Starting phenix.real_space_refine on Sat Mar 7 08:12:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bvp_30220/03_2026/7bvp_30220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bvp_30220/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7bvp_30220/03_2026/7bvp_30220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bvp_30220/03_2026/7bvp_30220.map" model { file = "/net/cci-nas-00/data/ceres_data/7bvp_30220/03_2026/7bvp_30220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bvp_30220/03_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 8.81, per 1000 atoms: 0.22 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: 3.38 Conformation dependent library (CDL) restraints added in 1.7 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: 1.62 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: 10.35 Time building geometry restraints manager: 4.50 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: 22982 17.98 - 35.97: 1584 35.97 - 53.95: 457 53.95 - 71.93: 65 71.93 - 89.91: 34 Dihedral angle restraints: 25122 sinusoidal: 10050 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 25119 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: 0.09 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 42.750 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 13.819 89.914 15426 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 covalent geometry : bond 0.00439 (40956) covalent geometry : angle 0.72031 (55656) hydrogen bonds : bond 0.33964 ( 1468) hydrogen bonds : angle 9.94810 ( 4239) metal coordination : bond 0.04170 ( 18) Misc. bond : bond 0.74327 ( 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 : 1.464 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: 0.2653 time to fit residues: 492.2143 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 : 1.560 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3692 r_free = 0.3692 target = 0.145540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107099 restraints weight = 60786.037| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.01 r_work: 0.2959 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40976 Z= 0.135 Angle : 0.596 9.317 55656 Z= 0.309 Chirality : 0.045 0.165 6402 Planarity : 0.005 0.057 7134 Dihedral : 9.536 86.877 6325 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.05 % Allowed : 13.52 % Favored : 83.43 % 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: -4.22 (0.09), residues: 5202 helix: -2.87 (0.08), residues: 2508 sheet: -2.47 (0.15), residues: 864 loop : -2.47 (0.12), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 865 TYR 0.025 0.001 TYR A 690 PHE 0.022 0.001 PHE A 566 TRP 0.010 0.001 TRP C 424 HIS 0.005 0.001 HIS F 737 Details of bonding type rmsd covalent geometry : bond 0.00286 (40956) covalent geometry : angle 0.59561 (55656) hydrogen bonds : bond 0.04837 ( 1468) hydrogen bonds : angle 4.53098 ( 4239) metal coordination : bond 0.00619 ( 18) Misc. bond : bond 0.00140 ( 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 745 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 618 time to evaluate : 1.477 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: 0.9159 (OUTLIER) cc_final: 0.8776 (t70) REVERT: A 90 SER cc_start: 0.8285 (m) cc_final: 0.7975 (p) REVERT: A 128 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8404 (pp) REVERT: A 165 ASP cc_start: 0.7069 (p0) cc_final: 0.6822 (p0) REVERT: A 412 LYS cc_start: 0.9037 (tptt) cc_final: 0.8805 (tptt) REVERT: A 463 ARG cc_start: 0.2367 (OUTLIER) cc_final: 0.0705 (mtm180) REVERT: A 526 ARG cc_start: 0.7325 (mtt180) cc_final: 0.7074 (mtm180) REVERT: A 591 LYS cc_start: 0.7717 (mmtp) cc_final: 0.7323 (mptt) REVERT: A 619 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: A 831 LYS cc_start: 0.6178 (ptpt) cc_final: 0.5955 (ptpt) REVERT: A 839 ASP cc_start: 0.6052 (t70) cc_final: 0.5180 (t70) REVERT: B 15 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.7943 (mtp-110) REVERT: B 59 MET cc_start: 0.6597 (mmm) cc_final: 0.5959 (ppp) REVERT: B 141 ARG cc_start: 0.8073 (ttt180) cc_final: 0.7867 (ttt180) REVERT: B 198 MET cc_start: 0.8333 (ttp) cc_final: 0.7935 (ttp) REVERT: B 241 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7190 (t0) REVERT: B 412 LYS cc_start: 0.8597 (tppp) cc_final: 0.8262 (tppp) REVERT: B 431 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7387 (mm-30) REVERT: B 558 MET cc_start: 0.8683 (mtt) cc_final: 0.8397 (mtt) REVERT: B 574 MET cc_start: 0.8437 (ttt) cc_final: 0.8127 (ttt) REVERT: B 576 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 774 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8299 (mtp180) REVERT: C 1 MET cc_start: 0.6689 (tpt) cc_final: 0.6402 (tpt) REVERT: C 86 CYS cc_start: 0.9027 (m) cc_final: 0.8687 (m) REVERT: C 341 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9003 (mp) REVERT: C 358 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8569 (mttm) REVERT: C 416 SER cc_start: 0.9514 (p) cc_final: 0.9128 (m) REVERT: C 604 GLU cc_start: 0.8811 (pm20) cc_final: 0.8599 (pm20) REVERT: C 759 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8778 (mmmt) REVERT: D 17 LYS cc_start: 0.8942 (ttmt) cc_final: 0.8701 (ttmt) REVERT: D 182 MET cc_start: 0.8875 (mtm) cc_final: 0.8662 (mtm) REVERT: D 186 ASP cc_start: 0.8928 (p0) cc_final: 0.8666 (p0) REVERT: D 200 LYS cc_start: 0.8981 (tppt) cc_final: 0.8532 (tmtt) REVERT: D 241 ASP cc_start: 0.8444 (t0) cc_final: 0.8238 (t0) REVERT: D 286 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8374 (mt) REVERT: D 555 MET cc_start: 0.8733 (ptm) cc_final: 0.8499 (mtp) REVERT: E 75 TYR cc_start: 0.8850 (m-80) cc_final: 0.8574 (m-80) REVERT: E 179 ASN cc_start: 0.7854 (t0) cc_final: 0.7318 (m-40) REVERT: E 189 LEU cc_start: 0.9247 (tp) cc_final: 0.9032 (tp) REVERT: E 241 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7697 (t0) REVERT: E 371 LEU cc_start: 0.8872 (tp) cc_final: 0.8529 (tp) REVERT: E 463 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8097 (tpt170) REVERT: E 618 GLN cc_start: 0.6786 (mm-40) cc_final: 0.6541 (mm110) REVERT: E 652 LEU cc_start: 0.8738 (mt) cc_final: 0.8463 (mt) REVERT: E 692 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8582 (mm-30) REVERT: E 866 ASP cc_start: 0.7586 (p0) cc_final: 0.7066 (p0) REVERT: F 52 MET cc_start: 0.7443 (mtp) cc_final: 0.7181 (mtp) REVERT: F 69 ASN cc_start: 0.8546 (m110) cc_final: 0.8190 (m110) REVERT: F 332 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7983 (m-80) REVERT: F 554 ILE cc_start: 0.7595 (mm) cc_final: 0.7162 (mt) REVERT: F 568 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7502 (mt-10) REVERT: F 582 LYS cc_start: 0.7518 (ttmm) cc_final: 0.7257 (tppt) REVERT: F 592 MET cc_start: 0.7201 (tpp) cc_final: 0.6509 (tpp) REVERT: F 682 LEU cc_start: 0.7958 (mt) cc_final: 0.7724 (mt) outliers start: 127 outliers final: 65 residues processed: 716 average time/residue: 0.2489 time to fit residues: 293.6547 Evaluate side-chains 560 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 483 time to evaluate : 1.440 ------------------------------------------------------------------------------- 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 70 HIS Chi-restraints excluded: chain A residue 128 LEU 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 695 LYS Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain B residue 67 ILE 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 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 486 THR 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: 0.0020 chunk 333 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 129 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 322 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 184 optimal weight: 1.9990 chunk 291 optimal weight: 0.9980 chunk 431 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS A 828 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 