Starting phenix.real_space_refine on Fri Dec 27 19:41:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.map" model { file = "/net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsd_33524/12_2024/7xsd_33524.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 168 5.16 5 C 31592 2.51 5 N 8824 2.21 5 O 9264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 49848 Number of models: 1 Model: "" Number of chains: 32 Chain: "5" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "6" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "7" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "8" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "O" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "P" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "G" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "1" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "2" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "3" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "4" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "M" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "N" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "E" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "J" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "Q" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "R" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "S" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "T" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "A" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "L" Number of atoms: 1421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1421 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain: "U" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "V" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "W" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 811 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "X" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 897 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "C" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3102 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 374} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 19.95, per 1000 atoms: 0.40 Number of scatterers: 49848 At special positions: 0 Unit cell: (202, 202, 133.32, 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 168 16.00 O 9264 8.00 N 8824 7.00 C 31592 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: 8.40 Conformation dependent library (CDL) restraints added in 4.5 seconds 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11760 Finding SS restraints... Secondary structure from input PDB file: 336 helices and 32 sheets defined 55.7% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain '5' and resid 4 through 30 removed outlier: 3.677A pdb=" N SER 5 16 " --> pdb=" O LYS 5 12 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN 5 29 " --> pdb=" O THR 5 25 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 38 Processing helix chain '5' and resid 53 through 60 Processing helix chain '5' and resid 65 through 79 removed outlier: 3.836A pdb=" N ARG 5 69 " --> pdb=" O ASP 5 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG 5 74 " --> pdb=" O ILE 5 70 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU 5 75 " --> pdb=" O MET 5 71 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N HIS 5 76 " --> pdb=" O THR 5 72 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE 5 77 " --> pdb=" O VAL 5 73 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 102 removed outlier: 3.585A pdb=" N ARG 5 90 " --> pdb=" O PRO 5 86 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY 5 92 " --> pdb=" O MET 5 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN 5 94 " --> pdb=" O ARG 5 90 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN 5 95 " --> pdb=" O SER 5 91 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLN 5 100 " --> pdb=" O ALA 5 96 " (cutoff:3.500A) Processing helix chain '6' and resid 3 through 31 removed outlier: 3.514A pdb=" N ASP 6 9 " --> pdb=" O GLN 6 5 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS 6 12 " --> pdb=" O LYS 6 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 6 14 " --> pdb=" O THR 6 10 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN 6 15 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 34 through 46 removed outlier: 3.547A pdb=" N THR 6 43 " --> pdb=" O LEU 6 39 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL 6 46 " --> pdb=" O HIS 6 42 " (cutoff:3.500A) Processing helix chain '6' and resid 51 through 63 removed outlier: 3.821A pdb=" N LYS 6 57 " --> pdb=" O GLU 6 53 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU 6 58 " --> pdb=" O ALA 6 54 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU 6 62 " --> pdb=" O GLU 6 58 " (cutoff:3.500A) Processing helix chain '6' and resid 65 through 77 removed outlier: 3.809A pdb=" N ARG 6 69 " --> pdb=" O ASP 6 65 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL 6 73 " --> pdb=" O ARG 6 69 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG 6 74 " --> pdb=" O ILE 6 70 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU 6 75 " --> pdb=" O MET 6 71 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS 6 76 " --> pdb=" O THR 6 72 " (cutoff:3.500A) Processing helix chain '6' and resid 85 through 100 removed outlier: 4.159A pdb=" N ARG 6 90 " --> pdb=" O PRO 6 86 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER 6 91 " --> pdb=" O GLU 6 87 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY 6 92 " --> pdb=" O MET 6 88 " (cutoff:3.500A) Processing helix chain '6' and resid 101 through 112 removed outlier: 3.795A pdb=" N LEU 6 105 " --> pdb=" O ARG 6 101 " (cutoff:3.500A) Processing helix chain '7' and resid 4 through 30 removed outlier: 3.530A pdb=" N THR 7 13 " --> pdb=" O ASP 7 9 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 7 16 " --> pdb=" O LYS 7 12 " (cutoff:3.500A) Processing helix chain '7' and resid 34 through 38 Processing helix chain '7' and resid 53 through 60 Processing helix chain '7' and resid 65 through 79 removed outlier: 3.807A pdb=" N ARG 7 69 " --> pdb=" O ASP 7 65 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG 7 74 " --> pdb=" O ILE 7 70 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU 7 75 " --> pdb=" O MET 7 71 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N HIS 7 76 " --> pdb=" O THR 7 72 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE 7 77 " --> pdb=" O VAL 7 73 " (cutoff:3.500A) Processing helix chain '7' and resid 84 through 102 removed outlier: 3.527A pdb=" N MET 7 88 " --> pdb=" O PHE 7 84 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG 7 90 " --> pdb=" O PRO 7 86 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY 7 92 " --> pdb=" O MET 7 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN 7 94 " --> pdb=" O ARG 7 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN 7 95 " --> pdb=" O SER 7 91 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN 7 100 " --> pdb=" O ALA 7 96 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 31 removed outlier: 3.505A pdb=" N ASP 8 9 " --> pdb=" O GLN 8 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS 8 12 " --> pdb=" O LYS 8 8 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU 8 14 " --> pdb=" O THR 8 10 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN 8 15 " --> pdb=" O ALA 8 11 " (cutoff:3.500A) Processing helix chain '8' and resid 34 through 46 removed outlier: 3.558A pdb=" N THR 8 43 " --> pdb=" O LEU 8 39 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL 8 46 " --> pdb=" O HIS 8 42 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 63 removed outlier: 3.834A pdb=" N LYS 8 57 " --> pdb=" O GLU 8 53 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU 8 58 " --> pdb=" O ALA 8 54 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU 8 62 " --> pdb=" O GLU 8 58 " (cutoff:3.500A) Processing helix chain '8' and resid 65 through 77 removed outlier: 3.788A pdb=" N ARG 8 69 " --> pdb=" O ASP 8 65 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL 8 73 " --> pdb=" O ARG 8 69 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG 8 74 " --> pdb=" O ILE 8 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU 8 75 " --> pdb=" O MET 8 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS 8 76 " --> pdb=" O THR 8 72 " (cutoff:3.500A) Processing helix chain '8' and resid 85 through 100 removed outlier: 4.148A pdb=" N ARG 8 90 " --> pdb=" O PRO 8 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER 8 91 " --> pdb=" O GLU 8 87 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY 8 92 " --> pdb=" O MET 8 88 " (cutoff:3.500A) Processing helix chain '8' and resid 101 through 112 removed outlier: 3.866A pdb=" N LEU 8 105 " --> pdb=" O ARG 8 101 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS O 25 " --> pdb=" O GLU O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA O 41 " --> pdb=" O GLY O 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU O 43 " --> pdb=" O ALA O 39 " (cutoff:3.500A) Processing helix chain 'O' and resid 52 through 56 removed outlier: 3.597A pdb=" N ALA O 56 " --> pdb=" O ILE O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN O 66 " --> pdb=" O VAL O 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL O 67 " --> pdb=" O GLN O 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER O 76 " --> pdb=" O GLN O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA O 91 " --> pdb=" O LEU O 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU O 98 " --> pdb=" O GLY O 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR O 99 " --> pdb=" O SER O 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU O 101 " --> pdb=" O VAL O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 104 No H-bonds generated for 'chain 'O' and resid 102 through 104' Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU O 115 " --> pdb=" O ALA O 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE O 117 " --> pdb=" O GLY O 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU O 128 " --> pdb=" O ASP O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA O 155 " --> pdb=" O GLY O 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP O 159 " --> pdb=" O ALA O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG O 171 " --> pdb=" O ASP O 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER O 172 " --> pdb=" O LEU O 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 167 through 172' Processing helix chain 'O' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG O 177 " --> pdb=" O ARG O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE O 181 " --> pdb=" O ARG O 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA O 182 " --> pdb=" O GLY O 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 177 through 182' Processing helix chain 'O' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE O 191 " --> pdb=" O ALA O 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS P 25 " --> pdb=" O GLU P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 44 removed outlier: 4.731A pdb=" N ALA P 41 " --> pdb=" O GLY P 