : 6.025 69.500 5658 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.67 % Allowed : 16.59 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.12), residues: 5202 helix: -0.18 (0.10), residues: 2562 sheet: -1.40 (0.19), residues: 762 loop : -1.57 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 702 TYR 0.021 0.001 TYR E 75 PHE 0.026 0.001 PHE F 71 TRP 0.012 0.001 TRP A 801 HIS 0.005 0.001 HIS E 367 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 (40956) covalent geometry : angle 0.59407 / 0.30 (55656) hydrogen bonds : bond 0.03509 / 2.33 ( 1468) hydrogen bonds : angle 3.71388 / 2.56 ( 4239) metal coordination : bond 0.00924 / 0.57 ( 18) Misc. bond : bond 0.00045 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 424 time to evaluate : 1.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6066 (mmt) cc_final: 0.4774 (ttt) REVERT: A 70 HIS cc_start: 0.9190 (OUTLIER) cc_final: 0.8699 (t70) REVERT: A 463 ARG cc_start: 0.2865 (OUTLIER) cc_final: 0.1135 (mtm180) REVERT: A 526 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7142 (mtm180) REVERT: A 591 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7598 (mmtm) REVERT: A 801 TRP cc_start: 0.7571 (t60) cc_final: 0.7364 (t60) REVERT: A 809 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6505 (mt) REVERT: A 831 LYS cc_start: 0.6651 (ttpt) cc_final: 0.6236 (ptpt) REVERT: A 839 ASP cc_start: 0.6506 (t70) cc_final: 0.5906 (t0) REVERT: B 15 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8199 (ttp-110) REVERT: B 198 MET cc_start: 0.8615 (ttp) cc_final: 0.8268 (ttp) REVERT: B 265 ARG cc_start: 0.7654 (mmm-85) cc_final: 0.7049 (tpt90) REVERT: B 431 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 624 ASP cc_start: 0.8090 (t70) cc_final: 0.7840 (t0) REVERT: B 834 GLU cc_start: 0.8043 (tt0) cc_final: 0.7616 (tm-30) REVERT: C 86 CYS cc_start: 0.8972 (m) cc_final: 0.8625 (m) REVERT: C 416 SER cc_start: 0.9433 (p) cc_final: 0.9127 (m) REVERT: C 443 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8988 (m) REVERT: C 760 GLN cc_start: 0.9398 (OUTLIER) cc_final: 0.9154 (pp30) REVERT: D 172 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8197 (tm-30) REVERT: D 200 LYS cc_start: 0.8788 (tppt) cc_final: 0.8336 (tmtt) REVERT: D 719 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8975 (mp) REVERT: D 840 GLN cc_start: 0.9254 (tp40) cc_final: 0.8973 (tp40) REVERT: E 52 MET cc_start: 0.7543 (mtp) cc_final: 0.6633 (tpp) REVERT: E 59 MET cc_start: 0.7708 (ptp) cc_final: 0.6603 (ptp) REVERT: E 75 TYR cc_start: 0.8903 (m-80) cc_final: 0.8669 (m-80) REVERT: E 102 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7866 (mm-30) REVERT: E 198 MET cc_start: 0.7289 (tmm) cc_final: 0.6417 (tmm) REVERT: E 207 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8127 (mtmm) REVERT: E 341 LEU cc_start: 0.7049 (mt) cc_final: 0.6819 (mt) REVERT: E 343 MET cc_start: 0.6900 (mmt) cc_final: 0.6582 (mmt) REVERT: E 371 LEU cc_start: 0.8761 (tp) cc_final: 0.8435 (tp) REVERT: E 395 LEU cc_start: 0.8666 (mm) cc_final: 0.8319 (mt) REVERT: E 576 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8021 (mt) REVERT: F 332 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: F 455 LYS cc_start: 0.7550 (mttt) cc_final: 0.6488 (mmtt) REVERT: F 547 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.8015 (m) REVERT: F 549 MET cc_start: 0.7566 (ttm) cc_final: 0.7208 (ttp) REVERT: F 554 ILE cc_start: 0.7582 (mm) cc_final: 0.7148 (mt) REVERT: F 555 MET cc_start: 0.8751 (mtp) cc_final: 0.8506 (mtm) REVERT: F 582 LYS cc_start: 0.7709 (ttmm) cc_final: 0.7484 (tppt) REVERT: F 680 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6518 (tppt) REVERT: F 682 LEU cc_start: 0.7986 (mt) cc_final: 0.7744 (mt) REVERT: F 808 GLU cc_start: 0.7139 (pt0) cc_final: 0.6219 (mp0) REVERT: F 834 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6912 (mt-10) outliers start: 111 outliers final: 93 residues processed: 512 average time/residue: 0.2611 time to fit residues: 221.6772 Evaluate side-chains 518 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 413 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 780 ASP Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain B residue 851 ILE Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 