ASN F 188 ASN F 440 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.146092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.106532 restraints weight = 60482.272| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.91 r_work: 0.2989 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 40976 Z= 0.099 Angle : 0.522 12.889 55656 Z= 0.267 Chirality : 0.042 0.161 6402 Planarity : 0.004 0.070 7134 Dihedral : 8.492 83.619 6291 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.57 % Allowed : 14.34 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.06 (0.10), residues: 5202 helix: -1.70 (0.09), residues: 2508 sheet: -2.24 (0.16), residues: 828 loop : -2.08 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 865 TYR 0.023 0.001 TYR C 302 PHE 0.020 0.001 PHE A 714 TRP 0.012 0.001 TRP C 424 HIS 0.004 0.000 HIS F 781 Details of bonding type rmsd covalent geometry : bond 0.00220 (40956) covalent geometry : angle 0.52212 (55656) hydrogen bonds : bond 0.03628 ( 1468) hydrogen bonds : angle 3.99404 ( 4239) metal coordination : bond 0.00389 ( 18) Misc. bond : bond 0.00067 ( 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 640 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 533 time to evaluate : 1.221 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: A 70 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8717 (t70) REVERT: A 412 LYS cc_start: 0.8966 (tptt) cc_final: 0.8721 (tptt) REVERT: A 463 ARG cc_start: 0.3327 (OUTLIER) cc_final: 0.1305 (mtm180) REVERT: A 526 ARG cc_start: 0.7412 (mtt180) cc_final: 0.7194 (mtm180) REVERT: A 558 MET cc_start: 0.7408 (mmt) cc_final: 0.7153 (mmt) REVERT: A 591 LYS cc_start: 0.7844 (mmtp) cc_final: 0.7488 (mptt) REVERT: A 839 ASP cc_start: 0.5766 (t70) cc_final: 0.4830 (t70) REVERT: B 59 MET cc_start: 0.6534 (mmm) cc_final: 0.6013 (ppp) REVERT: B 84 LYS cc_start: 0.8612 (mtmm) cc_final: 0.7845 (mmmt) REVERT: B 198 MET cc_start: 0.8368 (ttp) cc_final: 0.7963 (ttp) REVERT: B 241 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7278 (t0) REVERT: B 431 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7435 (mm-30) REVERT: B 574 MET cc_start: 0.8427 (ttt) cc_final: 0.8096 (ttt) REVERT: B 586 MET cc_start: 0.8654 (mtm) cc_final: 0.8443 (mtm) REVERT: B 692 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: B 774 ARG cc_start: 0.8428 (mtp85) cc_final: 0.8199 (mtp180) REVERT: B 834 GLU cc_start: 0.7961 (tt0) cc_final: 0.7535 (tm-30) REVERT: C 1 MET cc_start: 0.6776 (tpt) cc_final: 0.6546 (tpt) REVERT: C 86 CYS cc_start: 0.8960 (m) cc_final: 0.8642 (m) REVERT: C 128 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8974 (pt) REVERT: C 341 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9011 (mp) REVERT: C 362 MET cc_start: 0.8445 (mpp) cc_final: 0.7740 (mpp) REVERT: C 416 SER cc_start: 0.9483 (p) cc_final: 0.9128 (m) REVERT: C 604 GLU cc_start: 0.8808 (pm20) cc_final: 0.8565 (pm20) REVERT: D 128 LEU cc_start: 0.8761 (pp) cc_final: 0.8560 (pt) REVERT: D 182 MET cc_start: 0.8956 (mtm) cc_final: 0.8697 (mtm) REVERT: D 200 LYS cc_start: 0.8868 (tppt) cc_final: 0.8397 (tmtt) REVERT: D 241 ASP cc_start: 0.8427 (t0) cc_final: 0.8219 (t0) REVERT: D 286 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8337 (mt) REVERT: E 75 TYR cc_start: 0.8758 (m-80) cc_final: 0.8376 (m-80) REVERT: E 179 ASN cc_start: 0.7810 (t0) cc_final: 0.7375 (m-40) REVERT: E 189 LEU cc_start: 0.9284 (tp) cc_final: 0.9030 (tp) REVERT: E 198 MET cc_start: 0.7181 (tmm) cc_final: 0.6430 (tmm) REVERT: E 241 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7682 (t0) REVERT: E 371 LEU cc_start: 0.8771 (tp) cc_final: 0.8430 (tp) REVERT: E 384 TYR cc_start: 0.7879 (t80) cc_final: 0.7564 (t80) REVERT: E 395 LEU cc_start: 0.8694 (mm) cc_final: 0.8414 (mt) REVERT: E 576 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8080 (mt) REVERT: E 618 GLN cc_start: 0.6647 (mm-40) cc_final: 0.6437 (mm110) REVERT: E 652 LEU cc_start: 0.8623 (mt) cc_final: 0.8184 (mt) REVERT: E 866 ASP cc_start: 0.7586 (p0) cc_final: 0.7104 (p0) REVERT: F 52 MET cc_start: 0.7402 (mtp) cc_final: 0.7138 (mtp) REVERT: F 98 ILE cc_start: 0.8386 (mt) cc_final: 0.7922 (tt) REVERT: F 158 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8056 (mp) REVERT: F 332 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: F 423 SER cc_start: 0.8389 (p) cc_final: 0.8142 (p) REVERT: F 449 GLU cc_start: 0.7764 (mp0) cc_final: 0.7126 (tt0) REVERT: F 455 LYS cc_start: 0.7229 (mttt) cc_final: 0.6284 (mmtt) REVERT: F 547 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8056 (m) REVERT: F 554 ILE cc_start: 0.7559 (mm) cc_final: 0.7012 (mt) REVERT: F 568 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7275 (mp0) REVERT: F 582 LYS cc_start: 0.7450 (ttmm) cc_final: 0.7245 (tppt) REVERT: F 682 LEU cc_start: 0.7994 (mt) cc_final: 0.7762 (mt) outliers start: 107 outliers final: 60 residues processed: 617 average time/residue: 0.2532 time to fit residues: 258.0252 Evaluate side-chains 533 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 461 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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 128 LEU 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 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 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 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 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 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 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 557 VAL 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: 0.6980 chunk 280 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 474 optimal weight: 1.9990 chunk 360 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 422 optimal weight: 0.3980 chunk 358 optimal weight: 0.8980 chunk 296 optimal weight: 0.7980 chunk 337 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 ASN B 840 GLN C 387 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 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 = 0.3723 r_free = 0.3723 target = 0.147971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.110100 restraints weight = 59987.544| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.93 r_work: 0.3036 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 40976 Z= 0.105 Angle : 0.510 11.603 55656 Z= 0.259 Chirality : 0.043 0.168 6402 Planarity : 0.004 0.048 7134 Dihedral : 7.932 85.861 6272 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.93 % Allowed : 14.55 % 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: -2.40 (0.11), residues: 5202 helix: -1.07 (0.10), residues: 2526 sheet: -2.00 (0.16), residues: 828 loop : -1.89 (0.13), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 141 TYR 0.023 0.001 TYR C 302 PHE 0.019 0.001 PHE A 714 TRP 0.007 0.001 TRP F 556 HIS 0.004 0.001 HIS F 781 Details of bonding type rmsd covalent geometry : bond 0.00240 (40956) covalent geometry : angle 0.51028 (55656) hydrogen bonds : bond 0.03192 ( 1468) hydrogen bonds : angle 3.74127 ( 4239) metal coordination : bond 0.00538 ( 18) Misc. bond : bond 0.00069 ( 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 632 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 510 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9151 (OUTLIER) cc_final: 0.8712 (t70) REVERT: A 362 MET cc_start: 0.7953 (mtt) cc_final: 0.7672 (mtt) REVERT: A 412 LYS cc_start: 0.8934 (tptt) cc_final: 0.8719 (tptt) REVERT: A 463 ARG cc_start: 0.2853 (OUTLIER) cc_final: 0.1092 (mtm180) REVERT: A 526 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7188 (mtm180) REVERT: A 558 MET cc_start: 0.7370 (mmt) cc_final: 0.7127 (mmt) REVERT: A 591 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7574 (mmtm) REVERT: A 839 ASP cc_start: 0.5977 (t70) cc_final: 0.5269 (t0) REVERT: B 15 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.8165 (ttp-110) REVERT: B 84 LYS cc_start: 0.8583 (mtmm) cc_final: 0.7857 (mmmt) REVERT: B 198 MET cc_start: 0.8425 (ttp) cc_final: 0.8066 (ttp) REVERT: B 241 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7313 (t0) REVERT: B 431 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7436 (mm-30) REVERT: B 574 MET cc_start: 0.8389 (ttt) cc_final: 0.8026 (ttt) REVERT: B 624 ASP cc_start: 0.7928 (t70) cc_final: 0.7692 (t0) REVERT: B 692 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.7730 (mm-30) REVERT: B 774 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8230 (mtp180) REVERT: B 834 GLU cc_start: 0.7989 (tt0) cc_final: 0.7591 (tm-30) REVERT: C 1 MET cc_start: 0.6920 (tpt) cc_final: 0.6653 (tpt) REVERT: C 86 CYS cc_start: 0.8964 (m) cc_final: 0.8648 (m) REVERT: C 341 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9007 (mp) REVERT: C 416 SER cc_start: 0.9436 (p) cc_final: 0.9092 (m) REVERT: C 760 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8963 (pp30) REVERT: D 17 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8669 (ttmt) REVERT: D 128 LEU cc_start: 0.8717 (pp) cc_final: 0.8500 (pt) REVERT: D 182 MET cc_start: 0.8999 (mtm) cc_final: 0.8791 (mtm) REVERT: D 200 LYS cc_start: 0.8761 (tppt) cc_final: 0.8328 (tmtt) REVERT: D 241 ASP cc_start: 0.8426 (t0) cc_final: 0.8202 (t0) REVERT: D 286 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8283 (mt) REVERT: D 586 MET cc_start: 0.8836 (mtp) cc_final: 0.8468 (mtp) REVERT: E 52 MET cc_start: 0.7392 (mtp) cc_final: 0.6553 (tpp) REVERT: E 179 ASN cc_start: 0.7726 (t0) cc_final: 0.7253 (m-40) REVERT: E 198 MET cc_start: 0.7277 (tmm) cc_final: 0.6503 (tmm) REVERT: E 241 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7601 (t0) REVERT: E 343 MET cc_start: 0.7112 (mmt) cc_final: 0.6696 (mmt) REVERT: E 371 LEU cc_start: 0.8749 (tp) cc_final: 0.8408 (tp) REVERT: E 395 LEU cc_start: 0.8710 (mm) cc_final: 0.8433 (mt) REVERT: E 549 MET cc_start: 0.8530 (mtm) cc_final: 0.8309 (mtp) REVERT: E 576 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8112 (mt) REVERT: E 631 MET cc_start: 0.9027 (ttm) cc_final: 0.8799 (ttp) REVERT: E 652 LEU cc_start: 0.8580 (mt) cc_final: 0.8181 (mt) REVERT: E 866 ASP cc_start: 0.7569 (p0) cc_final: 0.7200 (p0) REVERT: F 52 MET cc_start: 0.7618 (mtp) cc_final: 0.7386 (mtp) REVERT: F 98 ILE cc_start: 0.8494 (mt) cc_final: 0.8043 (tt) REVERT: F 158 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.8069 (mp) REVERT: F 332 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: F 449 GLU cc_start: 0.7801 (mp0) cc_final: 0.7255 (tt0) REVERT: F 455 LYS cc_start: 0.7219 (mttt) cc_final: 0.6302 (mmtt) REVERT: F 547 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8049 (m) REVERT: F 554 ILE cc_start: 0.7433 (mm) cc_final: 0.7012 (mt) REVERT: F 555 MET cc_start: 0.8474 (mtp) cc_final: 0.8194 (mtm) REVERT: F 582 LYS cc_start: 0.7577 (ttmm) cc_final: 0.7339 (tppt) REVERT: F 682 LEU cc_start: 0.7993 (mt) cc_final: 0.7771 (mt) REVERT: F 747 ASN cc_start: 0.8075 (m110) cc_final: 0.7664 (m-40) REVERT: F 817 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7035 (mp0) outliers start: 122 outliers final: 79 residues processed: 602 average time/residue: 0.2386 time to fit residues: 236.9207 Evaluate side-chains 553 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 462 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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 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 547 SER Chi-restraints excluded: chain B residue 634 VAL 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 341 LEU 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 286 ILE 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 3 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 94 THR 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 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 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 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 Chi-restraints excluded: chain F residue 834 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 332 optimal weight: 0.6980 chunk 496 optimal weight: 0.6980 chunk 391 optimal weight: 0.7980 chunk 413 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 364 optimal weight: 0.6980 chunk 296 optimal weight: 0.9990 chunk 311 optimal weight: 0.0470 chunk 325 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 E 440 ASN E 618 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.147731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.110731 restraints weight = 59625.945| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.85 r_work: 0.3045 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 40976 Z= 0.095 Angle : 0.495 9.742 55656 Z= 0.251 Chirality : 0.042 0.169 6402 Planarity : 0.004 0.046 7134 Dihedral : 7.579 82.150 6268 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.88 % Allowed : 15.01 % Favored : 82.11 % 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: -0.63 (0.10), residues: 2538 sheet: -1.82 (0.17), residues: 822 loop : -1.68 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 21 TYR 0.019 0.001 TYR C 302 PHE 0.019 0.001 PHE A 714 TRP 0.010 0.001 TRP A 801 HIS 0.005 0.001 HIS F 781 Details of bonding type rmsd covalent geometry : bond 0.00219 (40956) covalent geometry : angle 0.49495 (55656) hydrogen bonds : bond 0.02891 ( 1468) hydrogen bonds : angle 3.60405 ( 4239) metal coordination : bond 0.00380 ( 18) Misc. bond : bond 0.00052 ( 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 616 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 496 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.7866 (mtt) cc_final: 0.7609 (mtt) REVERT: A 412 LYS cc_start: 0.8942 (tptt) cc_final: 0.8731 (tptt) REVERT: A 463 ARG cc_start: 0.2945 (OUTLIER) cc_final: 0.1213 (mtm180) REVERT: A 526 ARG cc_start: 0.7440 (mtt180) cc_final: 0.7127 (mtm180) REVERT: A 582 LYS cc_start: 0.8332 (mmmt) cc_final: 0.8003 (ptmm) REVERT: A 591 LYS cc_start: 0.7982 (mmtp) cc_final: 0.7622 (mmtm) REVERT: A 718 PHE cc_start: 0.8201 (m-80) cc_final: 0.7932 (m-80) REVERT: A 809 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6649 (mt) REVERT: A 831 LYS cc_start: 0.6609 (ttpt) cc_final: 0.6192 (pttt) REVERT: A 839 ASP cc_start: 0.6013 (t70) cc_final: 0.5320 (t0) REVERT: A 867 TYR cc_start: 0.5853 (t80) cc_final: 0.5519 (t80) REVERT: B 15 ARG cc_start: 0.8449 (mtp-110) cc_final: 0.8102 (ttp-110) REVERT: B 84 LYS cc_start: 0.8551 (mtmm) cc_final: 0.7855 (mmmt) REVERT: B 198 MET cc_start: 0.8382 (ttp) cc_final: 0.7976 (ttp) REVERT: B 241 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7325 (t0) REVERT: B 431 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7487 (mm-30) REVERT: B 522 LEU cc_start: 0.9145 (tp) cc_final: 0.8943 (tp) REVERT: B 624 ASP cc_start: 0.7995 (t70) cc_final: 0.7741 (t0) REVERT: B 834 GLU cc_start: 0.7988 (tt0) cc_final: 0.7607 (tm-30) REVERT: C 1 MET cc_start: 0.6927 (tpt) cc_final: 0.6634 (tpt) REVERT: C 86 CYS cc_start: 0.8966 (m) cc_final: 0.8661 (m) REVERT: C 341 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8998 (mp) REVERT: C 416 SER cc_start: 0.9424 (p) cc_final: 0.9076 (m) REVERT: C 524 ILE cc_start: 0.9136 (pt) cc_final: 0.8904 (mt) REVERT: C 647 CYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8783 (p) REVERT: C 759 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8684 (mmmm) REVERT: D 128 LEU cc_start: 0.8622 (pp) cc_final: 0.8390 (pt) REVERT: D 200 LYS cc_start: 0.8649 (tppt) cc_final: 0.8268 (tmtt) REVERT: D 286 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8257 (mt) REVERT: D 585 LYS cc_start: 0.9285 (ttpp) cc_final: 0.9082 (tttp) REVERT: D 586 MET cc_start: 0.8863 (mtp) cc_final: 0.8519 (mtp) REVERT: E 52 MET cc_start: 0.7397 (mtp) cc_final: 0.6565 (tpp) REVERT: E 71 PHE cc_start: 0.9332 (t80) cc_final: 0.9034 (t80) REVERT: E 75 TYR cc_start: 0.8899 (m-80) cc_final: 0.8657 (m-80) REVERT: E 179 ASN cc_start: 0.7744 (t0) cc_final: 0.7262 (m-40) REVERT: E 198 MET cc_start: 0.7221 (tmm) cc_final: 0.6422 (tmm) REVERT: E 241 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7585 (t0) REVERT: E 341 LEU cc_start: 0.7153 (mt) cc_final: 0.6834 (mt) REVERT: E 343 MET cc_start: 0.7099 (mmt) cc_final: 0.6662 (mmt) REVERT: E 371 LEU cc_start: 0.8812 (tp) cc_final: 0.8466 (tp) REVERT: E 576 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8086 (mt) REVERT: E 631 MET cc_start: 0.8979 (ttm) cc_final: 0.8735 (ttp) REVERT: E 652 LEU cc_start: 0.8537 (mt) cc_final: 0.8199 (mt) REVERT: E 866 ASP cc_start: 0.7595 (p0) cc_final: 0.7181 (p0) REVERT: F 52 MET cc_start: 0.7738 (mtp) cc_final: 0.7531 (mtp) REVERT: F 98 ILE cc_start: 0.8447 (mt) cc_final: 0.7978 (tt) REVERT: F 332 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: F 455 LYS cc_start: 0.7357 (mttt) cc_final: 0.6401 (mmtt) REVERT: F 547 SER cc_start: 0.8428 (OUTLIER) cc_final: 0.8086 (m) REVERT: F 554 ILE cc_start: 0.7421 (mm) cc_final: 0.6975 (mt) REVERT: F 555 MET cc_start: 0.8572 (mtp) cc_final: 0.8304 (mtm) REVERT: F 582 LYS cc_start: 0.7618 (ttmm) cc_final: 0.7373 (tppt) REVERT: F 682 LEU cc_start: 0.7988 (mt) cc_final: 0.7752 (mt) REVERT: F 747 ASN cc_start: 0.8061 (m110) cc_final: 0.7648 (m-40) REVERT: F 808 GLU cc_start: 0.7460 (pt0) cc_final: 0.6957 (mp0) REVERT: F 817 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7054 (mp0) outliers start: 120 outliers final: 77 residues processed: 592 average time/residue: 0.2369 time to fit residues: 232.9509 Evaluate side-chains 548 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 461 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 175 VAL 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 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 634 VAL 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 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 341 LEU 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 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 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 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 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 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 611 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 314 optimal weight: 0.0670 chunk 377 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 375 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 316 optimal weight: 0.7980 chunk 308 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 333 optimal weight: 0.0970 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 440 ASN F 747 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109805 restraints weight = 59867.514| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.01 r_work: 0.3050 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 40976 Z= 0.098 Angle : 0.494 11.385 55656 Z= 0.249 Chirality : 0.043 0.169 6402 Planarity : 0.004 0.045 7134 Dihedral : 7.362 75.075 6261 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.81 % Allowed : 15.56 % Favored : 81.63 % 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: -1.61 (0.11), residues: 5202 helix: -0.37 (0.10), residues: 2538 sheet: -1.67 (0.17), residues: 822 loop : -1.57 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 21 TYR 0.019 0.001 TYR E 75 PHE 0.018 0.001 PHE A 714 TRP 0.015 0.001 TRP A 801 HIS 0.004 0.001 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00230 (40956) covalent geometry : angle 0.49357 (55656) hydrogen bonds : bond 0.02823 ( 1468) hydrogen bonds : angle 3.55436 ( 4239) metal coordination : bond 0.00407 ( 18) Misc. bond : bond 0.00042 ( 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 603 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 486 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.7944 (mtt) cc_final: 0.7697 (mtt) REVERT: A 412 LYS cc_start: 0.8950 (tptt) cc_final: 0.8734 (tptt) REVERT: A 463 ARG cc_start: 0.3035 (OUTLIER) cc_final: 0.1213 (mtm180) REVERT: A 526 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7156 (mtm180) REVERT: A 574 MET cc_start: 0.6996 (mtm) cc_final: 0.6792 (mtp) REVERT: A 576 ILE cc_start: 0.8233 (mp) cc_final: 0.7950 (mm) REVERT: A 582 LYS cc_start: 0.8317 (mmmt) cc_final: 0.7986 (ptmm) REVERT: A 591 LYS cc_start: 0.7977 (mmtp) cc_final: 0.7617 (mmtm) REVERT: A 718 PHE cc_start: 0.8217 (m-80) cc_final: 0.7967 (m-80) REVERT: A 780 ASP cc_start: 0.6339 (OUTLIER) cc_final: 0.5387 (t0) REVERT: A 799 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.6129 (tt) REVERT: A 809 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6598 (mt) REVERT: A 831 LYS cc_start: 0.6535 (ttpt) cc_final: 0.6135 (pttt) REVERT: A 839 ASP cc_start: 0.6211 (t70) cc_final: 0.5555 (t0) REVERT: A 867 TYR cc_start: 0.5856 (t80) cc_final: 0.5589 (t80) REVERT: B 15 ARG cc_start: 0.8483 (mtp-110) cc_final: 0.8129 (ttp-110) REVERT: B 59 MET cc_start: 0.7248 (ppp) cc_final: 0.7020 (ppp) REVERT: B 84 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7867 (mmmt) REVERT: B 198 MET cc_start: 0.8399 (ttp) cc_final: 0.7968 (ttp) REVERT: B 431 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7481 (mm-30) REVERT: B 624 ASP cc_start: 0.8111 (t70) cc_final: 0.7822 (t70) REVERT: B 834 GLU cc_start: 0.8030 (tt0) cc_final: 0.7632 (tm-30) REVERT: C 1 MET cc_start: 0.6957 (tpt) cc_final: 0.6629 (tpt) REVERT: C 86 CYS cc_start: 0.8997 (m) cc_final: 0.8681 (m) REVERT: C 341 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8996 (mp) REVERT: C 416 SER cc_start: 0.9424 (p) cc_final: 0.9088 (m) REVERT: C 443 THR cc_start: 0.9328 (t) cc_final: 0.8937 (m) REVERT: C 524 ILE cc_start: 0.9172 (pt) cc_final: 0.8969 (mt) REVERT: C 647 CYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8784 (p) REVERT: C 760 GLN cc_start: 0.9158 (OUTLIER) cc_final: 0.8952 (pp30) REVERT: D 128 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8387 (pt) REVERT: D 172 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 200 LYS cc_start: 0.8724 (tppt) cc_final: 0.8317 (tmtt) REVERT: D 241 ASP cc_start: 0.8318 (t0) cc_final: 0.8074 (t0) REVERT: D 286 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (mt) REVERT: D 585 LYS cc_start: 0.9308 (ttpp) cc_final: 0.9105 (tttp) REVERT: E 52 MET cc_start: 0.7373 (mtp) cc_final: 0.6552 (tpp) REVERT: E 59 MET cc_start: 0.7839 (ptp) cc_final: 0.6412 (ptp) REVERT: E 179 ASN cc_start: 0.7736 (t0) cc_final: 0.7248 (m-40) REVERT: E 198 MET cc_start: 0.7250 (tmm) cc_final: 0.6433 (tmm) REVERT: E 241 ASP cc_start: 0.8200 (OUTLIER) cc_final: 0.7592 (t0) REVERT: E 341 LEU cc_start: 0.6723 (mt) cc_final: 0.6389 (mt) REVERT: E 343 MET cc_start: 0.6859 (mmt) cc_final: 0.6474 (mmt) REVERT: E 371 LEU cc_start: 0.8727 (tp) cc_final: 0.8345 (tp) REVERT: E 395 LEU cc_start: 0.8653 (mm) cc_final: 0.8287 (mt) REVERT: E 576 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.7919 (mt) REVERT: E 631 MET cc_start: 0.8993 (ttm) cc_final: 0.8644 (ttp) REVERT: E 652 LEU cc_start: 0.8573 (mt) cc_final: 0.8230 (mt) REVERT: F 98 ILE cc_start: 0.8418 (mt) cc_final: 0.7955 (tt) REVERT: F 332 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.7792 (m-10) REVERT: F 455 LYS cc_start: 0.7367 (mttt) cc_final: 0.6393 (mmtt) REVERT: F 547 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8134 (m) REVERT: F 549 MET cc_start: 0.7468 (ttm) cc_final: 0.7061 (ttp) REVERT: F 554 ILE cc_start: 0.7357 (mm) cc_final: 0.6870 (mt) REVERT: F 555 MET cc_start: 0.8711 (mtp) cc_final: 0.8465 (mtm) REVERT: F 582 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7379 (tppt) REVERT: F 680 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6533 (tppt) REVERT: F 682 LEU cc_start: 0.8044 (mt) cc_final: 0.7808 (mt) REVERT: F 808 GLU cc_start: 0.7425 (pt0) cc_final: 0.6964 (mp0) REVERT: F 817 