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU P 43 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA P 56 " --> pdb=" O ILE P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 78 removed outlier: 3.829A pdb=" N GLN P 66 " --> pdb=" O VAL P 62 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL P 69 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA P 91 " --> pdb=" O LEU P 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR P 92 " --> pdb=" O ALA P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU P 98 " --> pdb=" O GLY P 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR P 99 " --> pdb=" O SER P 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU P 101 " --> pdb=" O VAL P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 104 No H-bonds generated for 'chain 'P' and resid 102 through 104' Processing helix chain 'P' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP P 114 " --> pdb=" O ALA P 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE P 117 " --> pdb=" O GLY P 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS P 119 " --> pdb=" O LEU P 115 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU P 128 " --> pdb=" O ASP P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA P 155 " --> pdb=" O GLY P 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP P 159 " --> pdb=" O ALA P 155 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG P 171 " --> pdb=" O ASP P 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER P 172 " --> pdb=" O LEU P 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 167 through 172' Processing helix chain 'P' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG P 177 " --> pdb=" O ARG P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 182 removed outlier: 3.616A pdb=" N PHE P 181 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA P 182 " --> pdb=" O GLY P 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 177 through 182' Processing helix chain 'P' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE P 191 " --> pdb=" O ALA P 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU G 61 " --> pdb=" O ALA G 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE G 121 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS G 147 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP G 161 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA G 189 " --> pdb=" O ASN G 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL G 190 " --> pdb=" O TYR G 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG G 195 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY G 197 " --> pdb=" O LEU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 220 removed outlier: 3.606A pdb=" N PHE G 219 " --> pdb=" O TRP G 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU G 220 " --> pdb=" O ARG G 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 215 through 220' Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 276 through 280 removed outlier: 3.538A pdb=" N THR G 279 " --> pdb=" O THR G 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR G 280 " --> pdb=" O ALA G 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 276 through 280' Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU G 319 " --> pdb=" O LEU G 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE G 346 " --> pdb=" O ILE G 342 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL G 347 " --> pdb=" O THR G 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 342 through 347' Processing helix chain 'G' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY G 362 " --> pdb=" O LYS G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL G 392 " --> pdb=" O MET G 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU G 393 " --> pdb=" O PRO G 389 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN G 421 " --> pdb=" O GLY G 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG G 422 " --> pdb=" O ALA G 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 423 " --> pdb=" O THR G 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA G 424 " --> pdb=" O ALA G 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS G 428 " --> pdb=" O ALA G 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL G 429 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN G 430 " --> pdb=" O GLU G 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA G 431 " --> pdb=" O ALA G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL G 445 " --> pdb=" O GLU G 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 446 " --> pdb=" O GLY G 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 449 " --> pdb=" O VAL G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL G 458 " --> pdb=" O PRO G 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA G 459 " --> pdb=" O GLU G 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU G 462 " --> pdb=" O VAL G 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER H 63 " --> pdb=" O ALA H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 121 removed outlier: 3.912A pdb=" N VAL H 117 " --> pdb=" O SER H 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE H 121 " --> pdb=" O VAL H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS H 147 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP H 161 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 191 removed outlier: 3.616A pdb=" N ALA H 189 " --> pdb=" O ASN H 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL H 190 " --> pdb=" O TYR H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG H 195 " --> pdb=" O GLU H 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 