Starting phenix.real_space_refine on Tue Sep 24 20:05:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hs7_0264/09_2024/6hs7_0264.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 170 5.16 5 C 33345 2.51 5 N 9330 2.21 5 O 10045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 52890 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "E" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3629 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 21, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "T" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1000 Classifications: {'peptide': 130} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 122} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "b" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "c" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "d" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Chain: "e" Number of atoms: 3949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3949 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain breaks: 2 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 22.45, per 1000 atoms: 0.42 Number of scatterers: 52890 At special positions: 0 Unit cell: (181.04, 182.28, 177.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 170 16.00 O 10045 8.00 N 9330 7.00 C 33345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.25 Conformation dependent library (CDL) restraints added in 5.2 seconds 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12840 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 63 sheets defined 37.7% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.54 Creating SS restraints... Processing helix chain 'A' and resid 578 through 589 removed outlier: 4.206A pdb=" N LEU A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 587 " --> pdb=" O TYR A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 599 removed outlier: 3.995A pdb=" N ASP A 596 " --> pdb=" O HIS A 592 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 630 Processing helix chain 'A' and resid 631 through 637 Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.569A pdb=" N GLN A 668 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 682 Processing helix chain 'A' and resid 682 through 688 removed outlier: 3.555A pdb=" N ASN A 687 " --> pdb=" O LEU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.669A pdb=" N THR A 705 " --> pdb=" O THR A 701 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 706 " --> pdb=" O GLU A 702 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N MET A 707 " --> pdb=" O GLN A 703 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 725 removed outlier: 3.994A pdb=" N GLN A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 787 through 807 removed outlier: 3.796A pdb=" N THR A 793 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG A 794 " --> pdb=" O THR A 790 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 795 " --> pdb=" O TYR A 791 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 824 removed outlier: 4.577A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR A 821 " --> pdb=" O MET A 817 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 842 removed outlier: 4.053A pdb=" N ARG A 834 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASP A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 836 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLY A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER A 838 " --> pdb=" O ARG A 834 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A 842 " --> pdb=" O SER A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 856 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.598A pdb=" N GLU A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 863 " --> pdb=" O PRO A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 883 removed outlier: 3.818A pdb=" N ALA A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL A 883 " --> pdb=" O TRP A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 892 removed outlier: 4.037A pdb=" N ALA A 890 " --> pdb=" O GLY A 886 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER A 892 " --> pdb=" O ASN A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 913 Processing helix chain 'A' and resid 919 through 927 removed outlier: 3.577A pdb=" N LEU A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN A 925 " --> pdb=" O ALA A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 947 removed outlier: 4.010A pdb=" N THR A 946 " --> pdb=" O THR A 943 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 947 " --> pdb=" O ILE A 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 943 through 947' Processing helix chain 'A' and resid 952 through 965 removed outlier: 3.519A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 960 " --> pdb=" O LEU A 956 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR A 961 " --> pdb=" O LYS A 957 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER A 963 " --> pdb=" O ILE A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 1048 through 1053 removed outlier: 3.514A pdb=" N GLU A1052 " --> pdb=" O ILE A1048 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1048 through 1053' Processing helix chain 'A' and resid 1089 through 1099 removed outlier: 3.969A pdb=" N LEU A1096 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A1097 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ASN A1098 " --> pdb=" O LYS A1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 589 removed outlier: 3.875A pdb=" N LEU B 587 " --> pdb=" O TYR B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 599 removed outlier: 3.909A pdb=" N ASP B 596 " --> pdb=" O HIS B 592 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N MET B 597 " --> pdb=" O GLN B 593 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 629 Processing helix chain 'B' and resid 630 through 640 removed outlier: 5.040A pdb=" N VAL B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 673 removed outlier: 3.639A pdb=" N GLN B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 682 Processing helix chain 'B' and resid 682 through 687 removed outlier: 3.523A pdb=" N ASN B 687 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 709 removed outlier: 3.790A pdb=" N VAL B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 705 " --> pdb=" O THR B 701 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 706 " --> pdb=" O GLU B 702 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET B 707 " --> pdb=" O GLN B 703 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 725 removed outlier: 4.136A pdb=" N GLN B 725 " --> pdb=" O THR B 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 807 removed outlier: 3.954A pdb=" N THR B 793 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG B 794 " --> pdb=" O THR B 790 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 796 " --> pdb=" O LEU B 792 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 798 " --> pdb=" O ARG B 794 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 801 " --> pdb=" O GLN B 797 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 824 removed outlier: 4.541A pdb=" N GLN B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR B 821 " --> pdb=" O MET B 817 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 822 " --> pdb=" O LEU B 818 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 842 removed outlier: 3.791A pdb=" N ASP B 835 " --> pdb=" O THR B 831 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 836 " --> pdb=" O ASP B 832 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLY B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER B 838 " --> pdb=" O ARG B 834 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA B 841 " --> pdb=" O GLY B 837 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 856 Processing helix chain 'B' and resid 857 through 883 removed outlier: 3.533A pdb=" N GLU B 861 " --> pdb=" O VAL B 857 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 863 " --> pdb=" O PRO B 859 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 869 " --> pdb=" O GLN B 865 " (cutoff:3.500A) Proline residue: B 870 - end of helix removed outlier: 4.240A pdb=" N ALA B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 883 " --> pdb=" O TRP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 892 removed outlier: 4.009A pdb=" N ALA B 890 " --> pdb=" O GLY B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 908 through 913 Processing helix chain 'B' and resid 919 through 928 removed outlier: 3.598A pdb=" N LEU B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN B 925 " --> pdb=" O ALA B 921 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 927 " --> pdb=" O PHE B 923 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 928 " --> pdb=" O LEU B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 947 removed outlier: 4.028A pdb=" N THR B 946 " --> pdb=" O THR B 943 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG B 947 " --> pdb=" O ILE B 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 943 through 947' Processing helix chain 'B' and resid 952 through 966 removed outlier: 3.596A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 960 " --> pdb=" O LEU B 956 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B 963 " --> pdb=" O ILE B 959 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1097 removed outlier: 3.916A pdb=" N LEU B1096 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B1097 " --> pdb=" O LEU B1094 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 589 removed outlier: 3.893A pdb=" N LEU C 587 " --> pdb=" O TYR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 599 removed outlier: 3.865A pdb=" N ASP C 596 " --> pdb=" O HIS C 592 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 597 " --> pdb=" O GLN C 593 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 629 Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.506A pdb=" N ILE C 635 " --> pdb=" O VAL C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 673 removed outlier: 3.583A pdb=" N GLN C 668 " --> pdb=" O GLU C 664 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 670 " --> pdb=" O LEU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 682 Processing helix chain 'C' and resid 682 through 688 removed outlier: 3.540A pdb=" N ASN C 687 " --> pdb=" O LEU C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 709 removed outlier: 3.833A pdb=" N THR C 705 " --> pdb=" O THR C 701 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 706 " --> pdb=" O GLU C 702 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET C 707 " --> pdb=" O GLN C 703 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 725 removed outlier: 4.048A pdb=" N GLN C 725 " --> pdb=" O THR C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 775 Processing helix chain 'C' and resid 787 through 806 removed outlier: 3.907A pdb=" N THR C 793 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 794 " --> pdb=" O THR C 790 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 795 " --> pdb=" O TYR C 791 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 796 " --> pdb=" O LEU C 792 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL C 798 " --> pdb=" O ARG C 794 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 806 " --> pdb=" O LEU C 802 " (cutoff:3.500A) Processing helix chain 'C' and resid 810 through 824 removed outlier: 4.554A pdb=" N GLN C 816 " --> pdb=" O GLN C 812 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N THR C 821 " --> pdb=" O MET C 817 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 822 " --> pdb=" O LEU C 818 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 842 removed outlier: 4.241A pdb=" N ARG C 834 " --> pdb=" O LEU C 830 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASP C 835 " --> pdb=" O THR C 831 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR C 836 " --> pdb=" O ASP C 832 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLY C 837 " --> pdb=" O THR C 833 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N SER C 838 " --> pdb=" O ARG C 834 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C 841 " --> pdb=" O GLY C 837 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 842 " --> pdb=" O SER C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 856 Processing helix chain 'C' and resid 857 through 882 removed outlier: 3.642A pdb=" N GLU C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA C 863 " --> pdb=" O PRO C 859 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 869 " --> pdb=" O GLN C 865 " (cutoff:3.500A) Proline residue: C 870 - end of helix removed outlier: 4.155A pdb=" N ALA C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 892 removed outlier: 4.077A pdb=" N ALA C 890 " --> pdb=" O GLY C 886 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER C 892 " --> pdb=" O ASN C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 913 removed outlier: 4.074A pdb=" N ALA C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 924 removed outlier: 3.701A pdb=" N LEU C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 947 removed outlier: 3.987A pdb=" N THR C 946 " --> pdb=" O THR C 943 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG C 947 " --> pdb=" O ILE C 944 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 943 through 947' Processing helix chain 'C' and resid 952 through 965 removed outlier: 3.608A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 963 " --> pdb=" O ILE C 959 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1053 removed outlier: 3.952A pdb=" N ARG C1049 " --> pdb=" O TRP C1045 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C1050 " --> pdb=" O GLY C1046 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C1051 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C1052 " --> pdb=" O ILE C1048 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET C1053 " --> pdb=" O ARG C1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1045 through 1053' Processing helix chain 'C' and resid 1089 through 1097 removed outlier: 3.536A pdb=" N LEU C1093 " --> pdb=" O PRO C1090 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C1096 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C1097 " --> pdb=" O LEU C1094 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 599 removed outlier: 3.947A pdb=" N LEU D 587 " --> pdb=" O TYR D 583 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL D 590 " --> pdb=" O MET D 586 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N HIS D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN D 593 " --> pdb=" O ARG D 589 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP D 596 " --> pdb=" O HIS D 592 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET D 597 " --> pdb=" O GLN D 593 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 599 " --> pdb=" O ALA D 595 " (cutoff:3.500A) Processing helix chain 'D' and resid 626 through 629 Processing helix chain 'D' and resid 630 through 640 removed outlier: 3.505A pdb=" N SER D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE D 635 " --> pdb=" O VAL D 631 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL D 638 " --> pdb=" O SER D 634 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN D 640 " --> pdb=" O ASP D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 673 removed outlier: 3.548A pdb=" N GLN D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 670 " --> pdb=" O LEU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 682 Processing helix chain 'D' and resid 682 through 688 Processing helix chain 'D' and resid 696 through 709 removed outlier: 3.667A pdb=" N THR D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 706 " --> pdb=" O GLU D 702 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET D 707 " --> pdb=" O GLN D 703 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) Processing helix chain 'D' and resid 713 through 725 removed outlier: 4.052A pdb=" N GLN D 725 " --> pdb=" O THR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 807 removed outlier: 3.761A pdb=" N THR D 793 " --> pdb=" O GLN D 789 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL D 795 " --> pdb=" O TYR D 791 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL D 798 " --> pdb=" O ARG D 794 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA D 806 " --> pdb=" O LEU D 802 " (cutoff:3.500A) Processing helix chain 'D' and resid 810 through 824 removed outlier: 4.725A pdb=" N GLN D 816 " --> pdb=" O GLN D 812 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR D 821 " --> pdb=" O MET D 817 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL D 822 " --> pdb=" O LEU D 818 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 830 No H-bonds generated for 'chain 'D' and resid 828 through 830' Processing helix chain 'D' and resid 831 through 842 removed outlier: 3.830A pdb=" N ASP D 835 " --> pdb=" O THR D 831 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR D 836 " --> pdb=" O ASP D 832 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLY D 837 " --> pdb=" O THR D 833 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER D 838 " --> pdb=" O ARG D 834 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 841 " --> pdb=" O GLY D 837 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 842 " --> pdb=" O SER D 838 " (cutoff:3.500A) Processing helix chain 'D' and resid 846 through 856 Processing helix chain 'D' and resid 857 through 882 removed outlier: 3.600A pdb=" N ALA D 863 " --> pdb=" O PRO D 859 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR D 869 " --> pdb=" O GLN D 865 " (cutoff:3.500A) Proline residue: D 870 - end of helix removed outlier: 3.592A pdb=" N GLU D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA D 877 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 892 removed outlier: 4.196A pdb=" N ALA D 890 " --> pdb=" O GLY D 886 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER D 892 " --> pdb=" O ASN D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 908 through 913 Processing helix chain 'D' and resid 919 through 924 removed outlier: 3.698A pdb=" N LEU D 924 " --> pdb=" O ILE D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 952 through 966 removed outlier: 3.684A pdb=" N LEU D 956 " --> pdb=" O ASN D 952 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN D 960 " --> pdb=" O LEU D 956 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 961 " --> pdb=" O LYS D 957 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 964 " --> pdb=" O ASN D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1053 removed outlier: 3.681A pdb=" N MET D1053 " --> pdb=" O ARG D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1089 through 1097 removed outlier: 3.964A pdb=" N LEU D1096 " --> pdb=" O LEU D1093 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG D1097 " --> pdb=" O LEU D1094 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 589 removed outlier: 3.927A pdb=" N LEU E 587 " --> pdb=" O TYR E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 590 through 599 removed outlier: 3.932A pdb=" N ASP E 596 " --> pdb=" O HIS E 592 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET E 597 " --> pdb=" O GLN E 593 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 599 " --> pdb=" O ALA E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 630 Processing helix chain 'E' and resid 631 through 637 removed outlier: 3.617A pdb=" N ILE E 635 " --> pdb=" O VAL E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 673 removed outlier: 3.530A pdb=" N GLN E 668 " --> pdb=" O GLU E 664 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 670 " --> pdb=" O LEU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 675 through 682 Processing helix chain 'E' and resid 682 through 688 Processing helix chain 'E' and resid 696 through 709 removed outlier: 3.664A pdb=" N VAL E 700 " --> pdb=" O MET E 696 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR E 705 " --> pdb=" O THR E 701 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU E 706 " --> pdb=" O GLU E 702 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N MET E 707 " --> pdb=" O GLN E 703 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 713 through 725 removed outlier: 4.064A pdb=" N GLN E 725 " --> pdb=" O THR E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 771 through 775 Processing helix chain 'E' and resid 787 through 807 removed outlier: 3.796A pdb=" N THR E 793 " --> pdb=" O GLN E 789 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 794 " --> pdb=" O THR E 790 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL E 795 " --> pdb=" O TYR E 791 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 796 " --> pdb=" O LEU E 792 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL E 798 " --> pdb=" O ARG E 794 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA E 806 " --> pdb=" O LEU E 802 " (cutoff:3.500A) Processing helix chain 'E' and resid 810 through 824 removed outlier: 4.692A pdb=" N GLN E 816 " --> pdb=" O GLN E 812 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR E 821 " --> pdb=" O MET E 817 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL E 822 " --> pdb=" O LEU E 818 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU E 823 " --> pdb=" O ALA E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 