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7104 (mp0) REVERT: F 834 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7084 (mt-10) outliers start: 117 outliers final: 84 residues processed: 578 average time/residue: 0.2300 time to fit residues: 222.6134 Evaluate side-chains 550 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 451 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 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 694 SER Chi-restraints excluded: chain A residue 698 VAL 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 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 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 547 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL 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 341 LEU 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 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 128 LEU Chi-restraints excluded: chain D residue 285 VAL 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 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 16 VAL 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 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 70 HIS 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 337 optimal weight: 0.0570 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 477 optimal weight: 8.9990 chunk 461 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 0.0870 chunk 381 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 387 GLN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN E 437 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.146537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.107392 restraints weight = 60330.045| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.82 r_work: 0.3045 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40976 Z= 0.084 Angle : 0.484 13.190 55656 Z= 0.244 Chirality : 0.042 0.172 6402 Planarity : 0.004 0.058 7134 Dihedral : 7.063 70.951 6261 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.62 % Allowed : 16.02 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.31 (0.12), residues: 5202 helix: -0.09 (0.11), residues: 2520 sheet: -1.53 (0.17), residues: 822 loop : -1.46 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 21 TYR 0.019 0.001 TYR B 384 PHE 0.019 0.001 PHE A 714 TRP 0.018 0.001 TRP A 801 HIS 0.005 0.000 HIS B 70 Details of bonding type rmsd covalent geometry : bond 0.00189 (40956) covalent geometry : angle 0.48432 (55656) hydrogen bonds : bond 0.02562 ( 1468) hydrogen bonds : angle 3.45397 ( 4239) metal coordination : bond 0.00244 ( 18) Misc. bond : bond 0.00032 ( 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 612 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 503 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 MET cc_start: 0.7810 (mtt) cc_final: 0.7583 (mtt) REVERT: A 412 LYS cc_start: 0.8947 (tptt) cc_final: 0.8703 (tptt) REVERT: A 463 ARG cc_start: 0.2654 (OUTLIER) cc_final: 0.1071 (mtm180) REVERT: A 526 ARG cc_start: 0.7404 (mtt180) cc_final: 0.7136 (mtm180) REVERT: A 574 MET cc_start: 0.7160 (mtm) cc_final: 0.6625 (mtp) REVERT: A 582 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7986 (ptmm) REVERT: A 591 LYS cc_start: 0.7875 (mmtp) cc_final: 0.7522 (mmtm) REVERT: A 640 MET cc_start: 0.6141 (mtp) cc_final: 0.5864 (mtp) REVERT: A 780 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5401 (t0) REVERT: A 809 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6546 (mt) REVERT: A 831 LYS cc_start: 0.6501 (ttpt) cc_final: 0.6042 (ptpt) REVERT: A 839 ASP cc_start: 0.6135 (t70) cc_final: 0.5481 (t0) REVERT: A 867 TYR cc_start: 0.5792 (t80) cc_final: 0.5584 (t80) REVERT: B 15 ARG cc_start: 0.8468 (mtp-110) cc_final: 0.8175 (ttp-110) REVERT: B 59 MET cc_start: 0.7347 (ppp) cc_final: 0.7137 (ppp) REVERT: B 70 HIS cc_start: 0.8951 (t-170) cc_final: 0.8469 (t-170) REVERT: B 84 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7857 (mmmt) REVERT: B 128 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8581 (pt) REVERT: B 198 MET cc_start: 0.8390 (ttp) cc_final: 0.7951 (ttp) REVERT: B 431 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7465 (mm-30) REVERT: C 1 MET cc_start: 0.6917 (tpt) cc_final: 0.6592 (tpt) REVERT: C 86 CYS cc_start: 0.8914 (m) cc_final: 0.8624 (m) REVERT: C 341 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8988 (mp) REVERT: C 416 SER cc_start: 0.9445 (p) cc_final: 0.9120 (m) REVERT: C 443 THR cc_start: 0.9283 (t) cc_final: 0.8925 (m) REVERT: C 604 GLU cc_start: 0.8753 (pm20) cc_final: 0.8535 (pm20) REVERT: C 647 CYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8707 (p) REVERT: C 759 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8743 (mmtm) REVERT: C 760 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8941 (pp30) REVERT: D 128 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8273 (pt) REVERT: D 172 GLN cc_start: 0.8401 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 200 LYS cc_start: 0.8575 (tppt) cc_final: 0.8194 (tmtt) REVERT: D 286 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8216 (mt) REVERT: D 463 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.8263 (mmp-170) REVERT: D 789 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: E 52 MET cc_start: 0.7405 (mtp) cc_final: 0.6606 (tpp) REVERT: E 179 ASN cc_start: 0.7757 (t0) cc_final: 0.7288 (m-40) REVERT: E 198 MET cc_start: 0.7212 (tmm) cc_final: 0.6369 (tmm) REVERT: E 241 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7667 (t0) REVERT: E 334 HIS cc_start: 0.7169 (m170) cc_final: 0.6924 (m170) REVERT: E 343 MET cc_start: 0.6649 (mmt) cc_final: 0.6336 (mmt) REVERT: E 371 LEU cc_start: 0.8672 (tp) cc_final: 0.8300 (tp) REVERT: E 388 LYS cc_start: 0.7364 (mtpp) cc_final: 0.7113 (mtpp) REVERT: E 389 MET cc_start: 0.8642 (mtp) cc_final: 0.8339 (mtp) REVERT: E 395 LEU cc_start: 0.8545 (mm) cc_final: 0.8185 (mt) REVERT: E 431 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6949 (pt0) REVERT: E 576 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7977 (mt) REVERT: E 631 MET cc_start: 0.8994 (ttm) cc_final: 0.8642 (ttp) REVERT: E 642 MET cc_start: 0.8186 (ttm) cc_final: 0.7980 (ttm) REVERT: E 652 LEU cc_start: 0.8579 (mt) cc_final: 0.8262 (mt) REVERT: F 20 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8081 (tt0) REVERT: F 98 ILE cc_start: 0.8299 (mt) cc_final: 0.7808 (tt) REVERT: F 455 LYS cc_start: 0.7372 (mttt) cc_final: 0.6400 (mmtt) REVERT: F 463 ARG cc_start: 0.2283 (OUTLIER) cc_final: 0.0356 (mtm-85) REVERT: F 547 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8008 (m) REVERT: F 549 MET cc_start: 0.7485 (ttm) cc_final: 0.7064 (ttp) REVERT: F 555 MET cc_start: 0.8608 (mtp) cc_final: 0.8367 (mtm) REVERT: F 582 LYS cc_start: 0.7585 (ttmm) cc_final: 0.7361 (tppt) REVERT: F 680 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6450 (tppt) REVERT: F 682 LEU cc_start: 0.7944 (mt) cc_final: 0.7711 (mt) REVERT: F 747 ASN cc_start: 0.8064 (m-40) cc_final: 0.7676 (m-40) REVERT: F 808 GLU cc_start: 0.7463 (pt0) cc_final: 0.6958 (mp0) REVERT: F 817 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7181 (mp0) outliers start: 109 outliers final: 76 residues processed: 592 average time/residue: 0.2485 time to fit residues: 245.9887 Evaluate side-chains 549 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 457 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 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 694 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 780 ASP 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 128 LEU Chi-restraints excluded: chain B residue 175 VAL 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 547 SER Chi-restraints excluded: chain B residue 634 VAL 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 324 THR Chi-restraints excluded: chain C residue 341 LEU 