286 ILE Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 680 LYS Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 169 optimal weight: 4.9990 chunk 335 optimal weight: 0.9980 chunk 302 optimal weight: 5.9990 chunk 455 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 451 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 483 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 513 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN C 78 ASN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 132 ASN E 334 HIS ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 440 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103523 restraints weight = 60098.519| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.80 r_work: 0.2947 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 40976 Z= 0.210 Angle : 0.619 10.789 55656 Z= 0.313 Chirality : 0.047 0.172 6402 Planarity : 0.004 0.056 7134 Dihedral : 6.258 74.421 5658 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.69 % Allowed : 16.74 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.12), residues: 5202 helix: -0.28 (0.10), residues: 2574 sheet: -1.39 (0.19), residues: 696 loop : -1.56 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 865 TYR 0.023 0.002 TYR E 75 PHE 0.022 0.002 PHE F 71 TRP 0.013 0.002 TRP A 801 HIS 0.006 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.21 (40956) covalent geometry : angle 0.61911 / 0.31 (55656) hydrogen bonds : bond 0.03741 / 2.48 ( 1468) hydrogen bonds : angle 3.84763 / 2.65 ( 4239) metal coordination : bond 0.00999 / 0.62 ( 18) Misc. bond : bond 0.00054 / 0.03 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 427 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ARG cc_start: 0.2454 (OUTLIER) cc_final: 0.0626 (mtm180) REVERT: A 526 ARG cc_start: 0.7453 (mtt180) cc_final: 0.7151 (mtm180) REVERT: A 591 LYS cc_start: 0.7971 (mmtp) cc_final: 0.7488 (mmtm) REVERT: A 801 TRP cc_start: 0.7686 (t60) cc_final: 0.7405 (t60) REVERT: A 809 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6446 (mt) REVERT: A 831 LYS cc_start: 0.6686 (ttpt) cc_final: 0.6226 (ptpt) REVERT: A 839 ASP cc_start: 0.6861 (t70) cc_final: 0.6238 (t0) REVERT: B 15 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8259 (ttp-110) REVERT: B 198 MET cc_start: 0.8679 (ttp) cc_final: 0.8368 (ttp) REVERT: B 265 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.6943 (tpt90) REVERT: B 412 LYS cc_start: 0.8777 (tppp) cc_final: 0.8439 (tppp) REVERT: B 431 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7417 (mm-30) REVERT: B 558 MET cc_start: 0.8891 (mtt) cc_final: 0.8390 (mtt) REVERT: B 624 ASP cc_start: 0.8136 (t70) cc_final: 0.7910 (t0) REVERT: B 834 GLU cc_start: 0.8027 (tt0) cc_final: 0.7618 (tm-30) REVERT: C 86 CYS cc_start: 0.8999 (m) cc_final: 0.8646 (m) REVERT: C 416 SER cc_start: 0.9428 (p) cc_final: 0.9105 (m) REVERT: C 443 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.8971 (m) REVERT: C 760 GLN cc_start: 0.9404 (OUTLIER) cc_final: 0.9158 (pp30) REVERT: D 172 GLN cc_start: 0.8535 (tm-30) cc_final: 0.8289 (tm-30) REVERT: D 200 LYS cc_start: 0.8859 (tppt) cc_final: 0.8393 (tmtt) REVERT: D 719 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9002 (mp) REVERT: D 840 GLN cc_start: 0.9291 (tp40) cc_final: 0.9068 (tp40) REVERT: E 52 MET cc_start: 0.7582 (mtp) cc_final: 0.6647 (tpp) REVERT: E 59 MET cc_start: 0.7756 (ptp) cc_final: 0.6724 (ptp) REVERT: E 102 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7992 (mm-30) REVERT: E 198 MET cc_start: 0.7159 (tmm) cc_final: 0.6376 (tmm) REVERT: E 207 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8134 (mtmm) REVERT: E 341 LEU cc_start: 0.6956 (mt) cc_final: 0.6751 (mt) REVERT: E 343 MET cc_start: 0.6952 (mmt) cc_final: 0.6650 (mmt) REVERT: E 371 LEU cc_start: 0.8733 (tp) cc_final: 0.8397 (tp) REVERT: E 389 MET cc_start: 0.8497 (ttm) cc_final: 0.8272 (ttm) REVERT: E 395 LEU cc_start: 0.8631 (mm) cc_final: 0.8309 (mt) REVERT: E 576 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8058 (mt) REVERT: F 332 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: F 451 MET cc_start: 0.8789 (ttp) cc_final: 0.8505 (ttm) REVERT: F 455 LYS cc_start: 0.7566 (mttt) cc_final: 0.6518 (mmtt) REVERT: F 547 