842 removed outlier: 4.124A pdb=" N ARG E 834 " --> pdb=" O LEU E 830 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP E 835 " --> pdb=" O THR E 831 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR E 836 " --> pdb=" O ASP E 832 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N GLY E 837 " --> pdb=" O THR E 833 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER E 838 " --> pdb=" O ARG E 834 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 842 " --> pdb=" O SER E 838 " (cutoff:3.500A) Processing helix chain 'E' and resid 846 through 856 Processing helix chain 'E' and resid 857 through 883 removed outlier: 3.570A pdb=" N GLU E 861 " --> pdb=" O VAL E 857 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 863 " --> pdb=" O PRO E 859 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 869 " --> pdb=" O GLN E 865 " (cutoff:3.500A) Proline residue: E 870 - end of helix removed outlier: 4.170A pdb=" N ALA E 877 " --> pdb=" O GLU E 873 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL E 883 " --> pdb=" O TRP E 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 883 through 892 removed outlier: 4.111A pdb=" N ALA E 890 " --> pdb=" O GLY E 886 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER E 892 " --> pdb=" O ASN E 888 " (cutoff:3.500A) Processing helix chain 'E' and resid 908 through 913 Processing helix chain 'E' and resid 919 through 927 removed outlier: 3.608A pdb=" N LEU E 924 " --> pdb=" O ILE E 920 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLN E 925 " --> pdb=" O ALA E 921 " (cutoff:3.500A) Processing helix chain 'E' and resid 952 through 966 removed outlier: 3.594A pdb=" N LEU E 956 " --> pdb=" O ASN E 952 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN E 960 " --> pdb=" O LEU E 956 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 963 " --> pdb=" O ILE E 959 " (cutoff:3.500A) Processing helix chain 'E' and resid 1048 through 1053 removed outlier: 3.565A pdb=" N GLU E1052 " --> pdb=" O ILE E1048 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET E1053 " --> pdb=" O ARG E1049 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1048 through 1053' Processing helix chain 'E' and resid 1091 through 1097 removed outlier: 3.540A pdb=" N LEU E1094 " --> pdb=" O LEU E1091 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU E1096 " --> pdb=" O LEU E1093 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG E1097 " --> pdb=" O LEU E1094 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU F 68 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE F 69 " --> pdb=" O TYR F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'G' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU G 68 " --> pdb=" O ASP G 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 69 " --> pdb=" O TYR G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 79 Processing helix chain 'H' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU H 68 " --> pdb=" O ASP H 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE H 69 " --> pdb=" O TYR H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'I' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU I 68 " --> pdb=" O ASP I 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE I 69 " --> pdb=" O TYR I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 79 Processing helix chain 'J' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU J 68 " --> pdb=" O ASP J 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE J 69 " --> pdb=" O TYR J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'K' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU K 68 " --> pdb=" O ASP K 64 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 69 " --> pdb=" O TYR K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 79 Processing helix chain 'L' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU L 68 " --> pdb=" O ASP L 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE L 69 " --> pdb=" O TYR L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 79 Processing helix chain 'M' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU M 68 " --> pdb=" O ASP M 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE M 69 " --> pdb=" O TYR M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 79 Processing helix chain 'N' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU N 68 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE N 69 " --> pdb=" O TYR N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 73 through 79 Processing helix chain 'O' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU O 68 " --> pdb=" O ASP O 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE O 69 " --> pdb=" O TYR O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 73 through 79 Processing helix chain 'P' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU P 68 " --> pdb=" O ASP P 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE P 69 " --> pdb=" O TYR P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 73 through 79 Processing helix chain 'Q' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU Q 68 " --> pdb=" O ASP Q 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE Q 69 " --> pdb=" O TYR Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 73 through 79 Processing helix chain 'R' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU R 68 " --> pdb=" O ASP R 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 79 Processing helix chain 'S' and resid 64 through 70 removed outlier: 3.760A pdb=" N LEU S 68 " --> pdb=" O ASP S 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE S 69 " --> pdb=" O TYR S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 73 through 79 Processing helix chain 'T' and resid 64 through 70 removed outlier: 3.761A pdb=" N LEU T 68 " --> pdb=" O ASP T 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE T 69 " --> pdb=" O TYR T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 73 through 79 Processing helix chain 'a' and resid 570 through 577 Processing helix chain 'a' and resid 577 through 594 removed outlier: 5.794A pdb=" N TYR a 583 " --> pdb=" O ASP a 579 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN a 584 " --> pdb=" O ALA a 580 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 603 removed outlier: 3.698A pdb=" N MET a 602 " --> pdb=" O ARG a 598 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR a 603 " --> pdb=" O LEU a 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 598 through 603' Processing helix chain 'a' and resid 625 through 630 removed outlier: 3.862A pdb=" N GLU a 629 " --> pdb=" O ALA a 626 " (cutoff:3.500A) Processing helix chain 'a' and resid 634 through 643 removed outlier: 3.599A pdb=" N ILE a 639 " --> pdb=" O ILE a 635 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN a 640 " --> pdb=" O ASP a 636 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU a 641 " --> pdb=" O THR a 637 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG a 642 " --> pdb=" O VAL a 638 " (cutoff:3.500A) Processing helix chain 'a' and resid 666 through 687 removed outlier: 3.860A pdb=" N ARG a 673 " --> pdb=" O ARG a 669 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY a 679 " --> pdb=" O PHE a 675 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN a 680 " --> pdb=" O ALA a 676 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN a 684 " --> pdb=" O ASN a 680 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE a 685 " --> pdb=" O ALA a 681 " (cutoff:3.500A) Processing helix chain 'a' and resid 699 through 704 removed outlier: 4.266A pdb=" N GLN a 703 " --> pdb=" O ASP a 699 " (cutoff:3.500A) Processing helix chain 'a' and resid 715 through 728 removed outlier: 3.603A pdb=" N ARG a 727 " --> pdb=" O ALA a 723 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR a 728 " --> pdb=" O VAL a 724 " (cutoff:3.500A) Processing helix chain 'a' and resid 765 through 770 removed outlier: 4.079A pdb=" N PHE a 769 " --> pdb=" O LEU a 765 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY a 770 " --> pdb=" O ALA a 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 765 through 770' Processing helix chain 'a' and resid 784 through 804 removed outlier: 4.636A pdb=" N LEU a 788 " --> pdb=" O ASP a 784 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR a 793 " --> pdb=" O GLN a 789 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG a 801 " --> pdb=" O GLN a 797 " (cutoff:3.500A) Processing helix chain 'a' and resid 810 through 824 removed outlier: 3.881A pdb=" N MET a 814 " --> pdb=" O ASP a 810 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET a 817 " --> pdb=" O ALA a 813 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU a 823 " --> pdb=" O ALA a 819 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN a 824 " --> pdb=" O GLN a 820 " (cutoff:3.500A) Processing helix chain 'a' and resid 828 through 843 removed outlier: 3.756A pdb=" N ASP a 832 " --> pdb=" O VAL a 828 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR a 833 " --> pdb=" O ASP a 829 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG a 834 " --> pdb=" O LEU a 830 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU a 839 " --> pdb=" O ASP a 835 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR a 840 " --> pdb=" O TYR a 836 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA a 841 " --> pdb=" O GLY a 837 " (cutoff:3.500A) Processing helix chain 'a' and resid 848 through 853 Processing helix chain 'a' and resid 857 through 865 removed outlier: 3.623A pdb=" N GLU a 861 " --> pdb=" O VAL a 857 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN a 862 " --> pdb=" O ARG a 858 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA a 863 " --> pdb=" O PRO a 859 " (cutoff:3.500A) Processing helix chain 'a' and resid 867 through 883 removed outlier: 3.538A pdb=" N ALA a 871 " --> pdb=" O VAL a 867 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU a 875 " --> pdb=" O ALA a 871 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN a 876 " --> pdb=" O ALA a 872 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA a 877 " --> pdb=" O GLU a 873 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N THR a 881 " --> pdb=" O ALA a 877 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL a 883 " --> pdb=" O TRP a 879 " (cutoff:3.500A) Processing helix chain 'a' and resid 883 through 890 removed outlier: 3.741A pdb=" N ALA a 890 " --> pdb=" O GLY a 886 " (cutoff:3.500A) Processing helix chain 'a' and resid 894 through 898 removed outlier: 4.055A pdb=" N PHE a 897 " --> pdb=" O ARG a 894 " (cutoff:3.500A) Processing helix chain 'a' and resid 905 through 910 removed outlier: 3.861A pdb=" N LEU a 909 " --> pdb=" O SER a 905 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA a 910 " --> pdb=" O LEU a 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 905 through 910' Processing helix chain 'a' and resid 952 through 967 removed outlier: 3.744A pdb=" N LEU a 956 " --> pdb=" O ASN a 952 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN a 960 " --> pdb=" O LEU a 956 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU a 962 " --> pdb=" O ALA a 958 " (cutoff:3.500A) Processing helix chain 'a' and resid 1046 through 1051 removed outlier: 3.690A pdb=" N LEU a1050 " --> pdb=" O GLY a1046 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU a1051 " --> pdb=" O LEU a1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1046 through 1051' Processing helix chain 'a' and resid 1052 through 1055 removed outlier: 4.057A pdb=" N ARG a1055 " --> pdb=" O GLU a1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 1052 through 1055' Processing helix chain 'a' and resid 1072 through 1076 removed outlier: 4.145A pdb=" N GLY a1075 " --> pdb=" O ALA a1072 " (cutoff:3.500A) Processing helix chain 'a' and resid 1088 through 1097 removed outlier: 3.695A pdb=" N LEU a1091 " --> pdb=" O GLU a1088 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL a1092 " --> pdb=" O GLY a1089 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU a1093 " --> pdb=" O PRO a1090 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU a1096 " --> pdb=" O LEU a1093 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG a1097 " --> pdb=" O LEU a1094 " (cutoff:3.500A) Processing helix chain 'a' and resid 1117 through 1129 removed outlier: 4.598A pdb=" N ASP a1123 " --> pdb=" O GLU a1119 " (cutoff:3.500A) Processing helix chain 'b' and resid 570 through 577 Processing helix chain 'b' and resid 577 through 594 removed outlier: 5.800A pdb=" N TYR b 583 " --> pdb=" O ASP b 579 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLN b 584 " --> pdb=" O ALA b 580 " (cutoff:3.500A) Processing helix chain 'b' and resid 598 through 603 removed outlier: 3.620A pdb=" N MET b 602 " --> pdb=" O ARG b 598 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR b 603 " --> pdb=" O LEU b 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 598 through 603' Processing helix chain 'b' and resid 634 through 643 removed outlier: 3.524A pdb=" N ILE b 639 " --> pdb=" O ILE b 635 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASN b 640 " --> pdb=" O ASP b 636 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU b 641 " --> pdb=" O THR b 637 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG b 642 " --> pdb=" O VAL b 638 " (cutoff:3.500A) Processing helix chain 'b' and resid 664 through 687 removed outlier: 4.061A pdb=" N ARG b 669 " --> pdb=" O ALA b 665 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG b 673 " --> pdb=" O ARG b 669 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY b 679 " --> pdb=" O PHE b 675 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN b 680 " --> pdb=" O ALA b 676 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP b 682 " --> pdb=" O PHE b 678 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN b 684 " --> pdb=" O ASN b 680 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE b 685 " --> pdb=" O ALA b 681 " (cutoff:3.500A) Processing helix chain 'b' and resid 699 through 706 removed outlier: 4.168A pdb=" N GLN b 703 " --> pdb=" O ASP b 699 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR b 705 " --> pdb=" O THR b 701 " (cutoff:3.500A) Processing helix chain 'b' and resid 715 through 728 removed outlier: 3.637A pdb=" N THR b 728 " --> pdb=" O VAL b 724 " (cutoff:3.500A) Processing helix chain 'b' and resid 784 through 804 removed outlier: 4.576A pdb=" N LEU b 788 " --> pdb=" O ASP b 784 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR b 796 " --> pdb=" O LEU b 792 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG b 801 " --> pdb=" O GLN b 797 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN b 804 " --> pdb=" O LEU b 800 " (cutoff:3.500A) Processing helix chain 'b' and resid 810 through 824 removed outlier: 4.039A pdb=" N MET b 814 " --> pdb=" O ASP b 810 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR b 821 " --> pdb=" O MET b 817 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL b 822 " --> pdb=" O LEU b 818 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU b 823 " --> pdb=" O ALA b 819 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN b 824 " --> pdb=" O GLN b 820 " (cutoff:3.500A) Processing helix chain 'b' and resid 828 through 840 removed outlier: 3.662A pdb=" N ASP b 832 " --> pdb=" O VAL b 828 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR b 833 " --> pdb=" O ASP b 829 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG b 834 " --> pdb=" O LEU b 830 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP b 835 " --> pdb=" O THR b 831 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER b 838 " --> pdb=" O ARG b 834 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU b 839 " --> pdb=" O ASP b 835 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR b 840 " --> pdb=" O TYR b 836 " (cutoff:3.500A) Processing helix chain 'b' and resid 848 through 853 Processing helix chain 'b' and resid 857 through 865 removed outlier: 3.613A pdb=" N GLU b 861 " --> pdb=" O VAL b 857 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN b 862 " --> pdb=" O ARG b 858 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA b 863 " --> pdb=" O PRO b 859 " (cutoff:3.500A) Processing helix chain 'b' and resid 867 through 883 removed outlier: 4.066A pdb=" N ASN b 876 " --> pdb=" O ALA b 872 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA b 877 " --> pdb=" O GLU b 873 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N THR b 881 " --> pdb=" O ALA b 877 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL b 883 " --> pdb=" O TRP b 879 " (cutoff:3.500A) Processing helix chain 'b' and resid 883 through 891 removed outlier: 4.491A pdb=" N ASN b 889 " --> pdb=" O ASP b 885 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE b 891 " --> pdb=" O TRP b 887 " (cutoff:3.500A) Processing helix chain 'b' and resid 894 through 898 removed outlier: 4.119A pdb=" N PHE b 897 " --> pdb=" O ARG b 894 " (cutoff:3.500A) Processing helix chain 'b' and resid 905 through 910 removed outlier: 3.733A pdb=" N LEU b 909 " --> pdb=" O SER b 905 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA b 910 " --> pdb=" O LEU b 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 905 through 910' Processing helix chain 'b' and resid 952 through 967 removed outlier: 3.759A pdb=" N LEU b 956 " --> pdb=" O ASN b 952 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU b 962 " --> pdb=" O ALA b 958 " (cutoff:3.500A) Processing helix chain 'b' and resid 1046 through 1051 removed outlier: 3.772A pdb=" N LEU b1050 " --> pdb=" O GLY b1046 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU b1051 " --> pdb=" O LEU b1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1046 through 1051' Processing helix chain 'b' and resid 1052 through 1055 removed outlier: 4.264A pdb=" N ARG b1055 " --> pdb=" O GLU b1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 1052 through 1055' Processing helix chain 'b' and resid 1072 through 1076 removed outlier: 4.313A pdb=" N GLY b1075 " --> pdb=" O ALA b1072 " (cutoff:3.500A) Processing helix chain 'b' and resid 1088 through 1097 removed outlier: 3.511A pdb=" N LEU b1091 " --> pdb=" O GLU b1088 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL b1092 " --> pdb=" O GLY b1089 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU b1093 " --> pdb=" O PRO b1090 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU b1096 " --> pdb=" O LEU b1093 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG b1097 " --> pdb=" O LEU b1094 " (cutoff:3.500A) Processing helix chain 'b' and resid 1117 through 1129 removed outlier: 4.659A pdb=" N ASP b1123 " --> pdb=" O GLU b1119 " (cutoff:3.500A) Processing helix chain 'c' and resid 570 through 577 Processing helix chain 'c' and resid 577 through 594 removed outlier: 5.890A pdb=" N TYR c 583 " --> pdb=" O ASP c 579 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN c 584 " --> pdb=" O ALA c 580 " (cutoff:3.500A) Processing helix chain 'c' and resid 598 through 603 removed outlier: 3.611A pdb=" N MET c 602 " --> pdb=" O ARG c 598 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR c 603 " --> pdb=" O LEU c 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 598 through 603' Processing helix chain 'c' and resid 634 through 643 removed outlier: 3.887A pdb=" N ASN c 640 " --> pdb=" O ASP c 636 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU c 641 " --> pdb=" O THR c 637 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG c 642 " --> pdb=" O VAL c 638 " (cutoff:3.500A) Processing helix chain 'c' and resid 664 through 687 removed outlier: 3.853A pdb=" N ARG c 669 " --> pdb=" O ALA c 665 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG c 673 " --> pdb=" O ARG c 669 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY c 679 " --> pdb=" O PHE c 675 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN c 680 " --> pdb=" O ALA c 676 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN c 684 " --> pdb=" O ASN c 680 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE c 685 " --> pdb=" O ALA c 681 " (cutoff:3.500A) Processing helix chain 'c' and resid 699 through 706 removed outlier: 4.206A pdb=" N GLN c 703 " --> pdb=" O ASP c 699 " (cutoff:3.500A) Processing helix chain 'c' and resid 715 through 728 removed outlier: 3.619A pdb=" N THR c 728 " --> pdb=" O VAL c 724 " (cutoff:3.500A) Processing helix chain 'c' and resid 765 through 770 removed outlier: 3.818A pdb=" N PHE c 769 " --> pdb=" O LEU c 765 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY c 770 " --> pdb=" O ALA c 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 765 through 770' Processing helix chain 'c' and resid 784 through 804 removed outlier: 4.587A pdb=" N LEU c 788 " --> pdb=" O ASP c 784 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR c 793 " --> pdb=" O GLN c 789 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG c 801 " --> pdb=" O GLN c 797 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN c 804 " --> pdb=" O LEU c 800 " (cutoff:3.500A) Processing helix chain 'c' and resid 810 through 824 removed outlier: 3.862A pdb=" N MET c 814 " --> pdb=" O ASP c 810 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN c 816 " --> pdb=" O GLN c 812 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET c 817 " --> pdb=" O