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 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 128 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 418 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 642 MET Chi-restraints excluded: chain D residue 721 VAL Chi-restraints excluded: chain D residue 789 ASP 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 241 ASP 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 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 70 HIS Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 286 ILE 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 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 680 LYS Chi-restraints excluded: chain F residue 684 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 8 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 314 optimal weight: 0.1980 chunk 459 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 411 optimal weight: 0.3980 chunk 45 optimal weight: 10.0000 chunk 289 optimal weight: 0.3980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 378 GLN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN ** F 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111876 restraints weight = 58810.774| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.63 r_work: 0.2989 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 40976 Z= 0.086 Angle : 0.491 12.106 55656 Z= 0.247 Chirality : 0.042 0.169 6402 Planarity : 0.004 0.055 7134 Dihedral : 6.920 69.016 6258 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.57 % Allowed : 16.59 % Favored : 80.84 % 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: -1.11 (0.12), residues: 5202 helix: 0.06 (0.11), residues: 2544 sheet: -1.37 (0.17), residues: 822 loop : -1.38 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 21 TYR 0.027 0.001 TYR C 302 PHE 0.018 0.001 PHE A 714 TRP 0.019 0.001 TRP A 801 HIS 0.003 0.000 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00198 (40956) covalent geometry : angle 0.49090 (55656) hydrogen bonds : bond 0.02567 ( 1468) hydrogen bonds : angle 3.41810 ( 4239) metal coordination : bond 0.00275 ( 18) Misc. bond : bond 0.00032 ( 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 599 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 492 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ILE cc_start: 0.7990 (mt) cc_final: 0.7775 (mm) REVERT: A 362 MET cc_start: 0.7942 (mtt) cc_final: 0.7682 (mtt) REVERT: A 412 LYS cc_start: 0.8914 (tptt) cc_final: 0.8634 (tptt) REVERT: A 463 ARG cc_start: 0.2637 (OUTLIER) cc_final: 0.0978 (mtm180) REVERT: A 574 MET cc_start: 0.7132 (mtm) cc_final: 0.6554 (mtp) REVERT: A 582 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7955 (ptmm) REVERT: A 591 LYS cc_start: 0.7770 (mmtp) cc_final: 0.7386 (mptt) REVERT: A 640 MET cc_start: 0.6242 (mtp) cc_final: 0.5995 (mtp) REVERT: A 780 ASP cc_start: 0.6056 (OUTLIER) cc_final: 0.5365 (t0) REVERT: A 809 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.6528 (mt) REVERT: A 831 LYS cc_start: 0.6461 (ttpt) cc_final: 0.6066 (ptpt) REVERT: A 839 ASP cc_start: 0.6083 (t70) cc_final: 0.5409 (t0) REVERT: A 867 TYR cc_start: 0.5777 (t80) cc_final: 0.5564 (t80) REVERT: B 15 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.8098 (ttp-110) REVERT: B 59 MET cc_start: 0.7336 (ppp) cc_final: 0.7097 (ppp) REVERT: B 70 HIS cc_start: 0.8925 (t-170) cc_final: 0.8466 (t-170) REVERT: B 84 LYS cc_start: 0.8584 (mtmm) cc_final: 0.7866 (mmmt) REVERT: B 128 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8517 (pt) REVERT: B 198 MET cc_start: 0.8436 (ttp) cc_final: 0.7950 (ttp) REVERT: B 345 ARG cc_start: 0.7493 (ttm170) cc_final: 0.7120 (ttm170) REVERT: B 431 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7358 (mm-30) REVERT: B 834 GLU cc_start: 0.7828 (tt0) cc_final: 0.7448 (tm-30) REVERT: C 86 CYS cc_start: 0.8898 (m) cc_final: 0.8564 (m) REVERT: C 341 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9045 (mp) REVERT: C 416 SER cc_start: 0.9462 (p) cc_final: 0.9188 (m) REVERT: C 443 THR cc_start: 0.9280 (t) cc_final: 0.8956 (m) REVERT: C 604 GLU cc_start: 0.8871 (pm20) cc_final: 0.8633 (pm20) REVERT: C 647 CYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8663 (p) REVERT: C 759 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8693 (mmtm) REVERT: C 760 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8909 (pp30) REVERT: D 128 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (pt) REVERT: D 172 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8028 (tm-30) REVERT: D 200 LYS cc_start: 0.8462 (tppt) cc_final: 0.8068 (tmtt) REVERT: D 286 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8186 (mt) REVERT: D 463 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8241 (mmp-170) REVERT: E 52 MET cc_start: 0.7471 (mtp) cc_final: 0.6702 (tpp) REVERT: E 59 MET cc_start: 0.7556 (ptp) cc_final: 0.6230 (ptp) REVERT: E 179 ASN cc_start: 0.7682 (t0) cc_final: 0.7221 (m-40) REVERT: E 198 MET cc_start: 0.7219 (tmm) cc_final: 0.6369 (tmm) REVERT: E 241 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7686 (t0) REVERT: E 334 HIS cc_start: 0.7069 (m170) cc_final: 0.6790 (m170) REVERT: E 343 MET cc_start: 0.6559 (mmt) cc_final: 0.6311 (mmt) REVERT: E 371 LEU cc_start: 0.8662 (tp) cc_final: 0.8259 (tp) REVERT: E 388 LYS cc_start: 0.7295 (mtpp) cc_final: 0.7019 (mtpp) REVERT: E 389 MET cc_start: 0.8625 (mtp) cc_final: 0.8301 (mtp) REVERT: E 431 GLU cc_start: 0.7140 (mt-10) cc_final: 0.6740 (pt0) REVERT: E 576 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7928 (mt) REVERT: E 631 MET cc_start: 0.8965 (ttm) cc_final: 0.8613 (ttp) REVERT: E 652 LEU cc_start: 0.8517 (mt) cc_final: 0.8235 (mt) REVERT: F 20 GLN cc_start: 0.8307 (tm-30) cc_final: 0.8032 (tt0) REVERT: F 98 ILE cc_start: 0.8261 (mt) cc_final: 0.7758 (tt) REVERT: F 184 HIS cc_start: 0.8237 (t-90) cc_final: 0.7988 (t-90) REVERT: F 332 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: F 455 LYS cc_start: 0.7388 (mttt) cc_final: 0.6395 (mmtt) REVERT: F 463 ARG cc_start: 0.2491 (OUTLIER) cc_final: 0.0595 (mtm-85) REVERT: F 547 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7978 (m) REVERT: F 549 MET cc_start: 0.7534 (ttm) cc_final: 0.7111 (ttp) REVERT: F 555 MET cc_start: 0.8665 (mtp) cc_final: 0.8431 (mtm) REVERT: F 582 LYS cc_start: 0.7518 (ttmm) cc_final: 0.7285 (tppt) REVERT: F 680 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6460 (tppt) REVERT: F 682 LEU cc_start: 0.7897 (mt) cc_final: 0.7664 (mt) REVERT: F 747 ASN cc_start: 0.8017 (m-40) cc_final: 0.7574 (m-40) REVERT: F 808 GLU cc_start: 0.7476 (pt0) cc_final: 0.6969 (mp0) REVERT: F 817 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7150 (mp0) outliers start: 107 outliers final: 80 residues processed: 576 average time/residue: 0.2365 time to fit residues: 228.5515 Evaluate side-chains 565 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 469 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 694 SER Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 780 ASP 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 128 LEU Chi-restraints excluded: chain B residue 175 VAL 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 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 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 254 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 LEU 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 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 128 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 332 PHE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain D residue 721 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 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 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 114 THR Chi-restraints excluded: chain F residue 246 CYS 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 