197 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE H 219 " --> pdb=" O TRP H 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 220 " --> pdb=" O ARG H 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 215 through 220' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing helix chain 'H' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR H 279 " --> pdb=" O THR H 276 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR H 280 " --> pdb=" O ALA H 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 276 through 280' Processing helix chain 'H' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU H 319 " --> pdb=" O LEU H 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE H 346 " --> pdb=" O ILE H 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL H 347 " --> pdb=" O THR H 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 342 through 347' Processing helix chain 'H' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY H 362 " --> pdb=" O LYS H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 396 removed outlier: 3.541A pdb=" N VAL H 392 " --> pdb=" O MET H 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU H 393 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG H 422 " --> pdb=" O ALA H 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL H 423 " --> pdb=" O THR H 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 424 " --> pdb=" O ALA H 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS H 428 " --> pdb=" O ALA H 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL H 429 " --> pdb=" O LEU H 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN H 430 " --> pdb=" O GLU H 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA H 431 " --> pdb=" O ALA H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL H 445 " --> pdb=" O GLU H 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE H 446 " --> pdb=" O GLY H 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA H 449 " --> pdb=" O VAL H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL H 458 " --> pdb=" O PRO H 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA H 459 " --> pdb=" O GLU H 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) Processing helix chain '1' and resid 4 through 30 removed outlier: 3.636A pdb=" N SER 1 16 " --> pdb=" O LYS 1 12 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN 1 29 " --> pdb=" O THR 1 25 " (cutoff:3.500A) Processing helix chain '1' and resid 34 through 38 Processing helix chain '1' and resid 53 through 60 Processing helix chain '1' and resid 65 through 79 removed outlier: 3.826A pdb=" N ARG 1 69 " --> pdb=" O ASP 1 65 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR 1 72 " --> pdb=" O LEU 1 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 1 74 " --> pdb=" O ILE 1 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU 1 75 " --> pdb=" O MET 1 71 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N HIS 1 76 " --> pdb=" O THR 1 72 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE 1 77 " --> pdb=" O VAL 1 73 " (cutoff:3.500A) Processing helix chain '1' and resid 84 through 102 removed outlier: 3.765A pdb=" N ARG 1 90 " --> pdb=" O PRO 1 86 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY 1 92 " --> pdb=" O MET 1 88 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 1 94 " --> pdb=" O ARG 1 90 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN 1 95 " --> pdb=" O SER 1 91 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN 1 100 " --> pdb=" O ALA 1 96 " (cutoff:3.500A) Processing helix chain '2' and resid 3 through 34 removed outlier: 3.506A pdb=" N ASP 2 9 " --> pdb=" O GLN 2 5 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS 2 12 " --> pdb=" O LYS 2 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU 2 14 " --> pdb=" O THR 2 10 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN 2 15 " --> pdb=" O ALA 2 11 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU 2 32 " --> pdb=" O ALA 2 28 " (cutoff:3.500A) Processing helix chain '2' and resid 34 through 46 removed outlier: 3.505A pdb=" N THR 2 43 " --> pdb=" O LEU 2 39 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL 2 46 " --> pdb=" O HIS 2 42 " (cutoff:3.500A) Processing helix chain '2' and resid 51 through 63 removed outlier: 3.796A pdb=" N LYS 2 57 " --> pdb=" O GLU 2 53 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU 2 58 " --> pdb=" O ALA 2 54 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG 2 61 " --> pdb=" O LYS 2 57 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU 2 62 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 removed outlier: 3.821A pdb=" N ARG 2 69 " --> pdb=" O ASP 2 65 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL 2 73 " --> pdb=" O ARG 2 69 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG 2 74 " --> pdb=" O ILE 2 70 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU 2 75 " --> pdb=" O MET 2 71 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS 2 76 " --> pdb=" O THR 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 85 through 100 removed outlier: 4.170A pdb=" N ARG 2 90 " --> pdb=" O PRO 2 86 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER 2 91 " --> pdb=" O GLU 2 87 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLY 2 92 " --> pdb=" O MET 2 88 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 112 removed outlier: 3.823A pdb=" N LEU 2 105 " --> pdb=" O ARG 2 101 " (cutoff:3.500A) Processing helix chain '3' and resid 4 through 30 removed outlier: 3.656A pdb=" N SER 3 16 " --> pdb=" O LYS 3 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN 3 29 " --> pdb=" O THR 3 25 " (cutoff:3.500A) Processing helix chain '3' and resid 34 through 38 Processing helix chain '3' and resid 53 through 60 Processing helix chain '3' and resid 65 through 79 removed outlier: 3.830A pdb=" N ARG 3 69 " --> pdb=" O ASP 3 65 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR 3 72 " --> pdb=" O LEU 3 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 3 74 " --> pdb=" O ILE 3 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU 3 75 " --> pdb=" O MET 3 71 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS 3 76 " --> pdb=" O THR 3 72 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE 3 77 " --> pdb=" O VAL 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 84 through 102 removed outlier: 3.676A pdb=" N ARG 3 90 " --> pdb=" O PRO 3 86 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY 3 92 " --> pdb=" O MET 3 88 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN 3 94 " --> pdb=" O ARG 3 90 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN 3 95 " --> pdb=" O SER 3 91 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN 3 100 " --> pdb=" O ALA 3 96 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 34 removed outlier: 3.547A pdb=" N ASP 4 9 " --> pdb=" O GLN 4 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS 4 12 " --> pdb=" O LYS 4 8 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN 4 15 " --> pdb=" O ALA 4 11 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU 4 32 " --> pdb=" O ALA 4 28 " (cutoff:3.500A) Processing helix chain '4' and resid 34 through 46 removed outlier: 3.534A pdb=" N THR 4 43 " --> pdb=" O LEU 4 39 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL 4 46 " --> pdb=" O HIS 4 42 " (cutoff:3.500A) Processing helix chain '4' and resid 51 through 63 removed outlier: 3.796A pdb=" N LYS 4 57 " --> pdb=" O GLU 4 53 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU 4 58 " --> pdb=" O ALA 4 54 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG 4 61 " --> pdb=" O LYS 4 57 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU 4 62 " --> pdb=" O GLU 4 58 " (cutoff:3.500A) Processing helix chain '4' and resid 65 through 77 removed outlier: 3.823A pdb=" N ARG 4 69 " --> pdb=" O ASP 4 65 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL 4 73 " --> pdb=" O ARG 4 69 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG 4 74 " --> pdb=" O ILE 4 70 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU 4 75 " --> pdb=" O MET 4 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS 4 76 " --> pdb=" O THR 4 72 " (cutoff:3.500A) Processing helix chain '4' and resid 85 through 100 removed outlier: 4.173A pdb=" N ARG 4 90 " --> pdb=" O PRO 4 86 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N SER 4 91 " --> pdb=" O GLU 4 87 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N GLY 4 92 " --> pdb=" O MET 4 88 " (cutoff:3.500A) Processing helix chain '4' and resid 101 through 112 removed outlier: 3.851A pdb=" N LEU 4 105 " --> pdb=" O ARG 4 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 25 removed outlier: 3.741A pdb=" N LYS M 25 " --> pdb=" O GLU M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA M 41 " --> pdb=" O GLY M 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU M 43 " --> pdb=" O ALA M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA M 56 " --> pdb=" O ILE M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 78 removed outlier: 3.829A pdb=" N GLN M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL M 67 " --> pdb=" O GLN M 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL M 69 " --> pdb=" O ASN M 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER M 76 " --> pdb=" O GLN M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU M 98 " --> pdb=" O GLY M 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR M 99 " --> pdb=" O SER M 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU M 101 " --> pdb=" O VAL M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 104 No H-bonds generated for 'chain 'M' and resid 102 through 104' Processing helix chain 'M' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP M 114 " --> pdb=" O ALA M 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU M 115 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE M 117 " --> pdb=" O GLY M 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU M 128 " --> pdb=" O ASP M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA M 155 " --> pdb=" O GLY M 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG M 171 " --> pdb=" O ASP M 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER M 172 " --> pdb=" O LEU M 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 167 through 172' Processing helix chain 'M' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG M 177 " --> pdb=" O ARG M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE M 181 " --> pdb=" O ARG M 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA M 182 " --> pdb=" O GLY M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 177 through 182' Processing helix chain 'M' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE M 191 " --> pdb=" O ALA M 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS N 25 " --> pdb=" O GLU N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU N 43 " --> pdb=" O ALA N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA N 56 " --> pdb=" O ILE N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN N 66 " --> pdb=" O VAL N 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL N 67 " --> pdb=" O GLN N 