ALA c 813 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU c 823 " --> pdb=" O ALA c 819 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN c 824 " --> pdb=" O GLN c 820 " (cutoff:3.500A) Processing helix chain 'c' and resid 828 through 843 removed outlier: 3.589A pdb=" N THR c 833 " --> pdb=" O ASP c 829 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG c 834 " --> pdb=" O LEU c 830 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP c 835 " --> pdb=" O THR c 831 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU c 839 " --> pdb=" O ASP c 835 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR c 840 " --> pdb=" O TYR c 836 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA c 841 " --> pdb=" O GLY c 837 " (cutoff:3.500A) Processing helix chain 'c' and resid 848 through 853 Processing helix chain 'c' and resid 857 through 865 removed outlier: 3.573A pdb=" N GLU c 861 " --> pdb=" O VAL c 857 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN c 862 " --> pdb=" O ARG c 858 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA c 863 " --> pdb=" O PRO c 859 " (cutoff:3.500A) Processing helix chain 'c' and resid 867 through 883 removed outlier: 3.543A pdb=" N ALA c 871 " --> pdb=" O VAL c 867 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU c 873 " --> pdb=" O THR c 869 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASN c 876 " --> pdb=" O ALA c 872 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA c 877 " --> pdb=" O GLU c 873 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR c 881 " --> pdb=" O ALA c 877 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL c 883 " --> pdb=" O TRP c 879 " (cutoff:3.500A) Processing helix chain 'c' and resid 883 through 891 removed outlier: 4.437A pdb=" N ASN c 889 " --> pdb=" O ASP c 885 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE c 891 " --> pdb=" O TRP c 887 " (cutoff:3.500A) Processing helix chain 'c' and resid 894 through 898 removed outlier: 4.060A pdb=" N PHE c 897 " --> pdb=" O ARG c 894 " (cutoff:3.500A) Processing helix chain 'c' and resid 905 through 910 removed outlier: 3.825A pdb=" N LEU c 909 " --> pdb=" O SER c 905 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA c 910 " --> pdb=" O LEU c 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 905 through 910' Processing helix chain 'c' and resid 952 through 967 removed outlier: 3.790A pdb=" N LEU c 956 " --> pdb=" O ASN c 952 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU c 962 " --> pdb=" O ALA c 958 " (cutoff:3.500A) Processing helix chain 'c' and resid 1051 through 1055 removed outlier: 4.008A pdb=" N ALA c1054 " --> pdb=" O LEU c1051 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG c1055 " --> pdb=" O GLU c1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 1051 through 1055' Processing helix chain 'c' and resid 1072 through 1076 removed outlier: 4.209A pdb=" N GLY c1075 " --> pdb=" O ALA c1072 " (cutoff:3.500A) Processing helix chain 'c' and resid 1088 through 1096 removed outlier: 3.630A pdb=" N LEU c1091 " --> pdb=" O GLU c1088 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU c1093 " --> pdb=" O PRO c1090 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU c1094 " --> pdb=" O LEU c1091 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU c1096 " --> pdb=" O LEU c1093 " (cutoff:3.500A) Processing helix chain 'c' and resid 1117 through 1129 removed outlier: 4.622A pdb=" N ASP c1123 " --> pdb=" O GLU c1119 " (cutoff:3.500A) Processing helix chain 'd' and resid 572 through 577 Processing helix chain 'd' and resid 577 through 594 removed outlier: 5.951A pdb=" N TYR d 583 " --> pdb=" O ASP d 579 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN d 584 " --> pdb=" O ALA d 580 " (cutoff:3.500A) Processing helix chain 'd' and resid 598 through 603 removed outlier: 3.589A pdb=" N MET d 602 " --> pdb=" O ARG d 598 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR d 603 " --> pdb=" O LEU d 599 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 598 through 603' Processing helix chain 'd' and resid 634 through 643 removed outlier: 3.530A pdb=" N ILE d 639 " --> pdb=" O ILE d 635 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN d 640 " --> pdb=" O ASP d 636 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU d 641 " --> pdb=" O THR d 637 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG d 642 " --> pdb=" O VAL d 638 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG d 643 " --> pdb=" O ILE d 639 " (cutoff:3.500A) Processing helix chain 'd' and resid 666 through 687 removed outlier: 3.804A pdb=" N ARG d 673 " --> pdb=" O ARG d 669 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY d 679 " --> pdb=" O PHE d 675 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN d 680 " --> pdb=" O ALA d 676 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN d 684 " --> pdb=" O ASN d 680 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE d 685 " --> pdb=" O ALA d 681 " (cutoff:3.500A) Processing helix chain 'd' and resid 699 through 704 removed outlier: 4.122A pdb=" N GLN d 703 " --> pdb=" O ASP d 699 " (cutoff:3.500A) Processing helix chain 'd' and resid 715 through 728 removed outlier: 3.623A pdb=" N THR d 728 " --> pdb=" O VAL d 724 " (cutoff:3.500A) Processing helix chain 'd' and resid 765 through 770 removed outlier: 4.079A pdb=" N PHE d 769 " --> pdb=" O LEU d 765 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY d 770 " --> pdb=" O ALA d 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 765 through 770' Processing helix chain 'd' and resid 784 through 804 removed outlier: 4.624A pdb=" N LEU d 788 " --> pdb=" O ASP d 784 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR d 793 " --> pdb=" O GLN d 789 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN d 804 " --> pdb=" O LEU d 800 " (cutoff:3.500A) Processing helix chain 'd' and resid 810 through 824 removed outlier: 4.058A pdb=" N MET d 814 " --> pdb=" O ASP d 810 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU d 823 " --> pdb=" O ALA d 819 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN d 824 " --> pdb=" O GLN d 820 " (cutoff:3.500A) Processing helix chain 'd' and resid 828 through 843 removed outlier: 3.619A pdb=" N ASP d 832 " --> pdb=" O VAL d 828 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR d 833 " --> pdb=" O ASP d 829 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG d 834 " --> pdb=" O LEU d 830 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU d 839 " --> pdb=" O ASP d 835 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR d 840 " --> pdb=" O TYR d 836 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA d 841 " --> pdb=" O GLY d 837 " (cutoff:3.500A) Processing helix chain 'd' and resid 848 through 853 Processing helix chain 'd' and resid 857 through 865 removed outlier: 3.533A pdb=" N GLU d 861 " --> pdb=" O VAL d 857 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN d 862 " --> pdb=" O ARG d 858 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA d 863 " --> pdb=" O PRO d 859 " (cutoff:3.500A) Processing helix chain 'd' and resid 867 through 883 removed outlier: 4.074A pdb=" N ASN d 876 " --> pdb=" O ALA d 872 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA d 877 " --> pdb=" O GLU d 873 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR d 881 " --> pdb=" O ALA d 877 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL d 883 " --> pdb=" O TRP d 879 " (cutoff:3.500A) Processing helix chain 'd' and resid 883 through 891 removed outlier: 3.781A pdb=" N PHE d 891 " --> pdb=" O TRP d 887 " (cutoff:3.500A) Processing helix chain 'd' and resid 905 through 910 removed outlier: 3.832A pdb=" N LEU d 909 " --> pdb=" O SER d 905 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA d 910 " --> pdb=" O LEU d 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 905 through 910' Processing helix chain 'd' and resid 952 through 967 removed outlier: 3.857A pdb=" N LEU d 956 " --> pdb=" O ASN d 952 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA d 958 " --> pdb=" O ALA d 954 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU d 962 " --> pdb=" O ALA d 958 " (cutoff:3.500A) Processing helix chain 'd' and resid 1046 through 1051 removed outlier: 3.649A pdb=" N LEU d1050 " --> pdb=" O GLY d1046 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU d1051 " --> pdb=" O LEU d1047 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1046 through 1051' Processing helix chain 'd' and resid 1052 through 1055 removed outlier: 4.085A pdb=" N ARG d1055 " --> pdb=" O GLU d1052 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 1052 through 1055' Processing helix chain 'd' and resid 1072 through 1076 removed outlier: 4.314A pdb=" N GLY d1075 " --> pdb=" O ALA d1072 " (cutoff:3.500A) Processing helix chain 'd' and resid 1088 through 1097 removed outlier: 3.576A pdb=" N LEU d1091 " --> pdb=" O GLU d1088 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL d1092 " --> pdb=" O GLY d1089 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU d1093 " --> pdb=" O PRO d1090 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU d1096 " --> pdb=" O LEU d1093 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG d1097 " --> pdb=" O LEU d1094 " (cutoff:3.500A) Processing helix chain 'd' and resid 1117 through 1127 removed outlier: 4.688A pdb=" N ASP d1123 " --> pdb=" O GLU d1119 " (cutoff:3.500A) Processing helix chain 'e' and resid 570 through 577 Processing helix chain 'e' and resid 577 through 594 removed outlier: 5.964A pdb=" N TYR e 583 " --> pdb=" O ASP e 579 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN e 584 " --> pdb=" O ALA e 580 " (cutoff:3.500A) Processing helix chain 'e' and resid 598 through 603 removed outlier: 3.756A pdb=" N THR e 603 " --> pdb=" O LEU e 599 " (cutoff:3.500A) Processing helix chain 'e' and resid 625 through 630 removed outlier: 3.809A pdb=" N GLU e 629 " --> pdb=" O ALA e 626 " (cutoff:3.500A) Processing helix chain 'e' and resid 634 through 643 removed outlier: 3.670A pdb=" N ILE e 639 " --> pdb=" O ILE e 635 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN e 640 " --> pdb=" O ASP e 636 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU e 641 " --> pdb=" O THR e 637 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG e 642 " --> pdb=" O VAL e 638 " (cutoff:3.500A) Processing helix chain 'e' and resid 664 through 687 removed outlier: 3.997A pdb=" N ARG e 669 " --> pdb=" O ALA e 665 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG e 673 " --> pdb=" O ARG e 669 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY e 679 " --> pdb=" O PHE e 675 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN e 680 " --> pdb=" O ALA e 676 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN e 684 " --> pdb=" O ASN e 680 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE e 685 " --> pdb=" O ALA e 681 " (cutoff:3.500A) Processing helix chain 'e' and resid 699 through 704 removed outlier: 4.256A pdb=" N GLN e 703 " --> pdb=" O ASP e 699 " (cutoff:3.500A) Processing helix chain 'e' and resid 715 through 728 removed outlier: 3.610A pdb=" N THR e 728 " --> pdb=" O VAL e 724 " (cutoff:3.500A) Processing helix chain 'e' and resid 765 through 770 removed outlier: 3.644A pdb=" N PHE e 769 " --> pdb=" O LEU e 765 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY e 770 " --> pdb=" O ALA e 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 765 through 770' Processing helix chain 'e' and resid 784 through 804 removed outlier: 4.413A pdb=" N LEU e 788 " --> pdb=" O ASP e 784 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR e 793 " --> pdb=" O GLN e 789 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN e 804 " --> pdb=" O LEU e 800 " (cutoff:3.500A) Processing helix chain 'e' and resid 811 through 824 removed outlier: 3.892A pdb=" N MET e 817 " --> pdb=" O ALA e 813 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU e 823 " --> pdb=" O ALA e 819 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN e 824 " --> pdb=" O GLN e 820 " (cutoff:3.500A) Processing helix chain 'e' and resid 828 through 840 removed outlier: 3.660A pdb=" N ASP e 832 " --> pdb=" O VAL e 828 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR e 833 " --> pdb=" O ASP e 829 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG e 834 " --> pdb=" O LEU e 830 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP e 835 " --> pdb=" O THR e 831 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER e 838 " --> pdb=" O ARG e 834 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU e 839 " --> pdb=" O ASP e 835 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR e 840 " --> pdb=" O TYR e 836 " (cutoff:3.500A) Processing helix chain 'e' and resid 848 through 853 Processing helix chain 'e' and resid 857 through 865 removed outlier: 3.704A pdb=" N GLU e 861 " --> pdb=" O VAL e 857 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN e 862 " --> pdb=" O ARG e 858 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N ALA e 863 " --> pdb=" O PRO e 859 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 883 removed outlier: 3.935A pdb=" N ALA e 871 " --> pdb=" O VAL e 867 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN e 876 " --> pdb=" O ALA e 872 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA e 877 " --> pdb=" O GLU e 873 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR e 881 " --> pdb=" O ALA e 877 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL e 883 " --> pdb=" O TRP e 879 " (cutoff:3.500A) Processing helix chain 'e' and resid 883 through 891 removed outlier: 3.994A pdb=" N ALA e 890 " --> pdb=" O GLY e 886 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE e 891 " --> pdb=" O TRP e 887 " (cutoff:3.500A) Processing helix chain 'e' and resid 894 through 898 removed outlier: 4.009A pdb=" N PHE e 897 " --> pdb=" O ARG e 894 " (cutoff:3.500A) Processing helix chain 'e' and resid 905 through 910 removed outlier: 3.716A pdb=" N LEU e 909 " --> pdb=" O SER e 905 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA e 910 " --> pdb=" O LEU e 906 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 905 through 910' Processing helix chain 'e' and resid 952 through 967 removed outlier: 3.826A pdb=" N LEU e 956 " --> pdb=" O ASN e 952 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA e 958 " --> pdb=" O ALA e 954 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU e 962 " --> pdb=" O ALA e 958 " (cutoff:3.500A) Processing helix chain 'e' and resid 1046 through 1051 removed outlier: 3.521A pdb=" N LEU e1051 " --> pdb=" O LEU e1047 " (cutoff:3.500A) Processing helix chain 'e' and resid 1072 through 1076 removed outlier: 4.262A pdb=" N GLY e1075 " --> pdb=" O ALA e1072 " (cutoff:3.500A) Processing helix chain 'e' and resid 1088 through 1097 removed outlier: 3.574A pdb=" N LEU e1091 " --> pdb=" O GLU e1088 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL e1092 " --> pdb=" O GLY e1089 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU e1093 " --> pdb=" O PRO e1090 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU e1096 " --> pdb=" O LEU e1093 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG e1097 " --> pdb=" O LEU e1094 " (cutoff:3.500A) Processing helix chain 'e' and resid 1117 through 1127 removed outlier: 4.621A pdb=" N ASP e1123 " --> pdb=" O GLU e1119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1011 through 1012 removed outlier: 3.830A pdb=" N TYR A1080 " --> pdb=" O LEU A1068 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY A1065 " --> pdb=" O ALA A1059 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1024 through 1029 removed outlier: 7.344A pdb=" N ALA A1024 " --> pdb=" O ASP A1040 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASP A1040 " --> pdb=" O ALA A1024 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A1026 " --> pdb=" O TYR A1038 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A1038 " --> pdb=" O LEU A1026 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1011 through 1012 removed outlier: 6.093A pdb=" N ARG B1076 " --> pdb=" O ALA B1072 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ALA B1072 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP B1070 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR B1080 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B1065 " --> pdb=" O ALA B1059 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER B1067 " --> pdb=" O LYS B1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 1024 through 1025 removed outlier: 4.036A pdb=" N ALA B1024 " --> pdb=" O LEU B1041 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B1041 " --> pdb=" O ALA B1024 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 1028 through 1029 Processing sheet with id=AA6, first strand: chain 'C' and resid 1011 through 1012 removed outlier: 3.700A pdb=" N TYR C1080 " --> pdb=" O LEU C1068 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C1065 " --> pdb=" O ALA C1059 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 1024 through 1029 removed outlier: 7.397A pdb=" N ALA C1024 " --> pdb=" O ASP C1040 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASP C1040 " --> pdb=" O ALA C1024 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU C1026 " --> pdb=" O TYR C1038 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR C1038 " --> pdb=" O LEU C1026 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1011 through 1012 removed outlier: 3.849A pdb=" N TYR D1080 " --> pdb=" O LEU D1068 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D1065 " --> pdb=" O ALA D1059 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1024 through 1029 removed outlier: 7.291A pdb=" N ALA D1024 " --> pdb=" O ASP D1040 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASP D1040 " --> pdb=" O ALA D1024 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU D1026 " --> pdb=" O TYR D1038 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR D1038 " --> pdb=" O LEU D1026 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 1011 through 1012 removed outlier: 3.508A pdb=" N LYS E1011 " --> pdb=" O LEU E 981 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU E 981 " --> pdb=" O LYS E1011 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR E1080 " --> pdb=" O LEU E1068 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY E1065 " --> pdb=" O ALA E1059 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E1059 " --> pdb=" O GLY E1065 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 1024 through 1029 removed outlier: 7.384A pdb=" N ALA E1024 " --> pdb=" O ASP E1040 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP E1040 " --> pdb=" O ALA E1024 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU E1026 " --> pdb=" O TYR E1038 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR E1038 " --> pdb=" O LEU E1026 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL F 94 " --> pdb=" O ILE F 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE F 30 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY F 144 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA F 35 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU F 139 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN F 53 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN F 83 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE F 51 " --> pdb=" O GLN F 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP F 85 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL F 49 " --> pdb=" O ASP F 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP F 87 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL F 47 " --> pdb=" O TRP F 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL G 94 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE G 30 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY G 144 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA G 35 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU G 139 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN G 53 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN G 83 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE G 51 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP G 85 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 49 " --> pdb=" O ASP G 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP G 87 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL G 47 " --> pdb=" O TRP G 87 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL H 94 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE H 30 " --> pdb=" O VAL H 94 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N GLY H 144 " --> pdb=" O ARG H 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA H 35 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU H 139 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN H 53 " --> pdb=" O ILE H 81 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN H 83 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE H 51 " --> pdb=" O GLN H 83 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP H 85 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL H 49 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP H 87 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL H 47 " --> pdb=" O TRP H 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL I 94 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE I 30 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY I 144 " --> pdb=" O ARG I 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA I 35 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU I 139 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN I 53 " --> pdb=" O ILE I 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN I 83 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE I 51 " --> pdb=" O GLN I 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP I 85 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL I 49 " --> pdb=" O ASP I 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP I 87 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL I 47 " --> pdb=" O TRP I 87 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 94 through 99 removed outlier: 3.665A pdb=" N VAL J 94 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J 30 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY J 144 " --> pdb=" O ARG J 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA J 35 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU J 139 " --> pdb=" O LEU J 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN J 53 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN J 83 " --> pdb=" O ILE J 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE J 51 " --> pdb=" O GLN J 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP J 85 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL J 49 " --> pdb=" O ASP J 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP J 87 " --> pdb=" O VAL J 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL J 47 " --> pdb=" O TRP J 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL K 94 " --> pdb=" O ILE K 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE K 30 " --> pdb=" O VAL K 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY K 144 " --> pdb=" O ARG K 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA K 35 " --> pdb=" O GLY K 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU K 139 " --> pdb=" O LEU K 150 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN K 53 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN K 83 " --> pdb=" O ILE K 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE K 51 " --> pdb=" O GLN K 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP K 85 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL K 49 " --> pdb=" O ASP K 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP K 87 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL K 47 " --> pdb=" O TRP K 87 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL L 94 " --> pdb=" O ILE L 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE L 30 " --> pdb=" O VAL L 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY L 144 " --> pdb=" O ARG L 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA L 35 " --> pdb=" O GLY L 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU L 139 " --> pdb=" O LEU L 150 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN L 53 " --> pdb=" O ILE L 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN L 83 " --> pdb=" O ILE L 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE L 51 " --> pdb=" O GLN L 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP L 85 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 49 " --> pdb=" O ASP L 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP L 87 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL L 47 " --> pdb=" O TRP L 87 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL M 94 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE M 30 " --> pdb=" O VAL M 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY M 144 " --> pdb=" O ARG M 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA M 35 " --> pdb=" O GLY M 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU M 139 " --> pdb=" O LEU M 150 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN M 53 " --> pdb=" O ILE M 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN M 83 " --> pdb=" O ILE M 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE M 51 " --> pdb=" O GLN M 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP M 85 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 49 " --> pdb=" O ASP M 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP M 87 " --> pdb=" O VAL M 47 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL M 47 " --> pdb=" O TRP M 87 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL N 94 " --> pdb=" O ILE N 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE N 30 " --> pdb=" O VAL N 94 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLY N 144 " --> pdb=" O ARG N 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA N 35 " --> pdb=" O GLY N 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU N 139 " --> pdb=" O LEU N 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN N 53 " --> pdb=" O ILE N 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN N 83 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE N 51 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP N 85 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL N 49 " --> pdb=" O ASP N 85 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP N 87 " --> pdb=" O VAL N 47 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N VAL N 47 " --> pdb=" O TRP N 87 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL O 94 " --> pdb=" O ILE O 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE O 30 " --> pdb=" O VAL O 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY O 144 " --> pdb=" O ARG O 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA O 35 " --> pdb=" O GLY O 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU O 139 " --> pdb=" O LEU O 150 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN O 53 " --> pdb=" O ILE O 81 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLN O 83 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE O 51 " --> pdb=" O GLN O 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP O 85 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL O 49 " --> pdb=" O ASP O 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP O 87 " --> pdb=" O VAL O 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL O 47 " --> pdb=" O TRP O 87 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL P 94 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE P 30 " --> pdb=" O VAL P 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY P 144 " --> pdb=" O ARG P 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA P 35 " --> pdb=" O GLY P 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU P 139 " --> pdb=" O LEU P 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN P 53 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN P 83 " --> pdb=" O ILE P 51 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE P 51 " --> pdb=" O GLN P 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP P 85 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL P 49 " --> pdb=" O ASP P 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP P 87 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL P 47 " --> pdb=" O TRP P 87 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL Q 94 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE Q 30 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY Q 144 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA Q 35 " --> pdb=" O GLY Q 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU Q 139 " --> pdb=" O LEU Q 150 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN Q 53 " --> pdb=" O ILE Q 81 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN Q 83 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE Q 51 " --> pdb=" O GLN Q 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP Q 85 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL Q 49 " --> pdb=" O ASP Q 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP Q 87 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL Q 47 " --> pdb=" O TRP Q 87 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL R 94 " --> pdb=" O ILE R 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE R 30 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY R 144 " --> pdb=" O ARG R 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA R 35 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU R 139 " --> pdb=" O LEU R 150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN R 53 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN R 83 " --> pdb=" O ILE R 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE R 51 " --> pdb=" O GLN R 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP R 85 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL R 49 " --> pdb=" O ASP R 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP R 87 " --> pdb=" O VAL R 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL R 47 " --> pdb=" O TRP R 87 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 94 through 99 removed outlier: 3.664A pdb=" N VAL S 94 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE S 30 " --> pdb=" O VAL S 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY S 144 " --> pdb=" O ARG S 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA S 35 " --> pdb=" O GLY S 144 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LEU S 139 " --> pdb=" O LEU S 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 80 through 88 removed outlier: 6.795A pdb=" N GLN S 53 " --> pdb=" O ILE S 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN S 83 " --> pdb=" O ILE S 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE S 51 " --> pdb=" O GLN S 83 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASP S 85 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL S 49 " --> pdb=" O ASP S 85 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N TRP S 87 " --> pdb=" O VAL S 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL S 47 " --> pdb=" O TRP S 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 94 through 99 removed outlier: 3.663A pdb=" N VAL T 94 " --> pdb=" O ILE T 30 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE T 30 " --> pdb=" O VAL T 94 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY T 144 " --> pdb=" O ARG T 33 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ALA T 35 " --> pdb=" O GLY T 144 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU T 139 " --> pdb=" O LEU T 150 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'T' and resid 80 through 88 removed outlier: 6.794A pdb=" N GLN T 53 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN T 83 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE T 51 " --> pdb=" O GLN T 83 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP T 85 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL T 49 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TRP T 87 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL T 47 " --> pdb=" O TRP T 87 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 933 through 935 removed outlier: 3.921A pdb=" N HIS a 933 " --> pdb=" O VAL a 940 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL a 940 " --> pdb=" O HIS a 933 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU a 935 " --> pdb=" O ARG a 938 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'a' and resid 978 through 980 Processing sheet with id=AE8, first strand: chain 'a' and resid 999 through 1001 removed outlier: 3.793A pdb=" N THR a 996 " --> pdb=" O GLN a 999 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLN a 991 " --> pdb=" O VAL a1029 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA a1024 " --> pdb=" O ASP a1040 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP a1040 " --> pdb=" O ALA a1024 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU a1026 " --> pdb=" O TYR a1038 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TRP a1028 " --> pdb=" O ARG a1036 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'a' and resid 1066 through 1068 Processing sheet with id=AF1, first strand: chain 'b' and resid 933 through 935 removed outlier: 3.970A pdb=" N HIS b 933 " --> pdb=" O VAL b 940 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL b 940 " --> pdb=" O HIS b 933 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU b 935 " --> pdb=" O ARG b 938 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'b' and resid 978 through 981 removed outlier: 3.634A pdb=" N LYS b1011 " --> pdb=" O LEU b 981 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 999 through 1001 removed outlier: 4.084A pdb=" N THR b 996 " --> pdb=" O GLN b 999 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN b 991 " --> pdb=" O VAL b1029 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA b1024 " --> pdb=" O ASP b1040 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP b1040 " --> pdb=" O ALA b1024 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU b1026 " --> pdb=" O TYR b1038 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP b1028 " --> pdb=" O ARG b1036 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 1066 through 1068 Processing sheet with id=AF5, first strand: chain 'c' and resid 933 through 935 removed outlier: 3.868A pdb=" N HIS c 933 " --> pdb=" O VAL c 940 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL c 940 " --> pdb=" O HIS c 933 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU c 935 " --> pdb=" O ARG c 938 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'c' and resid 978 through 980 Processing sheet with id=AF7, first strand: chain 'c' and resid 999 through 1003 removed outlier: 3.773A pdb=" N THR c 996 " --> pdb=" O GLN c 999 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN c 991 " --> pdb=" O VAL c1029 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TRP c1028 " --> pdb=" O ARG c1036 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG c1036 " --> pdb=" O TRP c1028 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 999 through 1003 removed outlier: 3.773A pdb=" N THR c 996 " --> pdb=" O GLN c 999 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLN c 991 " --> pdb=" O VAL c1029 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'c' and resid 1066 through 1068 Processing sheet with id=AG1, first strand: chain 'd' and resid 933 through 935 removed outlier: 4.086A pdb=" N HIS d 933 " --> pdb=" O VAL d 940 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL d 940 " --> pdb=" O HIS d 933 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU d 935 " --> pdb=" O ARG d 938 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 978 through 980 removed outlier: 3.556A pdb=" N PHE d 979 " --> pdb=" O PHE d1013 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'd' and resid 999 through 1003 removed outlier: 3.834A pdb=" N THR d 996 " --> pdb=" O GLN d 999 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN d 991 " --> pdb=" O VAL d1029 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TRP d1028 " --> pdb=" O ARG d1036 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG d1036 " --> pdb=" O TRP d1028 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'd' and resid 999 through 1003 removed outlier: 3.834A pdb=" N THR d 996 " --> pdb=" O GLN d 999 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN d 991 " --> pdb=" O VAL d1029 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 1066 through 1068 Processing sheet with id=AG6, first strand: chain 'e' and resid 933 through 935 removed outlier: 3.928A pdb=" N HIS e 933 " --> pdb=" O VAL e 940 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL e 940 " --> pdb=" O HIS e 933 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU e 935 " --> pdb=" O ARG e 938 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 978 through 981 removed outlier: 3.647A pdb=" N LYS e1011 " --> pdb=" O LEU e 981 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'e' and resid 985 through 986 removed outlier: 4.107A pdb=" N THR e 985 " --> pdb=" O ASN e1079 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN e1079 " --> pdb=" O THR e 985 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 999 through 1001 removed outlier: 3.920A pdb=" N THR e 996 " --> pdb=" O GLN e 999 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN e 991 " --> pdb=" O VAL e1029 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA e1024 " --> pdb=" O ASP e1040 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP e1040 " --> pdb=" O ALA e1024 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU e1026 " --> pdb=" O TYR e1038 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP e1028 " --> pdb=" O ARG e1036 " (cutoff:3.500A) 1643 hydrogen bonds defined for protein. 4527 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: 20.09 Time building geometry restraints manager: 11.17 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: 17193 1.34 - 1.45: 8019 1.45 - 1.57: 28346 1.57 - 1.69: 2 1.69 - 1.81: 340 Bond restraints: 53900 Sorted by residual: bond pdb=" CA TRP a 848 " pdb=" C TRP a 848 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.48e-02 4.57e+03 8.41e+00 bond pdb=" C LEU e 981 " pdb=" N ARG e 982 " ideal model delta sigma weight residual 1.335 1.256 0.078 3.04e-02 1.08e+03 6.62e+00 bond pdb=" N ARG e 982 " pdb=" CA ARG e 982 " ideal model delta sigma weight residual 1.453 1.416 0.037 1.79e-02 3.12e+03 4.21e+00 bond pdb=" CA TRP d 848 " pdb=" C TRP d 848 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.48e-02 4.57e+03 4.20e+00 bond pdb=" C TYR c 895 " pdb=" N PRO c 896 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.06e+00 ... (remaining 53895 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 71891 2.90 - 5.79: 1290 5.79 - 8.69: 195 8.69 - 11.59: 29 11.59 - 14.48: 15 Bond angle restraints: 73420 Sorted by residual: angle pdb=" C GLU e1103 " pdb=" N THR e1104 " pdb=" CA THR e1104 " ideal model delta sigma weight residual 121.31 129.37 -8.06 1.49e+00 4.50e-01 2.92e+01 angle pdb=" N THR e1104 " pdb=" CA THR e1104 " pdb=" C THR e1104 " ideal model delta sigma weight residual 110.35 117.56 -7.21 1.40e+00 5.10e-01 2.65e+01 angle pdb=" CA THR d 614 " pdb=" CB THR d 614 " pdb=" CG2 THR d 614 " ideal model delta sigma weight residual 110.50 118.11 -7.61 1.70e+00 3.46e-01 2.00e+01 angle pdb=" C PHE c 622 " pdb=" N THR c 623 " pdb=" CA THR c 623 " ideal model delta sigma weight residual 121.54 129.96 -8.42 1.91e+00 2.74e-01 1.94e+01 angle pdb=" C PHE e 622 " pdb=" N THR e 623 " pdb=" CA THR e 623 " ideal model delta sigma weight residual 121.54 129.89 -8.35 1.91e+00 2.74e-01 1.91e+01 ... (remaining 73415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 28829 17.56 - 35.11: 2772 35.11 - 52.67: 483 52.67 - 70.22: 79 70.22 - 87.78: 57 Dihedral angle restraints: 32220 sinusoidal: 12400 harmonic: 19820 Sorted by residual: dihedral pdb=" CA ARG b 982 " pdb=" C ARG b 982 " pdb=" N PRO b 983 " pdb=" CA PRO b 983 " ideal model delta harmonic sigma weight residual 180.00 138.41 41.59 0 5.00e+00 4.00e-02 6.92e+01 dihedral pdb=" CA LEU b 632 " pdb=" C LEU b 632 " pdb=" N PRO b 633 " pdb=" CA PRO b 633 " ideal model delta harmonic sigma weight residual 180.00 139.97 40.03 0 5.00e+00 4.00e-02 6.41e+01 dihedral pdb=" CA LEU c 632 " pdb=" C LEU c 632 " pdb=" N PRO c 633 " pdb=" CA PRO c 633 " ideal model delta harmonic sigma weight residual 180.00 141.55 38.45 0 5.00e+00 4.00e-02 5.91e+01 ... (remaining 32217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 6668 0.062 - 0.124: 1554 0.124 - 0.186: 250 0.186 - 0.248: 27 0.248 - 0.310: 6 Chirality restraints: 8505 Sorted by residual: chirality pdb=" CB ILE b 805 " pdb=" CA ILE b 805 " pdb=" CG1 ILE b 805 " pdb=" CG2 ILE b 805 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE a 805 " pdb=" CA ILE a 805 " pdb=" CG1 ILE a 805 " pdb=" CG2 ILE a 805 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB ILE e 805 " pdb=" CA ILE e 805 " pdb=" CG1 ILE e 805 " pdb=" CG2 ILE e 805 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 8502 not shown) Planarity restraints: 9565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG b 858 " -0.057 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO b 859 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO b 859 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO b 859 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG a 858 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO a 859 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO a 859 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO a 859 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG e 858 " 0.057 5.00e-02 4.00e+02 8.57e-02 1.18e+01 pdb=" N PRO e 859 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO e 859 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO e 859 " 0.048 5.00e-02 4.00e+02 ... (remaining 9562 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1867 2.70 - 3.25: 49324 3.25 - 3.80: 81740 3.80 - 4.35: 97456 4.35 - 4.90: 159514 Nonbonded interactions: 389901 Sorted by model distance: nonbonded pdb=" OG1 THR A 992 " pdb=" O LEU A1001 " model vdw 2.156 3.040 nonbonded pdb=" OG1 THR B 992 " pdb=" O LEU B1001 " model vdw 2.205 3.040 nonbonded pdb=" OG1 THR E 992 " pdb=" O LEU E1001 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR D 992 " pdb=" O LEU