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 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 680 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 82 optimal weight: 0.0670 chunk 378 optimal weight: 9.9990 chunk 114 optimal weight: 10.0000 chunk 498 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 349 optimal weight: 10.0000 chunk 80 optimal weight: 0.0070 chunk 145 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 490 optimal weight: 7.9990 chunk 376 optimal weight: 10.0000 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN B 69 ASN B 378 GLN C 387 GLN D 188 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN E 132 ASN E 727 HIS F 377 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 = 0.3634 r_free = 0.3634 target = 0.140761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.102379 restraints weight = 60532.880| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.82 r_work: 0.2953 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 40976 Z= 0.181 Angle : 0.589 11.801 55656 Z= 0.298 Chirality : 0.046 0.187 6402 Planarity : 0.004 0.051 7134 Dihedral : 7.404 76.765 6258 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.86 % Allowed : 16.67 % Favored : 80.48 % 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: -1.18 (0.12), residues: 5202 helix: -0.07 (0.10), residues: 2562 sheet: -1.21 (0.17), residues: 840 loop : -1.42 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 381 TYR 0.027 0.001 TYR C 302 PHE 0.014 0.001 PHE A 714 TRP 0.022 0.002 TRP A 801 HIS 0.004 0.001 HIS E 454 Details of bonding type rmsd covalent geometry : bond 0.00437 (40956) covalent geometry : angle 0.58874 (55656) hydrogen bonds : bond 0.03611 ( 1468) hydrogen bonds : angle 3.68468 ( 4239) metal coordination : bond 0.00908 ( 18) Misc. bond : bond 0.00040 ( 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 565 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 446 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9219 (OUTLIER) cc_final: 0.8718 (t70) REVERT: A 186 ASP cc_start: 0.7790 (p0) cc_final: 0.7587 (p0) REVERT: A 362 MET cc_start: 0.7985 (mtt) cc_final: 0.7779 (mtt) REVERT: A 412 LYS cc_start: 0.8988 (tptt) cc_final: 0.8774 (tptt) REVERT: A 463 ARG cc_start: 0.2886 (OUTLIER) cc_final: 0.1290 (mtm180) REVERT: A 555 MET cc_start: 0.7931 (mtp) cc_final: 0.7561 (mtm) REVERT: A 582 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8040 (ptmm) REVERT: A 591 LYS cc_start: 0.7915 (mmtp) cc_final: 0.7528 (mptt) REVERT: A 780 ASP cc_start: 0.6077 (OUTLIER) cc_final: 0.5172 (t0) REVERT: A 809 LEU cc_start: 0.6776 (OUTLIER) cc_final: 0.6534 (mt) REVERT: A 831 LYS cc_start: 0.6509 (ttpt) cc_final: 0.6033 (ptpt) REVERT: A 839 ASP cc_start: 0.6241 (t70) cc_final: 0.5607 (t0) REVERT: A 867 TYR cc_start: 0.5850 (t80) cc_final: 0.5647 (t80) REVERT: B 15 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8199 (ttp-110) REVERT: B 59 MET cc_start: 0.7630 (ppp) cc_final: 0.7402 (ppp) REVERT: B 84 LYS cc_start: 0.8654 (mtmm) cc_final: 0.7869 (mmmt) REVERT: B 198 MET cc_start: 0.8528 (ttp) cc_final: 0.8052 (ttp) REVERT: B 240 PHE cc_start: 0.7880 (t80) cc_final: 0.7647 (t80) REVERT: B 265 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.6951 (tpt170) REVERT: B 412 LYS cc_start: 0.8498 (tppp) cc_final: 0.8167 (tppp) REVERT: B 431 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7475 (mm-30) REVERT: B 624 ASP cc_start: 0.8113 (t70) cc_final: 0.7861 (t0) REVERT: B 834 GLU cc_start: 0.7959 (tt0) cc_final: 0.7521 (tm-30) REVERT: C 86 CYS cc_start: 0.9025 (m) cc_final: 0.8693 (m) REVERT: C 341 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9039 (mp) REVERT: C 416 SER cc_start: 0.9466 (p) cc_final: 0.9205 (m) REVERT: C 443 THR cc_start: 0.9334 (t) cc_final: 0.8989 (m) REVERT: C 574 MET cc_start: 0.8926 (ttp) cc_final: 0.8708 (ttp) REVERT: C 760 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.9060 (pp30) REVERT: D 172 GLN cc_start: 0.8530 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 200 LYS cc_start: 0.8736 (tppt) cc_final: 0.8301 (tmtt) REVERT: D 789 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: D 840 GLN cc_start: 0.9202 (tp40) cc_final: 0.8872 (tp40) REVERT: E 52 MET cc_start: 0.7510 (mtp) cc_final: 0.6615 (tpp) REVERT: E 59 MET cc_start: 0.7734 (ptp) cc_final: 0.6489 (ptp) REVERT: E 102 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7845 (mm-30) REVERT: E 198 MET cc_start: 0.7184 (tmm) cc_final: 0.6382 (tmm) REVERT: E 334 HIS cc_start: 0.7237 (m170) cc_final: 0.7020 (m170) REVERT: E 371 LEU cc_start: 0.8714 (tp) cc_final: 0.8335 (tp) REVERT: E 389 MET cc_start: 0.8784 (mtp) cc_final: 0.8387 (mtp) REVERT: E 395 LEU cc_start: 0.8508 (mm) cc_final: 0.8120 (mt) REVERT: E 576 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8033 (mt) REVERT: F 198 MET cc_start: 0.7324 (tmm) cc_final: 0.7029 (tmm) REVERT: F 332 PHE cc_start: 0.8314 (OUTLIER) cc_final: 0.7733 (m-10) REVERT: F 455 LYS cc_start: 0.7412 (mttt) cc_final: 0.6476 (mmtt) REVERT: F 547 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7939 (m) REVERT: F 549 MET cc_start: 0.7628 (ttm) cc_final: 0.7208 (ttp) REVERT: F 555 MET cc_start: 0.8673 (mtp) cc_final: 0.8450 (mtm) REVERT: F 582 LYS cc_start: 0.7654 (ttmm) cc_final: 0.7425 (tppt) REVERT: F 680 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6478 (tppt) REVERT: F 682 LEU cc_start: 0.7856 (mt) cc_final: 0.7645 (mt) REVERT: F 747 ASN cc_start: 0.8242 (m-40) cc_final: 0.7951 (m-40) REVERT: F 808 GLU cc_start: 0.7585 (pt0) cc_final: 0.6995 (mp0) REVERT: F 817 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7219 (mp0) outliers start: 119 outliers final: 95 residues processed: 541 average time/residue: 0.2483 time to fit residues: 223.8900 Evaluate side-chains 527 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 421 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 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 543 LEU 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 694 SER 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 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 104 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL 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 508 VAL Chi-restraints excluded: chain B residue 547 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL 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 254 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 429 ILE Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 463 ARG 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 245 ILE Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG 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 D residue 789 ASP 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 286 ILE Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 443 THR 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 246 CYS 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 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 547 SER Chi-restraints excluded: chain F residue 571 LEU Chi-restraints excluded: chain F residue 642 MET Chi-restraints excluded: chain F residue 680 LYS Chi-restraints excluded: chain F residue 684 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 169 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 302 optimal weight: 0.9990 chunk 455 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 chunk 451 optimal weight: 0.0870 chunk 181 optimal weight: 1.9990 chunk 483 optimal weight: 7.9990 chunk 257 optimal weight: 0.9980 chunk 513 optimal weight: 6.