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL N 69 " --> pdb=" O ASN N 65 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER N 76 " --> pdb=" O GLN N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA N 91 " --> pdb=" O LEU N 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU N 98 " --> pdb=" O GLY N 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR N 99 " --> pdb=" O SER N 95 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU N 101 " --> pdb=" O VAL N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 104 No H-bonds generated for 'chain 'N' and resid 102 through 104' Processing helix chain 'N' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP N 114 " --> pdb=" O ALA N 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 115 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE N 117 " --> pdb=" O GLY N 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS N 119 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU N 128 " --> pdb=" O ASP N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA N 155 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP N 159 " --> pdb=" O ALA N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG N 171 " --> pdb=" O ASP N 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 167 through 172' Processing helix chain 'N' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG N 177 " --> pdb=" O ARG N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE N 181 " --> pdb=" O ARG N 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA N 182 " --> pdb=" O GLY N 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 177 through 182' Processing helix chain 'N' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE N 191 " --> pdb=" O ALA N 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 121 " --> pdb=" O VAL E 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS E 147 " --> pdb=" O VAL E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP E 161 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA E 189 " --> pdb=" O ASN E 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL E 190 " --> pdb=" O TYR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG E 195 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE E 219 " --> pdb=" O TRP E 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 215 through 220' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 removed outlier: 3.540A pdb=" N THR E 279 " --> pdb=" O THR E 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR E 280 " --> pdb=" O ALA E 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 276 through 280' Processing helix chain 'E' and resid 311 through 321 removed outlier: 3.614A pdb=" N LEU E 319 " --> pdb=" O LEU E 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE E 346 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL E 347 " --> pdb=" O THR E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 347' Processing helix chain 'E' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY E 362 " --> pdb=" O LYS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL E 392 " --> pdb=" O MET E 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE E 394 " --> pdb=" O ALA E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG E 422 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL E 423 " --> pdb=" O THR E 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA E 424 " --> pdb=" O ALA E 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS E 428 " --> pdb=" O ALA E 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL E 429 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN E 430 " --> pdb=" O GLU E 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL E 445 " --> pdb=" O GLU E 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE E 446 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA E 449 " --> pdb=" O VAL E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL E 458 " --> pdb=" O PRO E 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA E 459 " --> pdb=" O GLU E 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU E 462 " --> pdb=" O VAL E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU F 61 " --> pdb=" O ALA F 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER F 63 " --> pdb=" O ALA F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 121 removed outlier: 3.914A pdb=" N VAL F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE F 121 " --> pdb=" O VAL F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS F 147 " --> pdb=" O VAL F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP F 161 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL F 190 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG F 195 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE F 219 " --> pdb=" O TRP F 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 215 through 220' Processing helix chain 'F' and resid 221 through 223 No H-bonds generated for 'chain 'F' and resid 221 through 223' Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR F 279 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 280 " --> pdb=" O ALA F 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 276 through 280' Processing helix chain 'F' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU F 319 " --> pdb=" O LEU F 315 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE F 346 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL F 347 " --> pdb=" O THR F 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 342 through 347' Processing helix chain 'F' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY F 362 " --> pdb=" O LYS