D1001 " model vdw 2.211 3.040 nonbonded pdb=" OG1 THR C 992 " pdb=" O LEU C1001 " model vdw 2.236 3.040 ... (remaining 389896 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'B' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'C' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'D' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'E' and ((resid 578 through 605 and (name N or name CA or name C or name \ O or name CB )) or resid 606 or (resid 607 through 608 and (name N or name CA or \ name C or name O or name CB )) or resid 609 through 611 or (resid 612 through 6 \ 13 and (name N or name CA or name C or name O or name CB )) or resid 614 or (res \ id 615 through 616 and (name N or name CA or name C or name O or name CB )) or r \ esid 617 through 691 or (resid 692 and (name N or name CA or name C or name O or \ name CB )) or resid 693 through 809 or (resid 810 and (name N or name CA or nam \ e C or name O or name CB )) or resid 811 through 1017 or (resid 1018 and (name N \ or name CA or name C or name O or name CB )) or resid 1019 or (resid 1020 throu \ gh 1021 and (name N or name CA or name C or name O or name CB )) or resid 1022 t \ hrough 1107)) selection = (chain 'a' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'b' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'c' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'd' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) selection = (chain 'e' and ((resid 578 through 603 and (name N or name CA or name C or name \ O or name CB )) or resid 604 through 615 or (resid 616 and (name N or name CA or \ name C or name O or name CB )) or resid 617 through 621 or (resid 622 and (name \ N or name CA or name C or name O or name CB )) or resid 623 through 624 or (res \ id 625 through 626 and (name N or name CA or name C or name O or name CB )) or r \ esid 627 through 642 or resid 663 through 673 or (resid 674 and (name N or name \ CA or name C or name O or name CB )) or resid 675 through 677 or (resid 678 and \ (name N or name CA or name C or name O or name CB )) or resid 679 through 730 or \ resid 763 through 1107)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 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: 0.090 Extract box with map and model: 1.480 Check model and map are aligned: 0.300 Set scattering table: 0.360 Process input model: 89.940 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 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 : 0.006 0.078 53900 Z= 0.386 Angle : 0.998 14.484 73420 Z= 0.542 Chirality : 0.054 0.310 8505 Planarity : 0.006 0.086 9565 Dihedral : 14.594 87.780 19380 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 0.04 % Allowed : 5.14 % Favored : 94.83 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.97 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.02 (0.08), residues: 6815 helix: -4.05 (0.06), residues: 2360 sheet: -1.64 (0.18), residues: 775 loop : -3.28 (0.08), residues: 3680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D1045 HIS 0.007 0.001 HIS d 978 PHE 0.030 0.003 PHE A1013 TYR 0.022 0.002 TYR b1080 ARG 0.011 0.001 ARG B 624 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1555 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1553 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 812 GLN cc_start: 0.8067 (pm20) cc_final: 0.7658 (pm20) REVERT: A 860 MET cc_start: 0.7390 (tpp) cc_final: 0.6854 (tmm) REVERT: A 959 ILE cc_start: 0.9292 (pt) cc_final: 0.9032 (tt) REVERT: A 1001 LEU cc_start: 0.8005 (tt) cc_final: 0.7693 (tt) REVERT: A 1018 ASP cc_start: 0.7421 (t0) cc_final: 0.6945 (t0) REVERT: B 612 PHE cc_start: 0.6192 (m-10) cc_final: 0.5933 (m-10) REVERT: B 800 LEU cc_start: 0.8404 (mt) cc_final: 0.7781 (tp) REVERT: B 876 ASN cc_start: 0.8514 (m-40) cc_final: 0.7501 (t0) REVERT: B 972 THR cc_start: 0.8661 (p) cc_final: 0.8272 (t) REVERT: B 1001 LEU cc_start: 0.8312 (tt) cc_final: 0.8096 (tt) REVERT: B 1015 TRP cc_start: 0.8802 (t60) cc_final: 0.8527 (t60) REVERT: B 1067 SER cc_start: 0.7703 (t) cc_final: 0.7319 (t) REVERT: C 612 PHE cc_start: 0.6199 (m-10) cc_final: 0.5760 (m-10) REVERT: C 710 VAL cc_start: 0.6655 (t) cc_final: 0.6319 (p) REVERT: C 776 MET cc_start: 0.7465 (mmm) cc_final: 0.7161 (tmm) REVERT: C 844 LEU cc_start: 0.7981 (tp) cc_final: 0.7205 (tp) REVERT: C 858 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7641 (mtp85) REVERT: C 876 ASN cc_start: 0.8928 (m-40) cc_final: 0.8461 (t0) REVERT: C 1003 TYR cc_start: 0.2708 (m-80) cc_final: 0.2502 (m-80) REVERT: D 844 LEU cc_start: 0.7893 (tp) cc_final: 0.7632 (tp) REVERT: D 1001 LEU cc_start: 0.8356 (tt) cc_final: 0.7660 (tt) REVERT: E 959 ILE cc_start: 0.9403 (pt) cc_final: 0.8913 (tt) REVERT: E 972 THR cc_start: 0.8788 (p) cc_final: 0.8498 (t) REVERT: E 1001 LEU cc_start: 0.8307 (tt) cc_final: 0.7860 (tt) REVERT: G 28 LEU cc_start: 0.5588 (mt) cc_final: 0.5128 (mt) REVERT: G 54 LEU cc_start: 0.6529 (mt) cc_final: 0.6327 (tp) REVERT: G 121 ASN cc_start: 0.4846 (t0) cc_final: 0.4293 (m-40) REVERT: G 132 LEU cc_start: 0.3683 (mt) cc_final: 0.3464 (tp) REVERT: G 142 VAL cc_start: 0.6082 (t) cc_final: 0.5667 (p) REVERT: H 26 LEU cc_start: 0.8220 (tp) cc_final: 0.7874 (tp) REVERT: H 38 THR cc_start: 0.8791 (p) cc_final: 0.8319 (t) REVERT: H 69 PHE cc_start: 0.7761 (m-80) cc_final: 0.7526 (m-80) REVERT: H 106 PHE cc_start: 0.6602 (m-80) cc_final: 0.6352 (m-10) REVERT: H 112 MET cc_start: 0.8489 (mtm) cc_final: 0.7234 (mtm) REVERT: I 89 GLN cc_start: 0.8132 (mm110) cc_final: 0.7649 (mm-40) REVERT: J 98 MET cc_start: 0.3608 (ttt) cc_final: 0.2930 (mtm) REVERT: J 114 LEU cc_start: 0.8865 (mt) cc_final: 0.8654 (tp) REVERT: J 121 ASN cc_start: 0.4512 (t0) cc_final: 0.3712 (m-40) REVERT: J 132 LEU cc_start: 0.4537 (mt) cc_final: 0.4271 (tp) REVERT: J 140 ILE cc_start: 0.5216 (mt) cc_final: 0.4843 (mt) REVERT: J 142 VAL cc_start: 0.6459 (t) cc_final: 0.6004 (p) REVERT: K 38 THR cc_start: 0.8732 (p) cc_final: 0.8011 (t) REVERT: K 69 PHE cc_start: 0.7953 (m-80) cc_final: 0.7622 (m-10) REVERT: K 112 MET cc_start: 0.8483 (mtm) cc_final: 0.7313 (mtm) REVERT: K 124 ARG cc_start: 0.6820 (ptt180) cc_final: 0.6462 (ptt180) REVERT: L 36 ILE cc_start: 0.8336 (pt) cc_final: 0.7992 (mt) REVERT: M 45 LEU cc_start: 0.5928 (mt) cc_final: 0.5640 (mt) REVERT: M 112 MET cc_start: 0.7355 (mtm) cc_final: 0.7143 (mtt) REVERT: M 117 ASP cc_start: 0.7636 (t0) cc_final: 0.7370 (t0) REVERT: M 121 ASN cc_start: 0.4324 (t0) cc_final: 0.4000 (m-40) REVERT: M 132 LEU cc_start: 0.4824 (mt) cc_final: 0.4425 (tp) REVERT: N 26 LEU cc_start: 0.8037 (tp) cc_final: 0.7708 (tp) REVERT: N 38 THR cc_start: 0.8588 (p) cc_final: 0.8129 (t) REVERT: N 69 PHE cc_start: 0.7800 (m-80) cc_final: 0.7142 (m-80) REVERT: N 112 MET cc_start: 0.8496 (mtm) cc_final: 0.7436 (mtm) REVERT: O 30 ILE cc_start: 0.6809 (mt) cc_final: 0.6596 (tp) REVERT: O 36 ILE cc_start: 0.8162 (pt) cc_final: 0.7876 (mt) REVERT: P 76 LEU cc_start: 0.2635 (tp) cc_final: 0.2343 (tp) REVERT: P 121 ASN cc_start: 0.4483 (t0) cc_final: 0.4188 (m-40) REVERT: P 140 ILE cc_start: 0.5505 (mt) cc_final: 0.5271 (mt) REVERT: P 142 VAL cc_start: 0.6977 (t) cc_final: 0.6575 (p) REVERT: Q 26 LEU cc_start: 0.7710 (tp) cc_final: 0.7487 (tp) REVERT: Q 38 THR cc_start: 0.9039 (p) cc_final: 0.8561 (t) REVERT: Q 43 ILE cc_start: 0.9049 (mt) cc_final: 0.8579 (mm) REVERT: Q 112 MET cc_start: 0.8320 (mtm) cc_final: 0.8009 (mtm) REVERT: R 89 GLN cc_start: 0.8118 (mm110) cc_final: 0.7898 (mt0) REVERT: R 135 ASP cc_start: 0.5017 (m-30) cc_final: 0.4733 (t0) REVERT: S 132 LEU cc_start: 0.5068 (mt) cc_final: 0.4805 (tp) REVERT: T 26 LEU cc_start: 0.8019 (tp) cc_final: 0.7785 (mt) REVERT: T 38 THR cc_start: 0.8858 (p) cc_final: 0.8495 (t) REVERT: T 69 PHE cc_start: 0.8020 (m-80) cc_final: 0.7341 (m-80) REVERT: T 112 MET cc_start: 0.8552 (mtm) cc_final: 0.7211 (mtm) REVERT: a 815 MET cc_start: 0.8823 (mmt) cc_final: 0.8545 (tpp) REVERT: a 849 TYR cc_start: 0.8231 (t80) cc_final: 0.7985 (t80) REVERT: a 905 SER cc_start: 0.8693 (p) cc_final: 0.8367 (m) REVERT: a 972 THR cc_start: 0.7910 (p) cc_final: 0.7705 (p) REVERT: a 1101 LEU cc_start: 0.8554 (mt) cc_final: 0.8319 (mt) REVERT: b 972 THR cc_start: 0.8293 (p) cc_final: 0.8078 (p) REVERT: b 990 MET cc_start: 0.9304 (pmm) cc_final: 0.8957 (pmm) REVERT: b 993 THR cc_start: 0.8238 (p) cc_final: 0.8033 (p) REVERT: b 995 ILE cc_start: 0.8362 (mm) cc_final: 0.7938 (pt) REVERT: c 887 TRP cc_start: 0.8636 (t60) cc_final: 0.8405 (t-100) REVERT: c 972 THR cc_start: 0.8259 (p) cc_final: 0.7910 (p) REVERT: c 990 MET cc_start: 0.9203 (pmm) cc_final: 0.7380 (ptt) REVERT: d 814 MET cc_start: 0.8539 (mtt) cc_final: 0.8164 (mtm) REVERT: d 905 SER cc_start: 0.8396 (p) cc_final: 0.7757 (m) REVERT: d 972 THR cc_start: 0.7786 (p) cc_final: 0.7524 (p) REVERT: d 993 THR cc_start: 0.7927 (p) cc_final: 0.7716 (p) REVERT: d 999 GLN cc_start: 0.7511 (mt0) cc_final: 0.7248 (mm110) REVERT: d 1100 VAL cc_start: 0.8304 (t) cc_final: 0.8061 (p) REVERT: e 640 ASN cc_start: 0.7871 (m110) cc_final: 0.7646 (t0) REVERT: e 720 ASN cc_start: 0.8247 (m110) cc_final: 0.7786 (m-40) REVERT: e 815 MET cc_start: 0.8510 (mmt) cc_final: 0.8107 (tpp) REVERT: e 1101 LEU cc_start: 0.8481 (mt) cc_final: 0.8123 (mm) outliers start: 2 outliers final: 0 residues processed: 1554 average time/residue: 0.5393 time to fit residues: 1366.9753 Evaluate side-chains 1044 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1044 time to evaluate : 4.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 578 optimal weight: 0.8980 chunk 519 optimal weight: 0.9980 chunk 288 optimal weight: 0.1980 chunk 177 optimal weight: 0.5980 chunk 350 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 536 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 326 optimal weight: 0.5980 chunk 399 optimal weight: 0.1980 chunk 622 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 687 ASN A 712 GLN A 787 ASN A 804 GLN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 HIS A 999 GLN A1037 GLN A1098 ASN B 687 ASN B 712 GLN B 787 ASN ** B 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 945 ASN B 999 GLN C 687 ASN C 712 GLN C 787 ASN ** C 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN D 712 GLN D 787 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 GLN D1098 ASN E 687 ASN E 820 GLN E 876 ASN E 933 HIS E 978 HIS ** E 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN I 118 GLN K 53 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS O 118 GLN ** O 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 GLN R 118 GLN ** R 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 592 HIS a 640 ASN a 812 GLN a 820 GLN a 866 GLN a 991 GLN a 999 GLN b 593 GLN b 725 GLN b 812 GLN b 866 GLN b1071 GLN c 593 GLN ** c 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 687 ASN c 725 GLN c 812 GLN c 866 GLN c 991 GLN c1071 GLN d 684 ASN d 687 ASN d 812 GLN d 820 GLN d 866 GLN d 991 GLN e 803 GLN e 812 GLN e 820 GLN e 866 GLN e 991 GLN e 998 ASN e 999 GLN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 53900 Z= 0.201 Angle : 0.676 8.129 73420 Z= 0.350 Chirality : 0.045 0.223 8505 Planarity : 0.005 0.068 9565 Dihedral : 6.129 36.459 7400 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.66 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.09), residues: 6815 helix: -2.92 (0.08), residues: 2320 sheet: -0.72 (0.16), residues: 945 loop : -2.98 (0.09), residues: 3550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E1045 HIS 0.010 0.001 HIS S 27 PHE 0.025 0.002 PHE T 106 TYR 0.031 0.002 TYR B1003 ARG 0.006 0.001 ARG S 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1251 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LEU cc_start: 0.8006 (mt) cc_final: 0.7645 (tp) REVERT: A 812 GLN cc_start: 0.8090 (pm20) cc_final: 0.7690 (pm20) REVERT: A 1018 ASP cc_start: 0.7435 (t0) cc_final: 0.6991 (t0) REVERT: A 1038 TYR cc_start: 0.7369 (t80) cc_final: 0.6936 (t80) REVERT: A 1053 MET cc_start: 0.8367 (ttm) cc_final: 0.7362 (ttm) REVERT: A 1055 ARG cc_start: 0.7524 (mpp80) cc_final: 0.7234 (mpt-90) REVERT: A 1094 LEU cc_start: 0.8623 (mm) cc_final: 0.8282 (mt) REVERT: B 800 LEU cc_start: 0.8575 (mt) cc_final: 0.7892 (tp) REVERT: B 876 ASN cc_start: 0.8508 (m-40) cc_final: 0.8204 (t0) REVERT: B 972 THR cc_start: 0.8676 (p) cc_final: 0.8313 (t) REVERT: B 1018 ASP cc_start: 0.7587 (p0) cc_final: 0.7130 (p0) REVERT: C 836 TYR cc_start: 0.7732 (m-10) cc_final: 0.7467 (m-80) REVERT: C 844 LEU cc_start: 0.7456 (tp) cc_final: 0.7171 (tp) REVERT: C 1018 ASP cc_start: 0.7839 (p0) cc_final: 0.7431 (p0) REVERT: C 1038 TYR cc_start: 0.6931 (t80) cc_final: 0.6083 (t80) REVERT: C 1091 LEU cc_start: 0.6994 (mt) cc_final: 0.6648 (mt) REVERT: D 919 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.7186 (mtm110) REVERT: E 722 LEU cc_start: 0.8804 (tt) cc_final: 0.8405 (tt) REVERT: E 959 ILE cc_start: 0.9341 (pt) cc_final: 0.8772 (tt) REVERT: E 972 THR cc_start: 0.8897 (p) cc_final: 0.8605 (t) REVERT: E 1018 ASP cc_start: 0.8089 (p0) cc_final: 0.7722 (p0) REVERT: E 1038 TYR cc_start: 0.6857 (t80) cc_final: 0.6310 (t80) REVERT: E 1053 MET cc_start: 0.8488 (ttp) cc_final: 0.6979 (ttp) REVERT: E 1055 ARG cc_start: 0.7828 (mpp80) cc_final: 0.7475 (mpt-90) REVERT: G 121 ASN cc_start: 0.4518 (t0) cc_final: 0.4250 (m-40) REVERT: H 38 THR cc_start: 0.8916 (p) cc_final: 0.8296 (t) REVERT: H 69 PHE cc_start: 0.8121 (m-80) cc_final: 0.7413 (m-80) REVERT: H 112 MET cc_start: 0.8895 (mtm) cc_final: 0.6651 (mtm) REVERT: J 50 ARG cc_start: 0.6553 (mtt90) cc_final: 0.6017 (tpp80) REVERT: J 53 GLN cc_start: 0.5165 (mt0) cc_final: 0.4580 (pt0) REVERT: J 98 MET cc_start: 0.3066 (ttt) cc_final: 0.2731 (mtp) REVERT: J 112 MET cc_start: 0.7292 (mtm) cc_final: 0.6926 (mtt) REVERT: K 38 THR cc_start: 0.8833 (p) cc_final: 0.8151 (t) REVERT: K 51 ILE cc_start: 0.8150 (tp) cc_final: 0.7693 (pt) REVERT: K 64 ASP cc_start: 0.8477 (p0) cc_final: 0.8033 (p0) REVERT: K 101 ASP cc_start: 0.7402 (t70) cc_final: 0.7162 (t70) REVERT: K 124 ARG cc_start: 0.6770 (ptt180) cc_final: 0.6423 (ptt180) REVERT: L 89 GLN cc_start: 0.8769 (tp-100) cc_final: 0.8454 (mt0) REVERT: L 147 LEU cc_start: 0.7547 (mm) cc_final: 0.7076 (mm) REVERT: M 23 ILE cc_start: 0.2643 (mm) cc_final: 0.1863 (mm) REVERT: M 31 ARG cc_start: 0.6555 (mtp85) cc_final: 0.6019 (ttm110) REVERT: N 38 THR cc_start: 0.8750 (p) cc_final: 0.8160 (t) REVERT: N 39 SER cc_start: 0.9162 (p) cc_final: 0.8892 (p) REVERT: N 51 ILE cc_start: 0.8313 (tp) cc_final: 0.7500 (pt) REVERT: N 56 ASP cc_start: 0.6743 (m-30) cc_final: 0.5869 (m-30) REVERT: N 83 GLN cc_start: 0.8615 (mp10) cc_final: 0.8356 (mp10) REVERT: O 36 ILE cc_start: 0.8448 (pt) cc_final: 0.7952 (mt) REVERT: P 98 MET cc_start: 0.2245 (ttm) cc_final: 0.1647 (ttm) REVERT: Q 27 HIS cc_start: 0.5768 (m-70) cc_final: 0.5550 (m90) REVERT: Q 38 THR cc_start: 0.9056 (p) cc_final: 0.8716 (t) REVERT: Q 43 ILE cc_start: 0.9161 (mt) cc_final: 0.8802 (mm) REVERT: Q 51 ILE cc_start: 0.8239 (tp) cc_final: 0.7741 (pt) REVERT: Q 55 LYS cc_start: 0.7211 (tptt) cc_final: 0.6763 (ttpp) REVERT: Q 112 MET cc_start: 0.8236 (mtm) cc_final: 0.7612 (mtt) REVERT: R 84 LYS cc_start: 0.7025 (tptp) cc_final: 0.6747 (tptp) REVERT: S 31 ARG cc_start: 0.7014 (mtp85) cc_final: 0.6264 (ttm110) REVERT: S 50 ARG cc_start: 0.6807 (mtt180) cc_final: 0.6229 (mtt-85) REVERT: S 112 MET cc_start: 0.7638 (mtm) cc_final: 0.6752 (mtm) REVERT: S 133 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7982 (tm-30) REVERT: T 38 THR cc_start: 0.9084 (p) cc_final: 0.8514 (t) REVERT: T 39 SER cc_start: 0.9207 (p) cc_final: 0.8984 (p) REVERT: T 64 ASP cc_start: 0.8447 (p0) cc_final: 0.7876 (p0) REVERT: T 69 PHE cc_start: 0.8457 (m-80) cc_final: 0.7389 (m-80) REVERT: T 101 ASP cc_start: 0.7437 (t70) cc_final: 0.7154 (t70) REVERT: T 112 MET cc_start: 0.8803 (mtm) cc_final: 0.6371 (mtm) REVERT: a 575 THR cc_start: 0.6341 (t) cc_final: 0.6055 (t) REVERT: a 719 MET cc_start: 0.8394 (tpp) cc_final: 0.8155 (tpt) REVERT: a 815 MET cc_start: 0.8825 (mmt) cc_final: 0.8614 (tpp) REVERT: a 849 TYR cc_start: 0.8075 (t80) cc_final: 0.7734 (t80) REVERT: a 922 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7294 (ttm-80) REVERT: a 964 GLU cc_start: 0.6924 (tm-30) cc_final: 0.5895 (tp30) REVERT: a 965 ILE cc_start: 0.8228 (mm) cc_final: 0.7716 (tp) REVERT: a 972 THR cc_start: 0.7954 (p) cc_final: 0.7748 (p) REVERT: a 990 MET cc_start: 0.8946 (pmm) cc_final: 0.7569 (ptt) REVERT: a 995 ILE cc_start: 0.8621 (mm) cc_final: 0.8346 (mm) REVERT: a 1101 LEU cc_start: 0.8646 (mt) cc_final: 0.8428 (mt) REVERT: b 575 THR cc_start: 0.6143 (t) cc_final: 0.5931 (t) REVERT: b 776 MET cc_start: 0.5986 (ptm) cc_final: 0.5685 (ptm) REVERT: b 792 LEU cc_start: 0.8570 (tp) cc_final: 0.8258 (tt) REVERT: b 887 TRP cc_start: 0.8575 (t60) cc_final: 0.8322 (t-100) REVERT: b 964 GLU cc_start: 0.7003 (pp20) cc_final: 0.6583 (tm-30) REVERT: b 990 MET cc_start: 0.8755 (pmm) cc_final: 0.7986 (ptt) REVERT: b 995 ILE cc_start: 0.8501 (mm) cc_final: 0.8085 (mt) REVERT: b 1038 TYR cc_start: 0.7862 (t80) cc_final: 0.7428 (t80) REVERT: c 792 LEU cc_start: 0.8467 (tt) cc_final: 0.8209 (tt) REVERT: c 797 GLN cc_start: 0.8006 (tp-100) cc_final: 0.7751 (tp40) REVERT: c 887 TRP cc_start: 0.8620 (t60) cc_final: 0.8416 (t-100) REVERT: c 917 THR cc_start: 0.8155 (p) cc_final: 0.7848 (p) REVERT: c 922 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7505 (ttm-80) REVERT: c 972 THR cc_start: 0.8235 (p) cc_final: 0.8019 (p) REVERT: c 1000 LYS cc_start: 0.7924 (mmtm) cc_final: 0.7613 (mmtm) REVERT: d 575 THR cc_start: 0.6550 (t) cc_final: 0.6329 (t) REVERT: d 709 ASP cc_start: 0.7522 (t70) cc_final: 0.7264 (t0) REVERT: d 719 MET cc_start: 0.8293 (mmm) cc_final: 0.7995 (mmm) REVERT: d 838 SER cc_start: 0.8593 (p) cc_final: 0.8140 (t) REVERT: d 905 SER cc_start: 0.8259 (p) cc_final: 0.7596 (m) REVERT: d 913 LEU cc_start: 0.9508 (tp) cc_final: 0.9104 (mm) REVERT: d 922 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7517 (ttm-80) REVERT: d 972 THR cc_start: 0.7751 (p) cc_final: 0.7515 (p) REVERT: d 990 MET cc_start: 0.8610 (pmm) cc_final: 0.7760 (ptt) REVERT: d 999 GLN cc_start: 0.7808 (mt0) cc_final: 0.7404 (mt0) REVERT: d 1002 ILE cc_start: 0.9220 (tt) cc_final: 0.8783 (pt) REVERT: d 1100 VAL cc_start: 0.8143 (t) cc_final: 0.7868 (p) REVERT: e 785 MET cc_start: 0.8333 (tmm) cc_final: 0.7965 (tmm) REVERT: e 791 TYR cc_start: 0.7711 (m-10) cc_final: 0.7350 (m-10) REVERT: e 828 VAL cc_start: 0.8731 (m) cc_final: 0.8480 (p) REVERT: e 876 ASN cc_start: 0.7735 (t0) cc_final: 0.7502 (t0) REVERT: e 905 SER cc_start: 0.8377 (m) cc_final: 0.7588 (t) REVERT: e 922 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7853 (ttm-80) REVERT: e 927 ASN cc_start: 0.7897 (t0) cc_final: 0.7484 (t0) REVERT: e 990 MET cc_start: 0.9120 (pmm) cc_final: 0.7435 (ptt) REVERT: e 1038 TYR cc_start: 0.7771 (t80) cc_final: 0.7525 (t80) REVERT: e 1104 THR cc_start: 0.7879 (t) cc_final: 0.7503 (t) outliers start: 5 outliers final: 1 residues processed: 1254 average time/residue: 0.5153 time to fit residues: 1073.3076 Evaluate side-chains 1011 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1010 time to evaluate : 4.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 345 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 517 optimal weight: 3.9990 chunk 423 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 623 optimal weight: 7.9990 chunk 673 optimal weight: 0.8980 chunk 554 optimal weight: 0.9980 chunk 617 optimal weight: 0.9980 chunk 212 optimal weight: 0.0970 chunk 499 optimal weight: 0.8980 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 846 GLN A 999 GLN A1037 GLN A1098 ASN B 787 ASN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 978 HIS B 999 GLN C 787 ASN ** C 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 999 GLN D 668 GLN D 787 ASN ** D 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 999 GLN D1098 ASN E 787 ASN E 999 GLN ** G 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 HIS Q 53 GLN Q 121 ASN T 53 GLN a 593 GLN b 593 GLN c 593 GLN c 640 ASN c 720 ASN c 762 HIS c 820 GLN c 876 ASN d 593 GLN d 789 GLN d 927 ASN e 762 HIS ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 803 GLN e 804 GLN e 999 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 53900 Z= 0.235 Angle : 0.673 7.332 73420 Z= 0.344 Chirality : 0.045 0.177 8505 Planarity : 0.005 0.067 9565 Dihedral : 5.815 32.893 7400 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 0.05 % Allowed : 5.