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7881 (m) REVERT: F 549 MET cc_start: 0.7594 (ttm) cc_final: 0.7215 (ttp) REVERT: F 554 ILE cc_start: 0.7568 (mm) cc_final: 0.7119 (mt) REVERT: F 555 MET cc_start: 0.8678 (mtp) cc_final: 0.8460 (mtm) REVERT: F 582 LYS cc_start: 0.7716 (ttmm) cc_final: 0.7458 (tppt) REVERT: F 680 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6387 (tppt) REVERT: F 682 LEU cc_start: 0.7893 (mt) cc_final: 0.7655 (mt) REVERT: F 808 GLU cc_start: 0.7192 (pt0) cc_final: 0.6513 (mp0) REVERT: F 834 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7073 (mt-10) outliers start: 112 outliers final: 92 residues processed: 516 average time/residue: 0.2584 time to fit residues: 222.1810 Evaluate side-chains 513 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 410 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 809 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 611 VAL Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 760 GLN Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 245 ILE Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 647 CYS Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 760 GLN Chi-restraints excluded: chain C residue 789 ASP Chi-restraints excluded: chain D residue 118 SER Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 472 ASP Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 547 SER Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 719 LEU Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 829 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 SER Chi-restraints excluded: chain E residue 463 ARG Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 508 VAL Chi-restraints excluded: chain E residue 547 SER Chi-restraints excluded: chain E residue 576 ILE Chi-restraints excluded: chain E residue 612 THR Chi-restraints excluded: chain E residue 659 MET Chi-restraints excluded: chain E residue 826 LEU Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 252 VAL Chi-restraints excluded: chain F residue 332 PHE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 THR Chi-restraints excluded: chain F residue 440 ASN Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 485 VAL Chi-restraints excluded: chain F residue 486 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 611 VAL Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 680 LYS Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain F residue 834 GLU Chi-restraints excluded: chain F residue 847 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 383 optimal weight: 7.9990 chunk 425 optimal weight: 0.1980 chunk 317 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 360 optimal weight: 0.1980 chunk 126 optimal weight: 0.4980 chunk 103 optimal weight: 0.0570 chunk 492 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 overall best weight: 0.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 GLN ** D 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN E 334 HIS E 367 HIS ** E 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 747 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.103514 restraints weight = 60210.692| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.84 r_work: 0.2954 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 40976 Z= 0.178 Angle : 0.714 59.199 55656 Z= 0.382 Chirality : 0.045 0.274 6402 Planarity : 0.004 0.087 7134 Dihedral : 6.259 74.376 5658 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.13 % Favored : 94.85 % Rotamer: Outliers : 2.74 % Allowed : 16.76 % Favored : 80.50 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.12), residues: 5202 helix: -0.26 (0.10), residues: 2574 sheet: -1.40 (0.19), residues: 696 loop : -1.57 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 865 TYR 0.019 0.001 TYR E 75 PHE 0.021 0.001 PHE F 71 TRP 0.012 0.001 TRP A 801 HIS 0.005 0.001 HIS A 781 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (40956) covalent geometry : angle 0.71393 / 0.38 (55656) hydrogen bonds : bond 0.03601 / 2.39 ( 1468) hydrogen bonds : angle 3.84390 / 2.65 ( 4239) metal coordination : bond 0.01074 / 0.75 ( 18) Misc. bond : bond 0.00002 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12454.65 seconds wall clock time: 213 minutes 42.58 seconds (12822.58 seconds total)