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** D 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104582 restraints weight = 60177.908| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.79 r_work: 0.2981 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 40976 Z= 0.106 Angle : 0.529 11.908 55656 Z= 0.267 Chirality : 0.043 0.171 6402 Planarity : 0.004 0.050 7134 Dihedral : 7.203 68.849 6258 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 17.44 % Favored : 80.14 % 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: -0.98 (0.12), residues: 5202 helix: 0.13 (0.11), residues: 2502 sheet: -1.23 (0.17), residues: 858 loop : -1.27 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 865 TYR 0.026 0.001 TYR C 302 PHE 0.016 0.001 PHE A 714 TRP 0.019 0.001 TRP A 801 HIS 0.004 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00250 (40956) covalent geometry : angle 0.52870 (55656) hydrogen bonds : bond 0.02877 ( 1468) hydrogen bonds : angle 3.52876 ( 4239) metal coordination : bond 0.00353 ( 18) Misc. bond : bond 0.00024 ( 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 547 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 446 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 HIS cc_start: 0.9163 (OUTLIER) cc_final: 0.8558 (t70) REVERT: A 412 LYS cc_start: 0.8962 (tptt) cc_final: 0.8753 (tptt) REVERT: A 463 ARG cc_start: 0.2688 (OUTLIER) cc_final: 0.1074 (mtm180) REVERT: A 582 LYS cc_start: 0.8303 (mmmt) cc_final: 0.8016 (ptmm) REVERT: A 591 LYS cc_start: 0.7887 (mmtp) cc_final: 0.7462 (mptt) REVERT: A 780 ASP cc_start: 0.6084 (OUTLIER) cc_final: 0.5196 (t0) REVERT: A 799 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5675 (tt) REVERT: A 809 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6498 (mt) REVERT: A 831 LYS cc_start: 0.6494 (ttpt) cc_final: 0.6022 (ptpt) REVERT: A 839 ASP cc_start: 0.6353 (t70) cc_final: 0.5679 (t0) REVERT: B 15 ARG cc_start: 0.8421 (mtp-110) cc_final: 0.8177 (ttp-110) REVERT: B 59 MET cc_start: 0.7574 (ppp) cc_final: 0.7339 (ppp) REVERT: B 70 HIS cc_start: 0.9094 (t-170) cc_final: 0.8599 (t-170) REVERT: B 84 LYS cc_start: 0.8635 (mtmm) cc_final: 0.7891 (mmmt) REVERT: B 198 MET cc_start: 0.8498 (ttp) cc_final: 0.8019 (ttp) REVERT: B 240 PHE cc_start: 0.7861 (t80) cc_final: 0.7621 (t80) REVERT: B 265 ARG cc_start: 0.7592 (mmm-85) cc_final: 0.6935 (tpt170) REVERT: B 345 ARG cc_start: 0.7346 (ttm170) cc_final: 0.6841 (ttm170) REVERT: B 412 LYS cc_start: 0.8571 (tppp) cc_final: 0.8177 (tppp) REVERT: B 431 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7432 (mm-30) REVERT: C 86 CYS cc_start: 0.8867 (m) cc_final: 0.8534 (m) REVERT: C 341 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9001 (mp) REVERT: C 416 SER cc_start: 0.9445 (p) cc_final: 0.9168 (m) REVERT: C 443 THR cc_start: 0.9297 (t) cc_final: 0.8950 (m) REVERT: C 574 MET cc_start: 0.8854 (ttp) cc_final: 0.8650 (ttp) REVERT: C 647 CYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8743 (p) REVERT: C 759 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8744 (mmmm) REVERT: C 760 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.8997 (pp30) REVERT: D 172 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8214 (tm-30) REVERT: D 200 LYS cc_start: 0.8608 (tppt) cc_final: 0.8175 (tmtt) REVERT: D 286 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8267 (mt) REVERT: D 719 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8864 (mp) REVERT: D 789 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6971 (m-30) REVERT: D 840 GLN cc_start: 0.9091 (tp40) cc_final: 0.8854 (tp40) REVERT: E 52 MET cc_start: 0.7510 (mtp) cc_final: 0.6623 (tpp) REVERT: E 59 MET cc_start: 0.7683 (ptp) cc_final: 0.6568 (ptp) REVERT: E 102 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7877 (mm-30) REVERT: E 198 MET cc_start: 0.7163 (tmm) cc_final: 0.6385 (tmm) REVERT: E 334 HIS cc_start: 0.7243 (m170) cc_final: 0.7029 (m170) REVERT: E 371 LEU cc_start: 0.8654 (tp) cc_final: 0.8313 (tp) REVERT: E 389 MET cc_start: 0.8716 (mtp) cc_final: 0.8375 (mtp) REVERT: E 395 LEU cc_start: 0.8429 (mm) cc_final: 0.8049 (mt) REVERT: E 576 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7882 (mt) REVERT: F 332 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7720 (m-10) REVERT: F 455 LYS cc_start: 0.7297 (mttt) cc_final: 0.6409 (mmtt) REVERT: F 463 ARG cc_start: 0.2202 (OUTLIER) cc_final: 0.0245 (mtm-85) REVERT: F 547 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7922 (m) REVERT: F 549 MET cc_start: 0.7590 (ttm) cc_final: 0.7150 (ttp) REVERT: F 555 MET cc_start: 0.8647 (mtp) cc_final: 0.8432 (mtm) REVERT: F 582 LYS cc_start: 0.7625 (ttmm) cc_final: 0.7393 (tppt) REVERT: F 680 LYS cc_start: 0.6953 (OUTLIER) cc_final: 0.6389 (tppt) REVERT: F 682 LEU cc_start: 0.7865 (mt) cc_final: 0.7649 (mt) REVERT: F 747 ASN cc_start: 0.8194 (m-40) cc_final: 0.7900 (m-40) REVERT: F 808 GLU cc_start: 0.7550 (pt0) cc_final: 0.6991 (mp0) REVERT: F 817 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7188 (mp0) outliers start: 101 outliers final: 81 residues processed: 529 average time/residue: 0.2373 time to fit residues: 209.3778 Evaluate side-chains 534 residues out of total 4170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 437 time to evaluate : 1.383 ------------------------------------------------------------------------------- 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 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 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 694 SER 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 67 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 175 VAL 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 547 SER Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 341 LEU 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 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 418 THR Chi-restraints excluded: chain D residue 438 LEU Chi-restraints excluded: chain D residue 463 ARG 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 D residue 719 LEU Chi-restraints excluded: chain D residue 789 ASP Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 132 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 405 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 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 246 CYS 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 359 LEU Chi-restraints excluded: chain F residue 412 LYS Chi-restraints excluded: chain F residue 418 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 642 MET Chi-restraints excluded: chain F residue 680 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 516 random chunks: chunk 383 optimal weight: 2.9990 chunk 425 optimal weight: 3.9990 chunk 317 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 360 optimal weight: 10.0000 chunk 126 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 492 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 192 optimal weight: 0.0670 chunk 157 optimal weight: 0.7980 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108807 restraints weight = 59034.225| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.63 r_work: 0.2947 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3876 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= 0.105 Angle : 0.523 11.710 55656 Z= 0.265 Chirality : 0.043 0.170 6402 Planarity : 0.004 0.049 7134 Dihedral : 7.104 67.109 6258 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.55 % Allowed : 17.22 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.12), residues: 5202 helix: 0.22 (0.11), residues: 2496 sheet: -1.15 (0.18), residues: 852 loop : -1.27 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 865 TYR 0.026 0.001 TYR C 302 PHE 0.016 0.001 PHE A 714 TRP 0.020 0.001 TRP A 801 HIS 0.003 0.001 HIS A 781 Details of bonding type rmsd covalent geometry : bond 0.00248 (40956) covalent geometry : angle 0.52332 (55656) hydrogen bonds : bond 0.02812 ( 1468) hydrogen bonds : angle 3.47574 ( 4239) metal coordination : bond 0.00389 ( 18) Misc. bond : bond 0.00022 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12176.87 seconds wall clock time: 208 minutes 49.17 seconds (12529.17 seconds total)