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.09), residues: 6815 helix: -2.40 (0.09), residues: 2390 sheet: -0.52 (0.16), residues: 1035 loop : -2.86 (0.10), residues: 3390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C1045 HIS 0.014 0.001 HIS e 762 PHE 0.020 0.002 PHE R 69 TYR 0.025 0.002 TYR D1003 ARG 0.009 0.001 ARG B 934 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1179 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 MET cc_start: 0.7938 (mmm) cc_final: 0.7709 (mmm) REVERT: A 800 LEU cc_start: 0.8177 (mt) cc_final: 0.7789 (tp) REVERT: A 1018 ASP cc_start: 0.7525 (t0) cc_final: 0.7137 (t0) REVERT: A 1094 LEU cc_start: 0.8520 (mm) cc_final: 0.8201 (mt) REVERT: B 696 MET cc_start: 0.7433 (tmm) cc_final: 0.7220 (tmm) REVERT: B 800 LEU cc_start: 0.8516 (mt) cc_final: 0.7790 (tp) REVERT: B 876 ASN cc_start: 0.8598 (m-40) cc_final: 0.8203 (t0) REVERT: B 1018 ASP cc_start: 0.7656 (p0) cc_final: 0.7199 (p0) REVERT: B 1080 TYR cc_start: 0.4225 (m-80) cc_final: 0.3952 (m-10) REVERT: C 830 LEU cc_start: 0.8303 (tp) cc_final: 0.8042 (tp) REVERT: C 844 LEU cc_start: 0.7472 (tp) cc_final: 0.7168 (tp) REVERT: C 950 THR cc_start: 0.7818 (m) cc_final: 0.7397 (p) REVERT: C 1000 LYS cc_start: 0.6513 (mtmm) cc_final: 0.6301 (ptpp) REVERT: C 1018 ASP cc_start: 0.7947 (p0) cc_final: 0.7583 (p0) REVERT: D 814 MET cc_start: 0.8959 (mmm) cc_final: 0.8694 (mmm) REVERT: D 919 ARG cc_start: 0.7350 (mtp-110) cc_final: 0.7112 (mtm110) REVERT: D 1018 ASP cc_start: 0.8068 (p0) cc_final: 0.7425 (p0) REVERT: D 1038 TYR cc_start: 0.7272 (t80) cc_final: 0.6904 (t80) REVERT: D 1053 MET cc_start: 0.8369 (ttm) cc_final: 0.7961 (ttm) REVERT: E 957 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8112 (tppt) REVERT: E 959 ILE cc_start: 0.9354 (pt) cc_final: 0.8715 (tt) REVERT: E 967 ASP cc_start: 0.7489 (m-30) cc_final: 0.7286 (m-30) REVERT: E 1055 ARG cc_start: 0.7967 (mpp80) cc_final: 0.7692 (mpt-90) REVERT: F 43 ILE cc_start: 0.8032 (mt) cc_final: 0.7681 (mp) REVERT: G 50 ARG cc_start: 0.6501 (mtt90) cc_final: 0.5888 (ttm110) REVERT: G 112 MET cc_start: 0.7084 (mtp) cc_final: 0.6737 (mtt) REVERT: G 142 VAL cc_start: 0.7117 (t) cc_final: 0.6667 (p) REVERT: H 38 THR cc_start: 0.8945 (p) cc_final: 0.8457 (t) REVERT: H 39 SER cc_start: 0.9360 (p) cc_final: 0.9125 (p) REVERT: H 64 ASP cc_start: 0.8042 (p0) cc_final: 0.7715 (p0) REVERT: H 69 PHE cc_start: 0.8022 (m-80) cc_final: 0.7623 (m-80) REVERT: H 112 MET cc_start: 0.8881 (mtm) cc_final: 0.7021 (mtm) REVERT: J 31 ARG cc_start: 0.6978 (mtp85) cc_final: 0.5842 (ttm110) REVERT: J 98 MET cc_start: 0.2642 (ttt) cc_final: 0.2365 (ttm) REVERT: J 112 MET cc_start: 0.7488 (mtm) cc_final: 0.7161 (mtt) REVERT: K 26 LEU cc_start: 0.7804 (mt) cc_final: 0.7489 (mt) REVERT: K 38 THR cc_start: 0.8789 (p) cc_final: 0.8486 (t) REVERT: K 51 ILE cc_start: 0.8081 (tp) cc_final: 0.7776 (pt) REVERT: K 64 ASP cc_start: 0.8256 (p0) cc_final: 0.7993 (p0) REVERT: K 101 ASP cc_start: 0.7343 (t70) cc_final: 0.6756 (t0) REVERT: L 98 MET cc_start: 0.4817 (ttp) cc_final: 0.4510 (ttm) REVERT: M 31 ARG cc_start: 0.6543 (mtp85) cc_final: 0.6001 (ttm110) REVERT: M 112 MET cc_start: 0.7175 (mtt) cc_final: 0.6956 (mtt) REVERT: N 38 THR cc_start: 0.8841 (p) cc_final: 0.8341 (t) REVERT: N 39 SER cc_start: 0.9180 (p) cc_final: 0.8950 (p) REVERT: N 51 ILE cc_start: 0.8402 (tp) cc_final: 0.7914 (pt) REVERT: N 101 ASP cc_start: 0.8021 (t0) cc_final: 0.7797 (t70) REVERT: N 121 ASN cc_start: 0.7802 (p0) cc_final: 0.7579 (p0) REVERT: N 124 ARG cc_start: 0.7261 (ptt180) cc_final: 0.7030 (ptt180) REVERT: N 143 SER cc_start: 0.7863 (t) cc_final: 0.7539 (m) REVERT: O 36 ILE cc_start: 0.8624 (pt) cc_final: 0.8180 (mt) REVERT: Q 38 THR cc_start: 0.9159 (p) cc_final: 0.8737 (t) REVERT: Q 51 ILE cc_start: 0.8200 (tp) cc_final: 0.7772 (pt) REVERT: Q 55 LYS cc_start: 0.7345 (tptt) cc_final: 0.6993 (ttpp) REVERT: R 141 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6849 (tm-30) REVERT: S 31 ARG cc_start: 0.6901 (mtp85) cc_final: 0.6132 (ttm110) REVERT: S 112 MET cc_start: 0.7722 (mtm) cc_final: 0.6883 (mtm) REVERT: S 133 GLU cc_start: 0.8261 (tm-30) cc_final: 0.5587 (pm20) REVERT: T 39 SER cc_start: 0.9240 (p) cc_final: 0.8999 (p) REVERT: T 56 ASP cc_start: 0.7698 (m-30) cc_final: 0.7043 (m-30) REVERT: T 69 PHE cc_start: 0.8393 (m-80) cc_final: 0.7608 (m-80) REVERT: T 83 GLN cc_start: 0.8586 (mp-120) cc_final: 0.8343 (mp10) REVERT: T 101 ASP cc_start: 0.7622 (t70) cc_final: 0.7418 (t70) REVERT: T 112 MET cc_start: 0.9062 (mtm) cc_final: 0.7084 (mtm) REVERT: a 586 MET cc_start: 0.7098 (mmm) cc_final: 0.6817 (tpp) REVERT: a 625 GLN cc_start: 0.8229 (tm-30) cc_final: 0.8013 (tm-30) REVERT: a 715 LEU cc_start: 0.8100 (tp) cc_final: 0.7734 (tt) REVERT: a 815 MET cc_start: 0.8842 (mmt) cc_final: 0.8590 (tpp) REVERT: a 849 TYR cc_start: 0.7925 (t80) cc_final: 0.7652 (t80) REVERT: a 946 THR cc_start: 0.6275 (m) cc_final: 0.6069 (m) REVERT: a 964 GLU cc_start: 0.6813 (tm-30) cc_final: 0.5890 (tp30) REVERT: a 965 ILE cc_start: 0.8467 (mm) cc_final: 0.7885 (tp) REVERT: a 972 THR cc_start: 0.8017 (p) cc_final: 0.7798 (p) REVERT: a 990 MET cc_start: 0.8927 (pmm) cc_final: 0.7588 (ptt) REVERT: a 995 ILE cc_start: 0.8568 (mm) cc_final: 0.8086 (mm) REVERT: a 1000 LYS cc_start: 0.8416 (mmtm) cc_final: 0.7772 (mtpp) REVERT: b 792 LEU cc_start: 0.8557 (tp) cc_final: 0.8347 (tt) REVERT: b 817 MET cc_start: 0.6933 (tpp) cc_final: 0.6588 (tpp) REVERT: b 964 GLU cc_start: 0.6953 (pp20) cc_final: 0.6580 (tm-30) REVERT: b 990 MET cc_start: 0.8817 (pmm) cc_final: 0.7929 (ptt) REVERT: b 1038 TYR cc_start: 0.7867 (t80) cc_final: 0.7362 (t80) REVERT: c 625 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7981 (pm20) REVERT: c 707 MET cc_start: 0.6891 (tmm) cc_final: 0.6494 (tmm) REVERT: c 792 LEU cc_start: 0.8661 (tt) cc_final: 0.8409 (tt) REVERT: c 815 MET cc_start: 0.8523 (tpp) cc_final: 0.8220 (tpp) REVERT: c 887 TRP cc_start: 0.8681 (t60) cc_final: 0.8464 (t-100) REVERT: c 917 THR cc_start: 0.8186 (p) cc_final: 0.7884 (p) REVERT: c 927 ASN cc_start: 0.7461 (t0) cc_final: 0.7183 (t0) REVERT: c 972 THR cc_start: 0.8279 (p) cc_final: 0.8065 (p) REVERT: c 1000 LYS cc_start: 0.7941 (mmtm) cc_final: 0.7623 (mmtm) REVERT: d 625 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7554 (tm-30) REVERT: d 709 ASP cc_start: 0.7356 (t70) cc_final: 0.7080 (t0) REVERT: d 719 MET cc_start: 0.8313 (mmm) cc_final: 0.7991 (mmm) REVERT: d 791 TYR cc_start: 0.7234 (m-10) cc_final: 0.6942 (m-10) REVERT: d 913 LEU cc_start: 0.9432 (tp) cc_final: 0.9103 (mm) REVERT: d 964 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6536 (tm-30) REVERT: d 972 THR cc_start: 0.7858 (p) cc_final: 0.7555 (p) REVERT: d 990 MET cc_start: 0.8590 (pmm) cc_final: 0.7627 (ptt) REVERT: d 1002 ILE cc_start: 0.9241 (tt) cc_final: 0.8862 (pt) REVERT: d 1100 VAL cc_start: 0.8036 (t) cc_final: 0.7833 (p) REVERT: e 640 ASN cc_start: 0.7749 (m110) cc_final: 0.7524 (t0) REVERT: e 785 MET cc_start: 0.8418 (tmm) cc_final: 0.7946 (tmm) REVERT: e 905 SER cc_start: 0.8559 (m) cc_final: 0.7677 (t) outliers start: 3 outliers final: 3 residues processed: 1179 average time/residue: 0.5186 time to fit residues: 1014.4103 Evaluate side-chains 1011 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1008 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 615 optimal weight: 0.0980 chunk 468 optimal weight: 1.9990 chunk 323 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 297 optimal weight: 10.0000 chunk 418 optimal weight: 2.9990 chunk 625 optimal weight: 0.9990 chunk 662 optimal weight: 0.0060 chunk 326 optimal weight: 7.9990 chunk 592 optimal weight: 0.6980 chunk 178 optimal weight: 0.8980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 GLN A 712 GLN A 787 ASN B 787 ASN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 ASN C 787 ASN C 876 ASN C 999 GLN D 876 ASN D 999 GLN E 787 ASN G 118 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN a 640 ASN a 762 HIS a 999 GLN b 812 GLN b 927 ASN c 593 GLN c 762 HIS c 846 GLN c 876 ASN d 593 GLN ** d 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 999 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 53900 Z= 0.187 Angle : 0.634 7.671 73420 Z= 0.322 Chirality : 0.044 0.182 8505 Planarity : 0.004 0.071 9565 Dihedral : 5.486 32.279 7400 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.04 % Allowed : 3.50 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.09), residues: 6815 helix: -2.10 (0.09), residues: 2465 sheet: -0.35 (0.16), residues: 1035 loop : -2.70 (0.10), residues: 3315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c1066 HIS 0.016 0.001 HIS a 762 PHE 0.019 0.002 PHE D 851 TYR 0.022 0.001 TYR D1003 ARG 0.010 0.001 ARG B1049 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1164 time to evaluate : 4.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LEU cc_start: 0.8263 (mt) cc_final: 0.7556 (tp) REVERT: A 814 MET cc_start: 0.8682 (mmm) cc_final: 0.8473 (mmp) REVERT: A 938 ARG cc_start: 0.6607 (mtm110) cc_final: 0.5975 (mtm110) REVERT: A 1018 ASP cc_start: 0.7699 (t0) cc_final: 0.7305 (t0) REVERT: A 1094 LEU cc_start: 0.8605 (mm) cc_final: 0.8267 (mt) REVERT: B 800 LEU cc_start: 0.8495 (mt) cc_final: 0.7791 (tp) REVERT: B 876 ASN cc_start: 0.8650 (m-40) cc_final: 0.8253 (t0) REVERT: B 914 ASN cc_start: 0.7949 (t0) cc_final: 0.7276 (t0) REVERT: B 1018 ASP cc_start: 0.7717 (p0) cc_final: 0.7475 (p0) REVERT: B 1053 MET cc_start: 0.8318 (ttm) cc_final: 0.7967 (ttm) REVERT: C 719 MET cc_start: 0.7024 (tpp) cc_final: 0.6814 (tpp) REVERT: C 812 GLN cc_start: 0.8231 (pm20) cc_final: 0.7934 (pm20) REVERT: C 830 LEU cc_start: 0.8208 (tp) cc_final: 0.7896 (tp) REVERT: C 844 LEU cc_start: 0.7524 (tp) cc_final: 0.7079 (tp) REVERT: C 1018 ASP cc_start: 0.7859 (p0) cc_final: 0.7549 (p0) REVERT: D 814 MET cc_start: 0.8975 (mmm) cc_final: 0.8628 (mmm) REVERT: D 834 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7582 (mtp85) REVERT: D 1038 TYR cc_start: 0.7327 (t80) cc_final: 0.6851 (t80) REVERT: D 1053 MET cc_start: 0.8360 (ttm) cc_final: 0.8021 (ttm) REVERT: E 934 ARG cc_start: 0.7838 (mpt180) cc_final: 0.7044 (mpt180) REVERT: E 959 ILE cc_start: 0.9410 (pt) cc_final: 0.8948 (tp) REVERT: E 1038 TYR cc_start: 0.6986 (t80) cc_final: 0.6710 (t80) REVERT: E 1055 ARG cc_start: 0.8133 (mpp80) cc_final: 0.7834 (mpt-90) REVERT: F 29 ASP cc_start: 0.4854 (t70) cc_final: 0.4198 (t70) REVERT: F 43 ILE cc_start: 0.8177 (mt) cc_final: 0.7789 (mp) REVERT: G 50 ARG cc_start: 0.6408 (mtt90) cc_final: 0.5863 (ttm110) REVERT: G 86 VAL cc_start: 0.8756 (t) cc_final: 0.8539 (p) REVERT: G 142 VAL cc_start: 0.7147 (t) cc_final: 0.6661 (p) REVERT: H 64 ASP cc_start: 0.8015 (p0) cc_final: 0.7229 (p0) REVERT: H 101 ASP cc_start: 0.7451 (t70) cc_final: 0.7184 (t70) REVERT: H 112 MET cc_start: 0.8856 (mtm) cc_final: 0.7851 (mtm) REVERT: J 31 ARG cc_start: 0.6905 (mtp85) cc_final: 0.5794 (ttm110) REVERT: K 26 LEU cc_start: 0.7790 (mt) cc_final: 0.7544 (mt) REVERT: K 51 ILE cc_start: 0.8016 (tp) cc_final: 0.7779 (pt) REVERT: K 101 ASP cc_start: 0.6940 (t70) cc_final: 0.6718 (t0) REVERT: L 89 GLN cc_start: 0.8302 (mt0) cc_final: 0.8078 (mt0) REVERT: M 31 ARG cc_start: 0.6471 (mtp85) cc_final: 0.5946 (ttm110) REVERT: N 38 THR cc_start: 0.8912 (p) cc_final: 0.8309 (t) REVERT: N 51 ILE cc_start: 0.8463 (tp) cc_final: 0.7922 (pt) REVERT: N 64 ASP cc_start: 0.8383 (p0) cc_final: 0.8091 (p0) REVERT: N 101 ASP cc_start: 0.8089 (t0) cc_final: 0.7858 (t70) REVERT: N 112 MET cc_start: 0.8141 (mmt) cc_final: 0.7688 (mmm) REVERT: N 143 SER cc_start: 0.7979 (t) cc_final: 0.7552 (m) REVERT: O 36 ILE cc_start: 0.8589 (pt) cc_final: 0.8279 (mt) REVERT: O 147 LEU cc_start: 0.7080 (mm) cc_final: 0.6556 (mm) REVERT: Q 38 THR cc_start: 0.9134 (p) cc_final: 0.8851 (t) REVERT: Q 51 ILE cc_start: 0.8276 (tp) cc_final: 0.7868 (pt) REVERT: Q 106 PHE cc_start: 0.6861 (m-80) cc_final: 0.6612 (m-80) REVERT: Q 143 SER cc_start: 0.7965 (t) cc_final: 0.7617 (m) REVERT: R 29 ASP cc_start: 0.5424 (t0) cc_final: 0.5113 (t70) REVERT: R 98 MET cc_start: 0.5355 (ttm) cc_final: 0.4899 (ttp) REVERT: S 31 ARG cc_start: 0.6829 (mtp85) cc_final: 0.6102 (ttm110) REVERT: S 76 LEU cc_start: 0.5380 (pp) cc_final: 0.4510 (tt) REVERT: S 112 MET cc_start: 0.7794 (mtm) cc_final: 0.7046 (mtm) REVERT: S 133 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7501 (tm-30) REVERT: T 56 ASP cc_start: 0.7806 (m-30) cc_final: 0.7092 (m-30) REVERT: T 64 ASP cc_start: 0.8371 (p0) cc_final: 0.7754 (p0) REVERT: T 101 ASP cc_start: 0.7667 (t70) cc_final: 0.7381 (t0) REVERT: a 586 MET cc_start: 0.7102 (mmm) cc_final: 0.6692 (tpp) REVERT: a 625 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8165 (pm20) REVERT: a 815 MET cc_start: 0.8780 (mmt) cc_final: 0.8455 (mmm) REVERT: a 828 VAL cc_start: 0.8471 (m) cc_final: 0.8264 (t) REVERT: a 849 TYR cc_start: 0.7896 (t80) cc_final: 0.7626 (t80) REVERT: a 860 MET cc_start: 0.8409 (mmm) cc_final: 0.8087 (mmm) REVERT: a 876 ASN cc_start: 0.7485 (t0) cc_final: 0.7170 (t0) REVERT: a 947 ARG cc_start: 0.4852 (ptp90) cc_final: 0.4624 (ptp90) REVERT: a 965 ILE cc_start: 0.8457 (mm) cc_final: 0.8211 (tp) REVERT: a 972 THR cc_start: 0.8003 (p) cc_final: 0.7783 (p) REVERT: a 990 MET cc_start: 0.8885 (pmm) cc_final: 0.7436 (ptt) REVERT: a 995 ILE cc_start: 0.8550 (mm) cc_final: 0.8114 (mm) REVERT: a 1000 LYS cc_start: 0.8321 (mmtm) cc_final: 0.7573 (mtpp) REVERT: a 1101 LEU cc_start: 0.8684 (mt) cc_final: 0.8462 (mt) REVERT: b 625 GLN cc_start: 0.7369 (pm20) cc_final: 0.7047 (mp10) REVERT: b 785 MET cc_start: 0.8929 (tmm) cc_final: 0.8403 (tmm) REVERT: b 792 LEU cc_start: 0.8481 (tp) cc_final: 0.8174 (tt) REVERT: b 964 GLU cc_start: 0.6862 (pp20) cc_final: 0.6652 (tm-30) REVERT: b 990 MET cc_start: 0.8756 (pmm) cc_final: 0.7917 (ptt) REVERT: b 995 ILE cc_start: 0.8581 (mm) cc_final: 0.8120 (mm) REVERT: b 1038 TYR cc_start: 0.7425 (t80) cc_final: 0.7132 (t80) REVERT: c 815 MET cc_start: 0.8519 (tpp) cc_final: 0.8235 (mmm) REVERT: c 876 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7680 (t0) REVERT: c 887 TRP cc_start: 0.8694 (t60) cc_final: 0.8393 (t-100) REVERT: c 917 THR cc_start: 0.8339 (p) cc_final: 0.8069 (p) REVERT: c 972 THR cc_start: 0.8245 (p) cc_final: 0.8018 (p) REVERT: c 1045 TRP cc_start: 0.8025 (m100) cc_final: 0.7749 (m-10) REVERT: d 586 MET cc_start: 0.7184 (tpp) cc_final: 0.6735 (mmm) REVERT: d 625 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7669 (pm20) REVERT: d 719 MET cc_start: 0.8284 (mmm) cc_final: 0.7685 (mmm) REVERT: d 913 LEU cc_start: 0.9465 (tp) cc_final: 0.9028 (mm) REVERT: d 933 HIS cc_start: 0.7122 (m-70) cc_final: 0.6862 (m170) REVERT: d 972 THR cc_start: 0.7785 (p) cc_final: 0.7459 (p) REVERT: d 990 MET cc_start: 0.8584 (pmm) cc_final: 0.7516 (ptt) REVERT: d 1002 ILE cc_start: 0.9284 (tt) cc_final: 0.9025 (pt) REVERT: d 1100 VAL cc_start: 0.8047 (t) cc_final: 0.7760 (p) REVERT: e 785 MET cc_start: 0.8417 (tmm) cc_final: 0.7789 (tmm) REVERT: e 876 ASN cc_start: 0.7682 (t0) cc_final: 0.7436 (t0) REVERT: e 905 SER cc_start: 0.8479 (m) cc_final: 0.7624 (t) REVERT: e 916 ASP cc_start: 0.6285 (p0) cc_final: 0.6023 (p0) REVERT: e 937 SER cc_start: 0.8343 (p) cc_final: 0.7984 (t) REVERT: e 1104 THR cc_start: 0.7722 (t) cc_final: 0.7204 (t) outliers start: 2 outliers final: 0 residues processed: 1166 average time/residue: 0.5168 time to fit residues: 1006.1328 Evaluate side-chains 987 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 986 time to evaluate : 4.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 551 optimal weight: 0.0270 chunk 375 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 492 optimal weight: 0.3980 chunk 273 optimal weight: 1.9990 chunk 565 optimal weight: 0.0870 chunk 457 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 338 optimal weight: 1.9990 chunk 594 optimal weight: 0.4980 chunk 167 optimal weight: 0.0270 overall best weight: 0.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN B 668 GLN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS C 668 GLN C 787 ASN C 876 ASN D 876 ASN D 999 GLN E 787 ASN ** F 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 ASN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 999 GLN b 999 GLN c 593 GLN ** c1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 687 ASN d 725 GLN ** d 797 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 53900 Z= 0.160 Angle : 0.618 8.337 73420 Z= 0.311 Chirality : 0.043 0.306 8505 Planarity : 0.004 0.056 9565 Dihedral : 5.147 32.021 7400 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.09), residues: 6815 helix: -1.74 (0.10), residues: 2500 sheet: -0.25 (0.16), residues: 1035 loop : -2.61 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP b1066 HIS 0.006 0.001 HIS B 933 PHE 0.036 0.001 PHE K 60 TYR 0.022 0.001 TYR D1003 ARG 0.006 0.000 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1178 time to evaluate : 4.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 MET cc_start: 0.7915 (mmm) cc_final: 0.7666 (mmm) REVERT: A 800 LEU cc_start: 0.8373 (mt) cc_final: 0.7767 (tp) REVERT: A 814 MET cc_start: 0.8668 (mmm) cc_final: 0.8441 (mmp) REVERT: A 844 LEU cc_start: 0.7098 (tp) cc_final: 0.6845 (tp) REVERT: A 938 ARG cc_start: 0.6323 (mtm110) cc_final: 0.6044 (mtm110) REVERT: A 959 ILE cc_start: 0.9150 (tp) cc_final: 0.8940 (tp) REVERT: A 1018 ASP cc_start: 0.7688 (t0) cc_final: 0.7357 (t0) REVERT: A 1094 LEU cc_start: 0.8545 (mm) cc_final: 0.8126 (mt) REVERT: B 800 LEU cc_start: 0.8434 (mt) cc_final: 0.7828 (tp) REVERT: B 876 ASN cc_start: 0.8536 (m-40) cc_final: 0.8237 (t0) REVERT: B 1001 LEU cc_start: 0.8199 (tp) cc_final: 0.7840 (tp) REVERT: B 1011 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7793 (ttmt) REVERT: B 1038 TYR cc_start: 0.7512 (t80) cc_final: 0.7092 (t80) REVERT: B 1053 MET cc_start: 0.8399 (ttm) cc_final: 0.8123 (ttm) REVERT: C 812 GLN cc_start: 0.8101 (pm20) cc_final: 0.7804 (pm20) REVERT: C 830 LEU cc_start: 0.8160 (tp) cc_final: 0.7843 (tp) REVERT: C 844 LEU cc_start: 0.7456 (tp) cc_final: 0.7110 (tp) REVERT: C 885 ASP cc_start: 0.6980 (m-30) cc_final: 0.6387 (t70) REVERT: C 1018 ASP cc_start: 0.7823 (p0) cc_final: 0.7590 (p0) REVERT: D 800 LEU cc_start: 0.8256 (mt) cc_final: 0.8038 (mt) REVERT: D 814 MET cc_start: 0.9012 (mmm) cc_final: 0.8766 (mmm) REVERT: D 1038 TYR cc_start: 0.7350 (t80) cc_final: 0.6854 (t80) REVERT: E 719 MET cc_start: 0.8088 (tmm) cc_final: 0.7646 (tmm) REVERT: E 959 ILE cc_start: 0.9370 (pt) cc_final: 0.8854 (tp) REVERT: E 1018 ASP cc_start: 0.8234 (p0) cc_final: 0.7929 (p0) REVERT: E 1038 TYR cc_start: 0.6878 (t80) cc_final: 0.6393 (t80) REVERT: E 1053 MET cc_start: 0.8288 (ttp) cc_final: 0.7227 (ttp) REVERT: E 1055 ARG cc_start: 0.8150 (mpp80) cc_final: 0.7705 (mpt-90) REVERT: F 43 ILE cc_start: 0.8196 (mt) cc_final: 0.7816 (mp) REVERT: F 89 GLN cc_start: 0.8308 (mt0) cc_final: 0.8100 (mt0) REVERT: G 47 VAL cc_start: 0.7412 (t) cc_final: 0.7077 (t) REVERT: G 50 ARG cc_start: 0.6536 (mtt90) cc_final: 0.5865 (ttm-80) REVERT: G 142 VAL cc_start: 0.6903 (t) cc_final: 0.6507 (p) REVERT: H 38 THR cc_start: 0.9071 (p) cc_final: 0.8480 (t) REVERT: H 64 ASP cc_start: 0.7954 (p0) cc_final: 0.7303 (p0) REVERT: H 69 PHE cc_start: 0.7935 (m-80) cc_final: 0.7699 (m-80) REVERT: H 112 MET cc_start: 0.8834 (mtm) cc_final: 0.7689 (mtm) REVERT: I 28 LEU cc_start: 0.8102 (tp) cc_final: 0.7794 (mt) REVERT: J 31 ARG cc_start: 0.6864 (mtp85) cc_final: 0.6097 (ttp-110) REVERT: J 98 MET cc_start: 0.2411 (ttm) cc_final: 0.2078 (ttm) REVERT: L 89 GLN cc_start: 0.8336 (mt0) cc_final: 0.8115 (mt0) REVERT: M 31 ARG cc_start: 0.6443 (mtp85) cc_final: 0.5889 (ttm110) REVERT: M 98 MET cc_start: 0.1959 (mtp) cc_final: 0.1744 (mtp) REVERT: N 38 THR cc_start: 0.8860 (p) cc_final: 0.8308 (t) REVERT: N 39 SER cc_start: 0.9284 (p) cc_final: 0.9079 (p) REVERT: N 51 ILE cc_start: 0.8527 (tp) cc_final: 0.7916 (pt) REVERT: N 64 ASP cc_start: 0.8315 (p0) cc_final: 0.7965 (p0) REVERT: N 112 MET cc_start: 0.8086 (mmt) cc_final: 0.7396 (mmm) REVERT: N 143 SER cc_start: 0.7988 (t) cc_final: 0.7523 (m) REVERT: O 142 VAL cc_start: 0.6807 (t) cc_final: 0.6569 (t) REVERT: O 147 LEU cc_start: 0.7300 (mm) cc_final: 0.6973 (mm) REVERT: Q 38 THR cc_start: 0.9181 (p) cc_final: 0.8748 (t) REVERT: Q 51 ILE cc_start: 0.8258 (tp) cc_final: 0.7904 (pt) REVERT: Q 64 ASP cc_start: 0.8338 (p0) cc_final: 0.7963 (p0) REVERT: Q 143 SER cc_start: 0.7926 (t) cc_final: 0.7577 (m) REVERT: R 98 MET cc_start: 0.5270 (ttm) cc_final: 0.4877 (ttm) REVERT: S 31 ARG cc_start: 0.6767 (mtp85) cc_final: 0.6024 (ttm110) REVERT: S 76 LEU cc_start: 0.5595 (pp) cc_final: 0.4768 (tt) REVERT: S 112 MET cc_start: 0.7647 (mtm) cc_final: 0.7139 (mtm) REVERT: T 56 ASP cc_start: 0.7899 (m-30) cc_final: 0.7101 (m-30) REVERT: T 64 ASP cc_start: 0.8252 (p0) cc_final: 0.7691 (p0) REVERT: T 101 ASP cc_start: 0.7699 (t70) cc_final: 0.7387 (t0) REVERT: a 575 THR cc_start: 0.6271 (t) cc_final: 0.5965 (t) REVERT: a 815 MET cc_start: 0.8736 (mmt) cc_final: 0.8369 (mmm) REVERT: a 828 VAL cc_start: 0.8546 (m) cc_final: 0.8260 (t) REVERT: a 849 TYR cc_start: 0.7764 (t80) cc_final: 0.7555 (t80) REVERT: a 965 ILE cc_start: 0.8381 (mm) cc_final: 0.7979 (tp) REVERT: a 972 THR cc_start: 0.7970 (p) cc_final: 0.7704 (p) REVERT: a 995 ILE cc_start: 0.8452 (mm) cc_final: 0.8184 (mm) REVERT: a 1101 LEU cc_start: 0.8566 (mt) cc_final: 0.8245 (mp) REVERT: b 776 MET cc_start: 0.6179 (ptm) cc_final: 0.5893 (ptm) REVERT: b 785 MET cc_start: 0.8439 (tmm) cc_final: 0.8117 (tmm) REVERT: b 792 LEU cc_start: 0.8366 (tp) cc_final: 0.8141 (tt) REVERT: b 947 ARG cc_start: 0.5518 (mmt-90) cc_final: 0.5305 (mpt180) REVERT: b 964 GLU cc_start: 0.6863 (pp20) cc_final: 0.6568 (tm-30) REVERT: b 990 MET cc_start: 0.8703 (pmm) cc_final: 0.7867 (ptt) REVERT: b 995 ILE cc_start: 0.8557 (mm) cc_final: 0.8356 (mm) REVERT: b 998 ASN cc_start: 0.8142 (m110) cc_final: 0.7868 (m-40) REVERT: b 1038 TYR cc_start: 0.7352 (t80) cc_final: 0.7053 (t80) REVERT: c 625 GLN cc_start: 0.8284 (tm-30) cc_final: 0.7853 (pm20) REVERT: c 797 GLN cc_start: 0.7534 (tp40) cc_final: 0.7140 (tm-30) REVERT: c 887 TRP cc_start: 0.8631 (t60) cc_final: 0.8300 (t-100) REVERT: c 917 THR cc_start: 0.8076 (p) cc_final: 0.7794 (p) REVERT: c 978 HIS cc_start: 0.7374 (p-80) cc_final: 0.7164 (p90) REVERT: c 1045 TRP cc_start: 0.8341 (m100) cc_final: 0.7738 (m-10) REVERT: d 586 MET cc_start: 0.7080 (tpp) cc_final: 0.6571 (mmm) REVERT: d 631 VAL cc_start: 0.7326 (m) cc_final: 0.7122 (t) REVERT: d 699 ASP cc_start: 0.7166 (m-30) cc_final: 0.6910 (m-30) REVERT: d 709 ASP cc_start: 0.6860 (t70) cc_final: 0.6645 (t70) REVERT: d 838 SER cc_start: 0.8170 (p) cc_final: 0.7334 (p) REVERT: d 933 HIS cc_start: 0.7006 (m-70) cc_final: 0.6792 (m170) REVERT: d 964 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6380 (tm-30) REVERT: d 972 THR cc_start: 0.7718 (p) cc_final: 0.7379 (p) REVERT: d 978 HIS cc_start: 0.7693 (p90) cc_final: 0.7458 (p-80) REVERT: d 990 MET cc_start: 0.8627 (pmm) cc_final: 0.7497 (ptt) REVERT: d 1100 VAL cc_start: 0.8130 (t) cc_final: 0.7859 (p) REVERT: e 785 MET cc_start: 0.8253 (tmm) cc_final: 0.7546 (tmm) REVERT: e 815 MET cc_start: 0.8275 (tpp) cc_final: 0.7969 (tpp) REVERT: e 916 ASP cc_start: 0.6273 (p0) cc_final: 0.6043 (p0) REVERT: e 957 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7614 (ttmm) outliers start: 2 outliers final: 2 residues processed: 1178 average time/residue: 0.5095 time to fit residues: 1001.5272 Evaluate side-chains 985 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 983 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 222 optimal weight: 1.9990 chunk 596 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 388 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 662 optimal weight: 0.0000 chunk 550 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 219 optimal weight: 2.9990 chunk 347 optimal weight: 5.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN A 978 HIS ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS C 787 ASN C 876 ASN D 876 ASN D 999 GLN E 787 ASN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 876 ASN b 803 GLN ** b 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 789 GLN e 593 GLN e 625 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 53900 Z= 0.183 Angle : 0.630 11.644 73420 Z= 0.316 Chirality : 0.044 0.187 8505 Planarity : 0.004 0.075 9565 Dihedral : 5.084 30.882 7400 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.09), residues: 6815 helix: -1.52 (0.10), residues: 2500 sheet: -0.42 (0.17), residues: 900 loop : -2.51 (0.10), residues: 3415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E1045 HIS 0.006 0.001 HIS B 933 PHE 0.020 0.001 PHE D 851 TYR 0.019 0.002 TYR E 912 ARG 0.009 0.001 ARG e 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1146 time to evaluate : 4.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 MET cc_start: 0.6982 (tmm) cc_final: 0.6132 (tmm) REVERT: A 800 LEU cc_start: 0.8382 (mt) cc_final: 0.7758 (tp) REVERT: A 1018 ASP cc_start: 0.7894 (t0) cc_final: 0.7387 (t0) REVERT: A 1025 SER cc_start: 0.6065 (m) cc_final: 0.5751 (m) REVERT: A 1094 LEU cc_start: 0.8330 (mm) cc_final: 0.7986 (tp) REVERT: B 800 LEU cc_start: 0.8480 (mt) cc_final: 0.7891 (tp) REVERT: B 876 ASN cc_start: 0.8602 (m-40) cc_final: 0.8281 (t0) REVERT: B 934 ARG cc_start: 0.7547 (mpt180) cc_final: 0.6999 (mpt180) REVERT: B 1018 ASP cc_start: 0.7582 (p0) cc_final: 0.7237 (p0) REVERT: B 1038 TYR cc_start: 0.7493 (t80) cc_final: 0.7277 (t80) REVERT: C 812 GLN cc_start: 0.8201 (pm20) cc_final: 0.7770 (pm20) REVERT: C 815 MET cc_start: 0.7657 (mmm) cc_final: 0.7352 (mmm) REVERT: C 830 LEU cc_start: 0.8083 (tp) cc_final: 0.7842 (tp) REVERT: C 844 LEU cc_start: 0.7518 (tp) cc_final: 0.7081 (tp) REVERT: C 885 ASP cc_start: 0.6951 (m-30) cc_final: 0.6323 (t70) REVERT: C 1018 ASP cc_start: 0.7916 (p0) cc_final: 0.7551 (p0) REVERT: C 1038 TYR cc_start: 0.7073 (t80) cc_final: 0.6698 (t80) REVERT: D 814 MET cc_start: 0.9026 (mmm) cc_final: 0.8694 (mmm) REVERT: D 834 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7801 (mtp85) REVERT: D 1038 TYR cc_start: 0.7396 (t80) cc_final: 0.7026 (t80) REVERT: D 1053 MET cc_start: 0.8171 (ttm) cc_final: 0.7925 (ttm) REVERT: E 933 HIS cc_start: 0.7108 (t-170) cc_final: 0.6846 (t-170) REVERT: E 959 ILE cc_start: 0.9363 (pt) cc_final: 0.8912 (tp) REVERT: E 1018 ASP cc_start: 0.8233 (p0) cc_final: 0.7968 (p0) REVERT: E 1038 TYR cc_start: 0.6998 (t80) cc_final: 0.6469 (t80) REVERT: E 1053 MET cc_start: 0.8269 (ttp) cc_final: 0.7211 (ttp) REVERT: E 1055 ARG cc_start: 0.8075 (mpp80) cc_final: 0.7656 (mpt-90) REVERT: F 43 ILE cc_start: 0.8071 (mt) cc_final: 0.7712 (mp) REVERT: F 89 GLN cc_start: 0.8381 (mt0) cc_final: 0.8162 (mt0) REVERT: F 141 GLU cc_start: 0.7318 (tm-30) cc_final: 0.7087 (tm-30) REVERT: G 132 LEU cc_start: 0.1476 (tt) cc_final: 0.1236 (tp) REVERT: G 142 VAL cc_start: 0.6906 (t) cc_final: 0.6471 (p) REVERT: H 38 THR cc_start: 0.8989 (p) cc_final: 0.8614 (t) REVERT: H 64 ASP cc_start: 0.8037 (p0) cc_final: 0.7448 (p0) REVERT: H 112 MET cc_start: 0.8912 (mtm) cc_final: 0.7861 (mtm) REVERT: H 121 ASN cc_start: 0.8370 (t0) cc_final: 0.8129 (t0) REVERT: I 28 LEU cc_start: 0.8088 (tp) cc_final: 0.7582 (mt) REVERT: J 31 ARG cc_start: 0.6847 (mtp85) cc_final: 0.6088 (ttp-110) REVERT: J 98 MET cc_start: 0.2315 (ttm) cc_final: 0.1977 (ttm) REVERT: J 140 ILE cc_start: 0.6539 (mt) cc_final: 0.6161 (mt) REVERT: K 124 ARG cc_start: 0.6411 (ptt180) cc_final: 0.6104 (ptt180) REVERT: L 89 GLN cc_start: 0.8341 (mt0) cc_final: 0.8092 (mt0) REVERT: M 31 ARG cc_start: 0.6394 (mtp85) cc_final: 0.5973 (ttm110) REVERT: M 98 MET cc_start: 0.1920 (mtp) cc_final: 0.1662 (mtp) REVERT: N 38 THR cc_start: 0.8864 (p) cc_final: 0.8373 (t) REVERT: N 51 ILE cc_start: 0.8506 (tp) cc_final: 0.7945 (pt) REVERT: N 56 ASP cc_start: 0.7032 (m-30) cc_final: 0.6820 (m-30) REVERT: N 64 ASP cc_start: 0.8455 (p0) cc_final: 0.8128 (p0) REVERT: N 101 ASP cc_start: 0.8172 (t70) cc_final: 0.7967 (t70) REVERT: N 112 MET cc_start: 0.7912 (mmt) cc_final: 0.7384 (mmm) REVERT: N 143 SER cc_start: 0.8058 (t) cc_final: 0.7631 (m) REVERT: O 147 LEU cc_start: 0.7465 (mm) cc_final: 0.7155 (mm) REVERT: Q 38 THR cc_start: 0.9194 (p) cc_final: 0.8448 (t) REVERT: Q 51 ILE cc_start: 0.8245 (tp) cc_final: 0.7883 (pt) REVERT: Q 64 ASP cc_start: 0.8342 (p0) cc_final: 0.7990 (p0) REVERT: Q 101 ASP cc_start: 0.7650 (t0) cc_final: 0.7413 (t70) REVERT: Q 143 SER cc_start: 0.7885 (t) cc_final: 0.7501 (m) REVERT: R 98 MET cc_start: 0.5278 (ttm) cc_final: 0.5026 (ttm) REVERT: R 141 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6921 (tm-30) REVERT: S 31 ARG cc_start: 0.6797 (mtp85) cc_final: 0.6065 (ttm110) REVERT: S 76 LEU cc_start: 0.5777 (pp) cc_final: 0.4926 (tt) REVERT: S 112 MET cc_start: 0.7646 (mtm) cc_final: 0.7250 (mtm) REVERT: T 56 ASP cc_start: 0.7889 (m-30) cc_final: 0.7152 (m-30) REVERT: T 64 ASP cc_start: 0.8288 (p0) cc_final: 0.7783 (p0) REVERT: T 83 GLN cc_start: 0.8922 (mp10) cc_final: 0.8490 (mp10) REVERT: a 625 GLN cc_start: 0.7591 (pm20) cc_final: 0.6369 (pm20) REVERT: a 815 MET cc_start: 0.8583 (mmt) cc_final: 0.8271 (tpp) REVERT: a 828 VAL cc_start: 0.8608 (m) cc_final: 0.8278 (t) REVERT: a 965 ILE cc_start: 0.8430 (mm) cc_final: 0.7969 (tp) REVERT: a 995 ILE cc_start: 0.8459 (mm) cc_final: 0.8013 (mm) REVERT: a 1002 ILE cc_start: 0.9106 (tt) cc_final: 0.8731 (pt) REVERT: a 1101 LEU cc_start: 0.8581 (mt) cc_final: 0.8232 (mp) REVERT: b 776 MET cc_start: 0.6219 (ptm) cc_final: 0.5862 (ptm) REVERT: b 785 MET cc_start: 0.8566 (tmm) cc_final: 0.8083 (tmm) REVERT: b 792 LEU cc_start: 0.8376 (tp) cc_final: 0.8116 (tt) REVERT: b 964 GLU cc_start: 0.6875 (pp20) cc_final: 0.6589 (tm-30) REVERT: b 990 MET cc_start: 0.8383 (pmm) cc_final: 0.7752 (ptt) REVERT: b 1038 TYR cc_start: 0.7586 (t80) cc_final: 0.7367 (t80) REVERT: c 586 MET cc_start: 0.7115 (tpp) cc_final: 0.6677 (mmm) REVERT: c 625 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7899 (pm20) REVERT: c 760 ARG cc_start: 0.7094 (tmm160) cc_final: 0.6852 (ptm-80) REVERT: c 776 MET cc_start: 0.5350 (ptm) cc_final: 0.5128 (ptm) REVERT: c 887 TRP cc_start: 0.8676 (t60) cc_final: 0.8340 (t-100) REVERT: c 927 ASN cc_start: 0.7411 (t0) cc_final: 0.7202 (t0) REVERT: c 947 ARG cc_start: 0.5287 (mtm-85) cc_final: 0.4784 (mtm-85) REVERT: c 972 THR cc_start: 0.8272 (p) cc_final: 0.8018 (p) REVERT: c 1045 TRP cc_start: 0.8389 (m100) cc_final: 0.7593 (m-10) REVERT: d 586 MET cc_start: 0.7111 (tpp) cc_final: 0.6392 (mmm) REVERT: d 838 SER cc_start: 0.8060 (p) cc_final: 0.7041 (p) REVERT: d 933 HIS cc_start: 0.7118 (m-70) cc_final: 0.6830 (m170) REVERT: d 972 THR cc_start: 0.7650 (p) cc_final: 0.7422 (p) REVERT: d 978 HIS cc_start: 0.7804 (p90) cc_final: 0.7535 (p-80) REVERT: d 990 MET cc_start: 0.8751 (pmm) cc_final: 0.7634 (ptt) REVERT: d 1100 VAL cc_start: 0.8108 (t) cc_final: 0.7804 (p) REVERT: e 625 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7255 (mp10) REVERT: e 785 MET cc_start: 0.8260 (tmm) cc_final: 0.7642 (tmm) REVERT: e 815 MET cc_start: 0.8452 (tpp) cc_final: 0.8161 (tpp) REVERT: e 957 LYS cc_start: 0.8263 (ttmm) cc_final: 0.8011 (ttmm) outliers start: 0 outliers final: 0 residues processed: 1146 average time/residue: 0.5329 time to fit residues: 1031.6946 Evaluate side-chains 970 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 970 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 638 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 377 optimal weight: 0.9980 chunk 483 optimal weight: 0.7980 chunk 374 optimal weight: 0.7980 chunk 557 optimal weight: 0.9990 chunk 370 optimal weight: 0.9980 chunk 660 optimal weight: 0.0270 chunk 413 optimal weight: 0.9980 chunk 402 optimal weight: 5.9990 chunk 304 optimal weight: 0.1980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS C 787 ASN C 876 ASN D 876 ASN D 999 GLN E 787 ASN N 66 GLN Q 121 ASN a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 933 HIS b 812 GLN ** b 876 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 593 GLN d 846 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 991 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 53900 Z= 0.192 Angle : 0.637 13.111 73420 Z= 0.320 Chirality : 0.044 0.181 8505 Planarity : 0.004 0.077 9565 Dihedral : 5.051 28.529 7400 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 0.02 % Allowed : 1.91 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.10), residues: 6815 helix: -1.37 (0.10), residues: 2500 sheet: -0.45 (0.17), residues: 900 loop : -2.44 (0.10), residues: 3415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E1045 HIS 0.006 0.001 HIS B 933 PHE 0.022 0.002 PHE K 69 TYR 0.019 0.002 TYR C 912 ARG 0.009 0.001 ARG a1056 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1116 time to evaluate : 4.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LEU cc_start: 0.8392 (mt) cc_final: 0.7760 (tp) REVERT: A 1018 ASP cc_start: 0.7846 (t0) cc_final: 0.7352 (t0) REVERT: A 1094 LEU cc_start: 0.8344 (mm) cc_final: 0.7983 (tp) REVERT: B 800 LEU cc_start: 0.8429 (mt) cc_final: 0.7861 (tp) REVERT: B 876 ASN cc_start: 0.8616 (m-40) cc_final: 0.8308 (t0) REVERT: B 934 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7099 (mpt180) REVERT: B 1018 ASP cc_start: 0.7630 (p0) cc_final: 0.7298 (p0) REVERT: B 1038 TYR cc_start: 0.7551 (t80) cc_final: 0.7287 (t80) REVERT: B 1048 ILE cc_start: 0.8405 (tp) cc_final: 0.8123 (tp) REVERT: C 812 GLN cc_start: 0.8156 (pm20) cc_final: 0.7788 (pm20) REVERT: C 815 MET cc_start: 0.7515 (mmm) cc_final: 0.7291 (mmm) REVERT: C 830 LEU cc_start: 0.7995 (tp) cc_final: 0.7754 (tp) REVERT: C 844 LEU cc_start: 0.7584 (tp) cc_final: 0.7101 (tp) REVERT: C 885 ASP cc_start: 0.6966 (m-30) cc_final: 0.6325 (t70) REVERT: C 982 ARG cc_start: 0.7152 (ttp80) cc_final: 0.6874 (ttt-90) REVERT: C 1018 ASP cc_start: 0.7826 (p0) cc_final: 0.7580 (p0) REVERT: C 1038 TYR cc_start: 0.7120 (t80) cc_final: 0.6675 (t80) REVERT: D 776 MET cc_start: 0.7366 (mmm) cc_final: 0.7146 (mmm) REVERT: D 938 ARG cc_start: 0.6967 (mtm110) cc_final: 0.6668 (mtm110) REVERT: D 1038 TYR cc_start: 0.7414 (t80) cc_final: 0.7024 (t80) REVERT: D 1053 MET cc_start: 0.8258 (ttm) cc_final: 0.7953 (ttm) REVERT: E 800 LEU cc_start: 0.8620 (mt) cc_final: 0.7983 (tp) REVERT: E 815 MET cc_start: 0.8260 (mmm) cc_final: 0.8017 (mmm) REVERT: E 959 ILE cc_start: 0.9318 (pt) cc_final: 0.8883 (tp) REVERT: E 1038 TYR cc_start: 0.7051 (t80) cc_final: 0.6601 (t80) REVERT: E 1053 MET cc_start: 0.8293 (ttp) cc_final: 0.7384 (ttp) REVERT: E 1055 ARG cc_start: 0.8099 (mpp80) cc_final: 0.7543 (mpt-90) REVERT: F 141 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6878 (tm-30) REVERT: G 51 ILE cc_start: 0.7737 (pt) cc_final: 0.7456 (pt) REVERT: G 142 VAL cc_start: 0.6940 (t) cc_final: 0.6475 (p) REVERT: H 38 THR cc_start: 0.8878 (p) cc_final: 0.8633 (t) REVERT: H 70 THR cc_start: 0.7415 (m) cc_final: 0.7214 (m) REVERT: H 83 GLN cc_start: 0.8690 (mp10) cc_final: 0.8324 (mp10) REVERT: H 112 MET cc_start: 0.9012 (mtm) cc_final: 0.7576 (mtm) REVERT: H 117 ASP cc_start: 0.7840 (t0) cc_final: 0.6860 (t0) REVERT: H 121 ASN cc_start: 0.8332 (t0) cc_final: 0.8071 (t0) REVERT: I 28 LEU cc_start: 0.8008 (tp) cc_final: 0.7595 (mt) REVERT: J 31 ARG cc_start: 0.6743 (mtp85) cc_final: 0.5756 (mtm-85) REVERT: J 98 MET cc_start: 0.2284 (ttm) cc_final: 0.1980 (ttm) REVERT: J 112 MET cc_start: 0.7682 (mmm) cc_final: 0.7328 (mmm) REVERT: J 140 ILE cc_start: 0.6509 (mt) cc_final: 0.6138 (mt) REVERT: K 124 ARG cc_start: 0.6563 (ptt180) cc_final: 0.6311 (ptt180) REVERT: L 89 GLN cc_start: 0.8304 (mt0) cc_final: 0.8076 (mt0) REVERT: L 138 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.5782 (tpp80) REVERT: M 31 ARG cc_start: 0.6336 (mtp85) cc_final: 0.6004 (ttm110) REVERT: N 38 THR cc_start: 0.8935 (p) cc_final: 0.8445 (t) REVERT: N 51 ILE cc_start: 0.8456 (tp) cc_final: 0.7903 (pt) REVERT: N 64 ASP cc_start: 0.8480 (p0) cc_final: 0.8084 (p0) REVERT: N 101 ASP cc_start: 0.7923 (t70) cc_final: 0.7652 (t70) REVERT: N 143 SER cc_start: 0.8193 (t) cc_final: 0.7547 (m) REVERT: P 31 ARG cc_start: 0.6727 (mtp85) cc_final: 0.5778 (ttm110) REVERT: P 112 MET cc_start: 0.7912 (mpp) cc_final: 0.7706 (mpp) REVERT: Q 38 THR cc_start: 0.9156 (p) cc_final: 0.8735 (t) REVERT: Q 51 ILE cc_start: 0.8323 (tp) cc_final: 0.7937 (pt) REVERT: Q 64 ASP cc_start: 0.8384 (p0) cc_final: 0.8108 (p0) REVERT: Q 83 GLN cc_start: 0.8811 (mm-40) cc_final: 0.8421 (mm110) REVERT: Q 98 MET cc_start: 0.7471 (tpt) cc_final: 0.7184 (tpp) REVERT: Q 124 ARG cc_start: 0.6320 (ptt180) cc_final: 0.6013 (ptt180) REVERT: Q 143 SER cc_start: 0.7818 (t) cc_final: 0.7497 (m) REVERT: R 29 ASP cc_start: 0.5720 (t0) cc_final: 0.5343 (t70) REVERT: R 98 MET cc_start: 0.5489 (ttm) cc_final: 0.5201 (ttm) REVERT: S 31 ARG cc_start: 0.6789 (mtp85) cc_final: 0.6073 (ttm110) REVERT: T 56 ASP cc_start: 0.8014 (m-30) cc_final: 0.7285 (m-30) REVERT: T 64 ASP cc_start: 0.8449 (p0) cc_final: 0.7991 (p0) REVERT: T 83 GLN cc_start: 0.8911 (mp10) cc_final: 0.8526 (mp10) REVERT: a 794 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7678 (ttm-80) REVERT: a 802 LEU cc_start: 0.7144 (tp) cc_final: 0.6861 (tt) REVERT: a 815 MET cc_start: 0.8624 (mmt) cc_final: 0.8399 (tpp) REVERT: a 828 VAL cc_start: 0.8569 (m) cc_final: 0.8271 (t) REVERT: a 965 ILE cc_start: 0.8526 (mm) cc_final: 0.8021 (tp) REVERT: a 990 MET cc_start: 0.8752 (pmm) cc_final: 0.7948 (ptt) REVERT: a 1045 TRP cc_start: 0.8272 (m100) cc_final: 0.8040 (m100) REVERT: a 1101 LEU cc_start: 0.8587 (mt) cc_final: 0.8222 (mp) REVERT: b 785 MET cc_start: 0.8563 (tmm) cc_final: 0.8126 (tmm) REVERT: b 792 LEU cc_start: 0.8492 (tp) cc_final: 0.8119 (tt) REVERT: b 814 MET cc_start: 0.7884 (ttm) cc_final: 0.7648 (mtp) REVERT: b 964 GLU cc_start: 0.6874 (pp20) cc_final: 0.6572 (tm-30) REVERT: b 972 THR cc_start: 0.8153 (p) cc_final: 0.7706 (p) REVERT: b 990 MET cc_start: 0.8520 (pmm) cc_final: 0.7799 (ptt) REVERT: b 995 ILE cc_start: 0.8560 (mm) cc_final: 0.8189 (mm) REVERT: b 1070 TRP cc_start: 0.8067 (m-10) cc_final: 0.7820 (m-10) REVERT: c 625 GLN cc_start: 0.8382 (tm-30) cc_final: 0.7833 (pm20) REVERT: c 797 GLN cc_start: 0.6863 (tm-30) cc_final: 0.6548 (tm-30) REVERT: c 815 MET cc_start: 0.8278 (tpp) cc_final: 0.8024 (mmm) REVERT: c 887 TRP cc_start: 0.8721 (t60) cc_final: 0.8409 (t-100) REVERT: c 917 THR cc_start: 0.7978 (p) cc_final: 0.7617 (p) REVERT: c 990 MET cc_start: 0.8848 (pmm) cc_final: 0.7651 (ptt) REVERT: d 586 MET cc_start: 0.7138 (tpp) cc_final: 0.6407 (mmm) REVERT: d 709 ASP cc_start: 0.7720 (t70) cc_final: 0.7449 (t0) REVERT: d 972 THR cc_start: 0.7666 (p) cc_final: 0.7413 (p) REVERT: d 990 MET cc_start: 0.8773 (pmm) cc_final: 0.7254 (ptp) REVERT: d 1100 VAL cc_start: 0.8082 (t) cc_final: 0.7787 (p) REVERT: e 785 MET cc_start: 0.8352 (tmm) cc_final: 0.7785 (tmm) REVERT: e 794 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6984 (ttp80) REVERT: e 957 LYS cc_start: 0.8234 (ttmm) cc_final: 0.8004 (ttmm) REVERT: e 990 MET cc_start: 0.9130 (pmm) cc_final: 0.7584 (ptt) outliers start: 1 outliers final: 1 residues processed: 1116 average time/residue: 0.5586 time to fit residues: 1060.9446 Evaluate side-chains 961 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 960 time to evaluate : 4.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 408 optimal weight: 0.8980 chunk 263 optimal weight: 0.1980 chunk 394 optimal weight: 0.2980 chunk 198 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 chunk 127 optimal weight: 0.0670 chunk 419 optimal weight: 0.6980 chunk 449 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 518 optimal weight: 1.9990 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS C 787 ASN C 876 ASN C 925 GLN D 876 ASN D 999 GLN E 787 ASN N 53 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 999 GLN b 876 ASN b 927 ASN c 593 GLN c1071 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 991 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 53900 Z= 0.158 Angle : 0.624 11.406 73420 Z= 0.310 Chirality : 0.043 0.196 8505 Planarity : 0.004 0.078 9565 Dihedral : 4.841 27.542 7400 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.04 % Allowed : 0.91 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.10), residues: 6815 helix: -1.22 (0.10), residues: 2540 sheet: -0.38 (0.17), residues: 900 loop : -2.40 (0.10), residues: 3375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E1045 HIS 0.008 0.001 HIS B 933 PHE 0.031 0.001 PHE S 69 TYR 0.019 0.001 TYR a1038 ARG 0.009 0.001 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1111 time to evaluate : 4.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 LEU cc_start: 0.8296 (mt) cc_final: 0.7695 (tp) REVERT: A 814 MET cc_start: 0.8563 (mmm) cc_final: 0.8130 (mmm) REVERT: A 844 LEU cc_start: 0.7168 (tp) cc_final: 0.6886 (tp) REVERT: A 1018 ASP cc_start: 0.7905 (t0) cc_final: 0.7316 (t0) REVERT: A 1094 LEU cc_start: 0.8393 (mm) cc_final: 0.7983 (tp) REVERT: B 800 LEU cc_start: 0.8424 (mt) cc_final: 0.7845 (tp) REVERT: B 876 ASN cc_start: 0.8606 (m-40) cc_final: 0.8281 (t0) REVERT: B 1003 TYR cc_start: 0.6167 (t80) cc_final: 0.5567 (t80) REVERT: B 1018 ASP cc_start: 0.7623 (p0) cc_final: 0.7173 (p0) REVERT: B 1048 ILE cc_start: 0.8355 (tp) cc_final: 0.8046 (tp) REVERT: C 812 GLN cc_start: 0.8146 (pm20) cc_final: 0.7739 (pm20) REVERT: C 830 LEU cc_start: 0.8127 (tp) cc_final: 0.7869 (tp) REVERT: C 885 ASP cc_start: 0.7052 (m-30) cc_final: 0.6432 (t70) REVERT: C 967 ASP cc_start: 0.7688 (m-30) cc_final: 0.7477 (m-30) REVERT: C 1018 ASP cc_start: 0.7796 (p0) cc_final: 0.7481 (p0) REVERT: C 1038 TYR cc_start: 0.6967 (t80) cc_final: 0.6711 (t80) REVERT: D 719 MET cc_start: 0.7556 (mmm) cc_final: 0.7036 (tpp) REVERT: D 785 MET cc_start: 0.6299 (tmm) cc_final: 0.5613 (pmm) REVERT: D 1038 TYR cc_start: 0.7430 (t80) cc_final: 0.7071 (t80) REVERT: D 1053 MET cc_start: 0.8316 (ttm) cc_final: 0.7993 (ttm) REVERT: E 719 MET cc_start: 0.7440 (tmm) cc_final: 0.7194 (tmm) REVERT: E 815 MET cc_start: 0.8248 (mmm) cc_final: 0.7963 (mmm) REVERT: E 1053 MET cc_start: 0.8228 (ttp) cc_final: 0.7927 (tmm) REVERT: E 1055 ARG cc_start: 0.8125 (mpp80) cc_final: 0.7538 (mpt-90) REVERT: F 141 GLU cc_start: 0.7380 (tm-30) cc_final: 0.7007 (tm-30) REVERT: G 51 ILE cc_start: 0.7680 (pt) cc_final: 0.7463 (pt) REVERT: H 38 THR cc_start: 0.8825 (p) cc_final: 0.8588 (t) REVERT: H 85 ASP cc_start: 0.7152 (m-30) cc_final: 0.6743 (m-30) REVERT: H 112 MET cc_start: 0.8931 (mtm) cc_final: 0.7646 (mtm) REVERT: H 117 ASP cc_start: 0.7857 (t0) cc_final: 0.6949 (t0) REVERT: H 121 ASN cc_start: 0.8337 (t0) cc_final: 0.8072 (t0) REVERT: J 31 ARG cc_start: 0.6913 (mtp85) cc_final: 0.5823 (mtm-85) REVERT: J 98 MET cc_start: 0.2455 (ttm) cc_final: 0.1964 (ttm) REVERT: J 140 ILE cc_start: 0.6469 (mt) cc_final: 0.6114 (mt) REVERT: K 101 ASP cc_start: 0.7560 (t70) cc_final: 0.7141 (t0) REVERT: L 89 GLN cc_start: 0.8305 (mt0) cc_final: 0.8003 (mt0) REVERT: L 138 ARG cc_start: 0.7405 (mmm-85) cc_final: 0.6309 (tpp80) REVERT: M 31 ARG cc_start: 0.6291 (mtp85) cc_final: 0.5901 (ttm110) REVERT: N 38 THR cc_start: 0.8876 (p) cc_final: 0.8440 (t) REVERT: N 51 ILE cc_start: 0.8432 (tp) cc_final: 0.7930 (pt) REVERT: N 64 ASP cc_start: 0.8433 (p0) cc_final: 0.8066 (p0) REVERT: N 101 ASP cc_start: 0.7923 (t70) cc_final: 0.7687 (t70) REVERT: N 112 MET cc_start: 0.7925 (mmt) cc_final: 0.7702 (mmt) REVERT: N 121 ASN cc_start: 0.7953 (p0) cc_final: 0.7696 (p0) REVERT: N 143 SER cc_start: 0.8047 (t) cc_final: 0.7661 (t) REVERT: O 89 GLN cc_start: 0.8944 (tp40) cc_final: 0.8645 (tm-30) REVERT: P 31 ARG cc_start: 0.6432 (mtp85) cc_final: 0.5462 (mtm-85) REVERT: P 112 MET cc_start: 0.7901 (mpp) cc_final: 0.7633 (mpp) REVERT: Q 51 ILE cc_start: 0.8166 (tp) cc_final: 0.7861 (pt) REVERT: Q 112 MET cc_start: 0.8217 (mmt) cc_final: 0.7404 (mmm) REVERT: Q 121 ASN cc_start: 0.8070 (t0) cc_final: 0.7768 (t0) REVERT: Q 124 ARG cc_start: 0.6417 (ptt180) cc_final: 0.6163 (ptt180) REVERT: Q 143 SER cc_start: 0.7768 (t) cc_final: 0.7458 (m) REVERT: S 31 ARG cc_start: 0.6689 (mtp85) cc_final: 0.5954 (ttm110) REVERT: T 56 ASP cc_start: 0.7928 (m-30) cc_final: 0.7009 (m-30) REVERT: T 64 ASP cc_start: 0.8437 (p0) cc_final: 0.7985 (p0) REVERT: T 83 GLN cc_start: 0.8839 (mp10) cc_final: 0.8548 (mp10) REVERT: T 101 ASP cc_start: 0.7726 (t70) cc_final: 0.7508 (t0) REVERT: a 794 ARG cc_start: 0.7999 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: a 815 MET cc_start: 0.8595 (mmt) cc_final: 0.8345 (tpp) REVERT: a 828 VAL cc_start: 0.8470 (m) cc_final: 0.8180 (t) REVERT: a 887 TRP cc_start: 0.8414 (t60) cc_final: 0.7828 (t60) REVERT: a 965 ILE cc_start: 0.8571 (mm) cc_final: 0.8133 (tp) REVERT: a 981 LEU cc_start: 0.8001 (tp) cc_final: 0.7745 (tp) REVERT: a 990 MET cc_start: 0.8632 (pmm) cc_final: 0.7898 (ptt) REVERT: a 1002 ILE cc_start: 0.9096 (tt) cc_final: 0.8726 (pt) REVERT: a 1045 TRP cc_start: 0.8190 (m100) cc_final: 0.7853 (m100) REVERT: a 1101 LEU cc_start: 0.8534 (mt) cc_final: 0.7706 (mt) REVERT: b 586 MET cc_start: 0.6803 (tpp) cc_final: 0.6092 (mmm) REVERT: b 776 MET cc_start: 0.6190 (ptm) cc_final: 0.5942 (ptm) REVERT: b 785 MET cc_start: 0.8486 (tmm) cc_final: 0.7924 (tmm) REVERT: b 792 LEU cc_start: 0.8413 (tp) cc_final: 0.8129 (tt) REVERT: b 814 MET cc_start: 0.7802 (ttm) cc_final: 0.7522 (mtp) REVERT: b 964 GLU cc_start: 0.6820 (pp20) cc_final: 0.6526 (tm-30) REVERT: b 972 THR cc_start: 0.8105 (p) cc_final: 0.7725 (p) REVERT: b 990 MET cc_start: 0.8418 (pmm) cc_final: 0.7799 (ptt) REVERT: b 995 ILE cc_start: 0.8550 (mm) cc_final: 0.8241 (mm) REVERT: c 625 GLN cc_start: 0.8331 (tm-30) cc_final: 0.7825 (pm20) REVERT: c 815 MET cc_start: 0.8388 (tpp) cc_final: 0.8105 (mmm) REVERT: c 887 TRP cc_start: 0.8672 (t60) cc_final: 0.8346 (t-100) REVERT: c 972 THR cc_start: 0.8151 (p) cc_final: 0.7819 (p) REVERT: c 990 MET cc_start: 0.8859 (pmm) cc_final: 0.7699 (ptt) REVERT: d 586 MET cc_start: 0.7064 (tpp) cc_final: 0.6236 (mmm) REVERT: d 709 ASP cc_start: 0.7693 (t70) cc_final: 0.7432 (t0) REVERT: d 964 GLU cc_start: 0.6792 (pp20) cc_final: 0.6537 (tm-30) REVERT: d 972 THR cc_start: 0.7714 (p) cc_final: 0.7430 (p) REVERT: d 990 MET cc_start: 0.8797 (pmm) cc_final: 0.7219 (ptp) REVERT: d 1053 MET cc_start: 0.7358 (mtp) cc_final: 0.7115 (mtp) REVERT: d 1100 VAL cc_start: 0.8027 (t) cc_final: 0.7764 (p) REVERT: e 785 MET cc_start: 0.8404 (tmm) cc_final: 0.7788 (tmm) REVERT: e 815 MET cc_start: 0.8164 (tpp) cc_final: 0.7942 (tpp) REVERT: e 957 LYS cc_start: 0.8096 (ttmm) cc_final: 0.7893 (ttmm) REVERT: e 990 MET cc_start: 0.9138 (pmm) cc_final: 0.7592 (ptt) REVERT: e 1038 TYR cc_start: 0.7163 (t80) cc_final: 0.6899 (t80) outliers start: 2 outliers final: 0 residues processed: 1112 average time/residue: 0.4924 time to fit residues: 919.6814 Evaluate side-chains 980 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 600 optimal weight: 0.7980 chunk 632 optimal weight: 0.0020 chunk 577 optimal weight: 0.9990 chunk 615 optimal weight: 2.9990 chunk 370 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 483 optimal weight: 3.9990 chunk 188 optimal weight: 10.0000 chunk 555 optimal weight: 0.6980 chunk 581 optimal weight: 0.0980 chunk 613 optimal weight: 0.6980 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS C 787 ASN C 876 ASN D 876 ASN D 998 ASN D 999 GLN E 787 ASN ** E 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 978 HIS c 593 GLN d 803 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 978 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 53900 Z= 0.179 Angle : 0.648 12.919 73420 Z= 0.320 Chirality : 0.044 0.285 8505 Planarity : 0.004 0.079 9565 Dihedral : 4.834 25.858 7400 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.02 % Allowed : 0.64 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.10), residues: 6815 helix: -1.07 (0.10), residues: 2510 sheet: -0.52 (0.15), residues: 1035 loop : -2.39 (0.10), residues: 3270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1015 HIS 0.008 0.001 HIS B 933 PHE 0.027 0.001 PHE a1013 TYR 0.019 0.001 TYR c1038 ARG 0.010 0.001 ARG E1012 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1096 time to evaluate : 4.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 MET cc_start: 0.7177 (tmm) cc_final: 0.6971 (tmm) REVERT: A 800 LEU cc_start: 0.8304 (mt) cc_final: 0.7718 (tp) REVERT: A 814 MET cc_start: 0.8636 (mmm) cc_final: 0.8206 (mmm) REVERT: A 1018 ASP cc_start: 0.7887 (t0) cc_final: 0.7345 (t0) REVERT: A 1094 LEU cc_start: 0.8406 (mm) cc_final: 0.7971 (tp) REVERT: B 800 LEU cc_start: 0.8421 (mt) cc_final: 0.7838 (tp) REVERT: B 876 ASN cc_start: 0.8591 (m-40) cc_final: 0.8305 (t0) REVERT: B 934 ARG cc_start: 0.7630 (mpt180) cc_final: 0.7059 (mpt180) REVERT: B 1018 ASP cc_start: 0.7543 (p0) cc_final: 0.7176 (p0) REVERT: B 1048 ILE cc_start: 0.8516 (tp) cc_final: 0.8231 (tp) REVERT: C 830 LEU cc_start: 0.8090 (tp) cc_final: 0.7852 (tp) REVERT: C 844 LEU cc_start: 0.7460 (tp) cc_final: 0.6967 (tp) REVERT: C 885 ASP cc_start: 0.7119 (m-30) cc_final: 0.6440 (t70) REVERT: C 934 ARG cc_start: 0.7832 (mpt180) cc_final: 0.7517 (mpt180) REVERT: C 1018 ASP cc_start: 0.7685 (p0) cc_final: 0.7457 (p0) REVERT: D 719 MET cc_start: 0.7469 (mmm) cc_final: 0.6967 (tpp) REVERT: D 785 MET cc_start: 0.6336 (tmm) cc_final: 0.5619 (pmm) REVERT: D 998 ASN cc_start: 0.7878 (m110) cc_final: 0.7348 (t0) REVERT: E 785 MET cc_start: 0.7403 (tmm) cc_final: 0.5946 (pmm) REVERT: E 800 LEU cc_start: 0.8412 (mt) cc_final: 0.7981 (tp) REVERT: E 959 ILE cc_start: 0.9222 (pt) cc_final: 0.8819 (tp) REVERT: E 1053 MET cc_start: 0.8046 (ttp) cc_final: 0.7843 (tmm) REVERT: E 1055 ARG cc_start: 0.8168 (mpp80) cc_final: 0.7510 (mpt-90) REVERT: F 86 VAL cc_start: 0.6873 (p) cc_final: 0.6400 (p) REVERT: F 141 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6997 (tm-30) REVERT: G 51 ILE cc_start: 0.7745 (pt) cc_final: 0.7518 (pt) REVERT: H 38 THR cc_start: 0.8998 (p) cc_final: 0.8583 (t) REVERT: H 85 ASP cc_start: 0.7186 (m-30) cc_final: 0.6801 (m-30) REVERT: H 112 MET cc_start: 0.9008 (mtm) cc_final: 0.7762 (mtm) REVERT: H 117 ASP cc_start: 0.7829 (t0) cc_final: 0.6962 (t0) REVERT: H 121 ASN cc_start: 0.8339 (t0) cc_final: 0.8077 (t0) REVERT: I 141 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7078 (tm-30) REVERT: J 31 ARG cc_start: 0.6886 (mtp85) cc_final: 0.5799 (mtm-85) REVERT: J 98 MET cc_start: 0.2502 (ttm) cc_final: 0.2032 (ttm) REVERT: J 140 ILE cc_start: 0.6468 (mt) cc_final: 0.6121 (mt) REVERT: K 70 THR cc_start: 0.7785 (m) cc_final: 0.7502 (m) REVERT: K 101 ASP cc_start: 0.7560 (t70) cc_final: 0.7292 (t0) REVERT: L 89 GLN cc_start: 0.8253 (mt0) cc_final: 0.8030 (mt0) REVERT: L 138 ARG cc_start: 0.7342 (mmm-85) cc_final: 0.6284 (tpp80) REVERT: M 31 ARG cc_start: 0.6261 (mtp85) cc_final: 0.5907 (ttm110) REVERT: N 38 THR cc_start: 0.8934 (p) cc_final: 0.8542 (t) REVERT: N 51 ILE cc_start: 0.8311 (tp) cc_final: 0.7826 (pt) REVERT: N 56 ASP cc_start: 0.7254 (m-30) cc_final: 0.7020 (m-30) REVERT: N 117 ASP cc_start: 0.6837 (t0) cc_final: 0.5890 (t0) REVERT: N 121 ASN cc_start: 0.7919 (p0) cc_final: 0.7630 (p0) REVERT: N 143 SER cc_start: 0.8235 (t) cc_final: 0.7943 (t) REVERT: O 89 GLN cc_start: 0.8850 (tp40) cc_final: 0.8646 (tm-30) REVERT: O 142 VAL cc_start: 0.6483 (t) cc_final: 0.6191 (t) REVERT: P 31 ARG cc_start: 0.6395 (mtp85) cc_final: 0.5434 (ttm110) REVERT: P 112 MET cc_start: 0.8008 (mpp) cc_final: 0.7688 (mpp) REVERT: P 142 VAL cc_start: 0.7474 (t) cc_final: 0.7255 (t) REVERT: Q 51 ILE cc_start: 0.8164 (tp) cc_final: 0.7883 (pt) REVERT: Q 64 ASP cc_start: 0.8328 (p0) cc_final: 0.8007 (p0) REVERT: Q 101 ASP cc_start: 0.7637 (t70) cc_final: 0.7428 (t70) REVERT: Q 112 MET cc_start: 0.8080 (mmt) cc_final: 0.7390 (mmm) REVERT: Q 124 ARG cc_start: 0.6741 (ptt180) cc_final: 0.6465 (ptt180) REVERT: R 89 GLN cc_start: 0.8395 (mt0) cc_final: 0.8133 (mt0) REVERT: R 98 MET cc_start: 0.5371 (ttp) cc_final: 0.4883 (ttp) REVERT: S 31 ARG cc_start: 0.6703 (mtp85) cc_final: 0.5985 (ttm110) REVERT: T 56 ASP cc_start: 0.7850 (m-30) cc_final: 0.6960 (m-30) REVERT: T 64 ASP cc_start: 0.8456 (p0) cc_final: 0.8045 (p0) REVERT: T 83 GLN cc_start: 0.8841 (mp10) cc_final: 0.8534 (mp10) REVERT: a 794 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7834 (ttm-80) REVERT: a 815 MET cc_start: 0.8536 (mmt) cc_final: 0.8323 (tpp) REVERT: a 828 VAL cc_start: 0.8499 (m) cc_final: 0.8148 (t) REVERT: a 887 TRP cc_start: 0.8453 (t60) cc_final: 0.7826 (t60) REVERT: a 965 ILE cc_start: 0.8481 (mm) cc_final: 0.8088 (tp) REVERT: a 990 MET cc_start: 0.8704 (pmm) cc_final: 0.7928 (ptt) REVERT: a 1002 ILE cc_start: 0.8963 (tt) cc_final: 0.8678 (pt) REVERT: a 1045 TRP cc_start: 0.8252 (m100) cc_final: 0.7804 (m100) REVERT: a 1101 LEU cc_start: 0.8550 (mt) cc_final: 0.7708 (mt) REVERT: b 586 MET cc_start: 0.6760 (tpp) cc_final: 0.6068 (mmm) REVERT: b 785 MET cc_start: 0.8483 (tmm) cc_final: 0.7963 (tmm) REVERT: b 792 LEU cc_start: 0.8444 (tp) cc_final: 0.8060 (tt) REVERT: b 964 GLU cc_start: 0.6831 (pp20) cc_final: 0.6543 (tm-30) REVERT: b 972 THR cc_start: 0.8131 (p) cc_final: 0.7695 (p) REVERT: b 990 MET cc_start: 0.8440 (pmm) cc_final: 0.7648 (ptt) REVERT: b 995 ILE cc_start: 0.8515 (mm) cc_final: 0.8314 (mm) REVERT: b 1000 LYS cc_start: 0.8377 (mmpt) cc_final: 0.8130 (mmtm) REVERT: c 815 MET cc_start: 0.8355 (tpp) cc_final: 0.8102 (mmm) REVERT: c 887 TRP cc_start: 0.8705 (t60) cc_final: 0.8363 (t-100) REVERT: c 917 THR cc_start: 0.7862 (p) cc_final: 0.7605 (p) REVERT: c 965 ILE cc_start: 0.8460 (mm) cc_final: 0.8151 (tp) REVERT: c 972 THR cc_start: 0.8081 (p) cc_final: 0.7874 (p) REVERT: c 990 MET cc_start: 0.8862 (pmm) cc_final: 0.7709 (ptt) REVERT: d 586 MET cc_start: 0.7028 (tpp) cc_final: 0.6770 (mmm) REVERT: d 964 GLU cc_start: 0.6791 (pp20) cc_final: 0.6532 (tm-30) REVERT: d 972 THR cc_start: 0.7645 (p) cc_final: 0.7407 (p) REVERT: d 990 MET cc_start: 0.8919 (pmm) cc_final: 0.7533 (ptt) REVERT: d 1100 VAL cc_start: 0.8085 (t) cc_final: 0.7840 (p) REVERT: e 785 MET cc_start: 0.8428 (tmm) cc_final: 0.7811 (tmm) REVERT: e 957 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7872 (ttmm) REVERT: e 990 MET cc_start: 0.9182 (pmm) cc_final: 0.7610 (ptt) REVERT: e 1038 TYR cc_start: 0.7219 (t80) cc_final: 0.7014 (t80) outliers start: 1 outliers final: 0 residues processed: 1096 average time/residue: 0.4947 time to fit residues: 932.1380 Evaluate side-chains 966 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 966 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 404 optimal weight: 5.9990 chunk 650 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 chunk 308 optimal weight: 0.5980 chunk 452 optimal weight: 0.8980 chunk 682 optimal weight: 0.9990 chunk 628 optimal weight: 1.9990 chunk 543 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 419 optimal weight: 0.9980 chunk 333 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 ASN ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 978 HIS B 998 ASN C 787 ASN C 876 ASN ** D 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN D 999 GLN D1037 GLN E 787 ASN N 53 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 ASN ** S 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 803 GLN a 804 GLN a 876 ASN b 927 ASN c 593 GLN c 803 GLN c 978 HIS d 593 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 978 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.5494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 53900 Z= 0.237 Angle : 0.688 14.029 73420 Z= 0.343 Chirality : 0.045 0.355 8505 Planarity : 0.005 0.079 9565 Dihedral : 5.083 25.434 7400 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.05 % Allowed : 0.62 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.10), residues: 6815 helix: -1.01 (0.10), residues: 2425 sheet: -0.67 (0.15), residues: 1020 loop : -2.24 (0.10), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E1045 HIS 0.007 0.001 HIS B 933 PHE 0.029 0.002 PHE a1013 TYR 0.038 0.002 TYR E 912 ARG 0.011 0.001 ARG a1056 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13630 Ramachandran restraints generated. 6815 Oldfield, 0 Emsley, 6815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1106 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1103 time to evaluate : 4.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 696 MET cc_start: 0.7246 (tmm) cc_final: 0.7035 (tmm) REVERT: A 800 LEU cc_start: 0.8345 (mt) cc_final: 0.7771 (tp) REVERT: A 814 MET cc_start: 0.8303 (mmm) cc_final: 0.7953 (mmm) REVERT: A 815 MET cc_start: 0.7795 (tpt) cc_final: 0.7559 (tpt) REVERT: A 1018 ASP cc_start: 0.7875 (t0) cc_final: 0.7312 (t0) REVERT: A 1094 LEU cc_start: 0.8475 (mm) cc_final: 0.7978 (tp) REVERT: B 800 LEU cc_start: 0.8438 (mt) cc_final: 0.7879 (tp) REVERT: B 812 GLN cc_start: 0.8264 (pm20) cc_final: 0.8021 (pm20) REVERT: B 876 ASN cc_start: 0.8586 (m-40) cc_final: 0.8311 (t0) REVERT: B 919 ARG cc_start: 0.7427 (mtp-110) cc_final: 0.7120 (mtp85) REVERT: B 934 ARG cc_start: 0.7805 (mpt180) cc_final: 0.7344 (mpt180) REVERT: B 1018 ASP cc_start: 0.7660 (p0) cc_final: 0.7308 (p0) REVERT: B 1038 TYR cc_start: 0.7564 (t80) cc_final: 0.7331 (t80) REVERT: B 1048 ILE cc_start: 0.8717 (tp) cc_final: 0.8411 (tp) REVERT: C 830 LEU cc_start: 0.8135 (tp) cc_final: 0.7908 (tp) REVERT: C 844 LEU cc_start: 0.7592 (tp) cc_final: 0.7086 (tp) REVERT: C 885 ASP cc_start: 0.7034 (m-30) cc_final: 0.6403 (t70) REVERT: C 934 ARG cc_start: 0.8070 (mpt180) cc_final: 0.7789 (mpt180) REVERT: C 1000 LYS cc_start: 0.6371 (mtmm) cc_final: 0.6025 (ptpp) REVERT: D 698 SER cc_start: 0.8159 (m) cc_final: 0.7783 (p) REVERT: D 719 MET cc_start: 0.7544 (mmm) cc_final: 0.7066 (tpp) REVERT: D 785 MET cc_start: 0.6404 (tmm) cc_final: 0.5617 (pmm) REVERT: D 998 ASN cc_start: 0.7861 (m110) cc_final: 0.7415 (t0) REVERT: D 1018 ASP cc_start: 0.8019 (p0) cc_final: 0.7485 (p0) REVERT: E 785 MET cc_start: 0.7557 (tmm) cc_final: 0.5996 (pmm) REVERT: E 800 LEU cc_start: 0.8394 (mt) cc_final: 0.7967 (tp) REVERT: E 959 ILE cc_start: 0.9227 (pt) cc_final: 0.8857 (tp) REVERT: E 1055 ARG cc_start: 0.8154 (mpp80) cc_final: 0.7415 (mpt-90) REVERT: F 86 VAL cc_start: 0.7150 (p) cc_final: 0.6669 (p) REVERT: F 89 GLN cc_start: 0.8210 (mt0) cc_final: 0.8005 (mt0) REVERT: F 141 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6936 (tm-30) REVERT: G 51 ILE cc_start: 0.7748 (pt) cc_final: 0.7506 (pt) REVERT: G 142 VAL cc_start: 0.7233 (t) cc_final: 0.6782 (p) REVERT: H 38 THR cc_start: 0.8793 (p) cc_final: 0.8585 (t) REVERT: H 85 ASP cc_start: 0.7052 (m-30) cc_final: 0.6744 (m-30) REVERT: H 101 ASP cc_start: 0.7672 (t70) cc_final: 0.7454 (t70) REVERT: H 112 MET cc_start: 0.9005 (mtm) cc_final: 0.7881 (mtm) REVERT: H 117 ASP cc_start: 0.7999 (t0) cc_final: 0.6971 (t0) REVERT: H 121 ASN cc_start: 0.8382 (t0) cc_final: 0.8000 (t0) REVERT: I 89 GLN cc_start: 0.8070 (mt0) cc_final: 0.7824 (mt0) REVERT: J 31 ARG cc_start: 0.6868 (mtp85) cc_final: 0.5664 (mtm-85) REVERT: J 98 MET cc_start: 0.2294 (ttm) cc_final: 0.2027 (ttm) REVERT: J 140 ILE cc_start: 0.6254 (mt) cc_final: 0.5960 (mt) REVERT: K 101 ASP cc_start: 0.7538 (t70) cc_final: 0.7209 (t0) REVERT: K 124 ARG cc_start: 0.6456 (ptt180) cc_final: 0.6081 (ptt180) REVERT: L 89 GLN cc_start: 0.8254 (mt0) cc_final: 0.8044 (mt0) REVERT: L 138 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.5977 (tpp80) REVERT: M 31 ARG cc_start: 0.6322 (mtp85) cc_final: 0.5999 (ttm110) REVERT: M 98 MET cc_start: 0.2858 (mtp) cc_final: 0.2424 (mtp) REVERT: N 38 THR cc_start: 0.8978 (p) cc_final: 0.8593 (t) REVERT: N 51 ILE cc_start: 0.8335 (tp) cc_final: 0.7758 (pt) REVERT: N 112 MET cc_start: 0.8037 (mmt) cc_final: 0.7440 (mmm) REVERT: N 117 ASP cc_start: 0.6963 (t0) cc_final: 0.6081 (t0) REVERT: N 121 ASN cc_start: 0.7917 (p0) cc_final: 0.7633 (p0) REVERT: N 143 SER cc_start: 0.8130 (t) cc_final: 0.7777 (t) REVERT: O 37 ASN cc_start: 0.7885 (t0) cc_final: 0.7663 (t0) REVERT: P 31 ARG cc_start: 0.6376 (mtp85) cc_final: 0.5498 (ttm110) REVERT: Q 51 ILE cc_start: 0.8233 (tp) cc_final: 0.7925 (pt) REVERT: Q 57 ASN cc_start: 0.6652 (p0) cc_final: 0.6206 (p0) REVERT: Q 64 ASP cc_start: 0.8359 (p0) cc_final: 0.7917 (p0) REVERT: Q 101 ASP cc_start: 0.8010 (t70) cc_final: 0.7721 (t70) REVERT: Q 112 MET cc_start: 0.8167 (mmt) cc_final: 0.7719 (mmt) REVERT: Q 124 ARG cc_start: 0.6806 (ptt180) cc_final: 0.6517 (ptt180) REVERT: R 79 ASP cc_start: 0.5884 (m-30) cc_final: 0.5450 (m-30) REVERT: R 98 MET cc_start: 0.5253 (ttp) cc_final: 0.4813 (ttp) REVERT: S 31 ARG cc_start: 0.6790 (mtp85) cc_final: 0.6060 (ttm110) REVERT: T 56 ASP cc_start: 0.7768 (m-30) cc_final: 0.6861 (m-30) REVERT: T 64 ASP cc_start: 0.8405 (p0) cc_final: 0.7985 (p0) REVERT: T 83 GLN cc_start: 0.8877 (mp10) cc_final: 0.8541 (mp10) REVERT: T 101 ASP cc_start: 0.7902 (t70) cc_final: 0.7683 (t0) REVERT: T 112 MET cc_start: 0.7825 (mmt) cc_final: 0.7466 (mmt) REVERT: a 802 LEU cc_start: 0.7129 (tp) cc_final: 0.6827 (tt) REVERT: a 828 VAL cc_start: 0.8460 (m) cc_final: 0.8206 (t) REVERT: a 860 MET cc_start: 0.7663 (mmm) cc_final: 0.7389 (mmt) REVERT: a 965 ILE cc_start: 0.8493 (mm) cc_final: 0.8121 (tp) REVERT: a 990 MET cc_start: 0.8809 (pmm) cc_final: 0.8040 (ptt) REVERT: a 1045 TRP cc_start: 0.8579 (m100) cc_final: 0.8130 (m100) REVERT: b 586 MET cc_start: 0.6738 (tpp) cc_final: 0.6049 (mmm) REVERT: b 776 MET cc_start: 0.6163 (ptm) cc_final: 0.5958 (ptm) REVERT: b 785 MET cc_start: 0.8591 (tmm) cc_final: 0.7989 (tmm) REVERT: b 791 TYR cc_start: 0.7327 (m-10) cc_final: 0.6900 (m-80) REVERT: b 792 LEU cc_start: 0.8505 (tp) cc_final: 0.8166 (tt) REVERT: b 964 GLU cc_start: 0.6843 (pp20) cc_final: 0.6382 (tm-30) REVERT: b 972 THR cc_start: 0.8075 (p) cc_final: 0.7768 (p) REVERT: b 990 MET cc_start: 0.8560 (pmm) cc_final: 0.7709 (ptt) REVERT: b 1000 LYS cc_start: 0.8461 (mmpt) cc_final: 0.7974 (mmmm) REVERT: b 1038 TYR cc_start: 0.7762 (t80) cc_final: 0.7496 (t80) REVERT: c 625 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7826 (pm20) REVERT: c 815 MET cc_start: 0.8384 (tpp) cc_final: 0.8166 (mmm) REVERT: c 887 TRP cc_start: 0.8694 (t60) cc_final: 0.8389 (t-100) REVERT: c 972 THR cc_start: 0.8111 (p) cc_final: 0.7813 (p) REVERT: c 990 MET cc_start: 0.8877 (pmm) cc_final: 0.7777 (ptt) REVERT: d 586 MET cc_start: 0.6903 (tpp) cc_final: 0.6022 (mmm) REVERT: d 905 SER cc_start: 0.8400 (p) cc_final: 0.8111 (t) REVERT: d 964 GLU cc_start: 0.6941 (pp20) cc_final: 0.6386 (tm-30) REVERT: d 972 THR cc_start: 0.7796 (p) cc_final: 0.7418 (p) REVERT: d 990 MET cc_start: 0.8950 (pmm) cc_final: 0.7631 (ptt) REVERT: d 1100 VAL cc_start: 0.8124 (t) cc_final: 0.7870 (p) REVERT: e 623 THR cc_start: 0.5495 (t) cc_final: 0.5246 (t) REVERT: e 625 GLN cc_start: 0.8301 (tp-100) cc_final: 0.7782 (mp10) REVERT: e 686 LEU cc_start: 0.7334 (tp) cc_final: 0.7033 (tp) REVERT: e 785 MET cc_start: 0.8541 (tmm) cc_final: 0.7830 (tmm) REVERT: e 947 ARG cc_start: 0.4721 (ptp90) cc_final: 0.4436 (ptp90) REVERT: e 990 MET cc_start: 0.8788 (pmm) cc_final: 0.8292 (ptt) outliers start: 3 outliers final: 1 residues processed: 1104 average time/residue: 0.5477 time to fit residues: 1025.9168 Evaluate side-chains 956 residues out of total 5750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 955 time to evaluate : 4.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 685 random chunks: chunk 431 optimal weight: 0.9980 chunk 578 optimal weight: 0.5980 chunk 166 optimal weight: 0.5980 chunk 501 optimal weight: 0.1980 chunk 80 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 544 optimal weight: 0.8980 chunk 227 optimal weight: 0.0980 chunk 558 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 933 HIS B 945 ASN C 876 ASN ** D 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 876 ASN D 999 GLN E 787 ASN a 593 GLN ** a 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 876 ASN c 593 GLN d 593 GLN d 789 GLN e 593 GLN ** e 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 978 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.135655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.115729 restraints weight = 108324.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.116083 restraints weight = 98060.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.116077 restraints weight = 85145.765| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 53900 Z= 0.178 Angle : 0.654 13.703 73420 Z= 0.324 Chirality : 0.044 0.293 8505 Planarity : 0.004 0.091 9565 Dihedral : 4.906 25.750 7400 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 6815 helix: -0.88 (0.11), residues: 2360 sheet: -0.46 (0.17), residues: 870 loop : -2.11 (0.10), residues: 3585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP d1028 HIS 0.009 0.001 HIS B 933 PHE 0.028 0.002 PHE a1013 TYR 0.033 0.001 TYR B1003 ARG 0.010 0.001 ARG E1012 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14614.50 seconds wall clock time: 251 minutes 2.14 seconds (15062.14 seconds total)