F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL F 392 " --> pdb=" O MET F 388 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE F 394 " --> pdb=" O ALA F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL F 423 " --> pdb=" O THR F 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS F 428 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL F 429 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN F 430 " --> pdb=" O GLU F 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA F 431 " --> pdb=" O ALA F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 removed outlier: 3.718A pdb=" N VAL F 445 " --> pdb=" O GLU F 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE F 446 " --> pdb=" O GLY F 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 449 " --> pdb=" O VAL F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 463 removed outlier: 3.752A pdb=" N VAL F 458 " --> pdb=" O PRO F 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 459 " --> pdb=" O GLU F 455 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS I 25 " --> pdb=" O GLU I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA I 41 " --> pdb=" O GLY I 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU I 43 " --> pdb=" O ALA I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA I 56 " --> pdb=" O ILE I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN I 66 " --> pdb=" O VAL I 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL I 67 " --> pdb=" O GLN I 63 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL I 69 " --> pdb=" O ASN I 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER I 76 " --> pdb=" O GLN I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 removed outlier: 4.206A pdb=" N ALA I 91 " --> pdb=" O LEU I 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU I 98 " --> pdb=" O GLY I 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU I 101 " --> pdb=" O VAL I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 104 No H-bonds generated for 'chain 'I' and resid 102 through 104' Processing helix chain 'I' and resid 108 through 119 removed outlier: 3.601A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU I 115 " --> pdb=" O ALA I 111 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE I 117 " --> pdb=" O GLY I 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA I 155 " --> pdb=" O GLY I 151 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TRP I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG I 171 " --> pdb=" O ASP I 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 167 through 172' Processing helix chain 'I' and resid 172 through 177 removed outlier: 4.045A pdb=" N ARG I 177 " --> pdb=" O ARG I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE I 181 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA I 182 " --> pdb=" O GLY I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 182' Processing helix chain 'I' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS J 25 " --> pdb=" O GLU J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 44 removed outlier: 4.729A pdb=" N ALA J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU J 43 " --> pdb=" O ALA J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.599A pdb=" N ALA J 56 " --> pdb=" O ILE J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN J 66 " --> pdb=" O VAL J 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL J 67 " --> pdb=" O GLN J 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL J 69 " --> pdb=" O ASN J 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER J 76 " --> pdb=" O GLN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU J 98 " --> pdb=" O GLY J 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR J 99 " --> pdb=" O SER J 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU J 101 " --> pdb=" O VAL J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 104 No H-bonds generated for 'chain 'J' and resid 102 through 104' Processing helix chain 'J' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP J 114 " --> pdb=" O ALA J 110 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU J 115 " --> pdb=" O ALA J 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE J 117 " --> pdb=" O GLY J 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS J 119 " --> pdb=" O LEU J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA J 155 " --> pdb=" O GLY J 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP J 159 " --> pdb=" O ALA J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG J 171 " --> pdb=" O ASP J 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 167 through 172' Processing helix chain 'J' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 182 removed outlier: 3.615A pdb=" N PHE J 181 " --> pdb=" O ARG J 177 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA J 182 " --> pdb=" O GLY J 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 177 through 182' Processing helix chain 'J' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 30 removed outlier: 3.617A pdb=" N SER Q 16 " --> pdb=" O LYS Q 12 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN Q 29 " --> pdb=" O THR Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 38 Processing helix chain 'Q' and resid 53 through 60 Processing helix chain 'Q' and resid 65 through 79 removed outlier: 3.851A pdb=" N ARG Q 69 " --> pdb=" O ASP Q 65 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG Q 74 " --> pdb=" O ILE Q 70 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU Q 75 " --> pdb=" O MET Q 71 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS Q 76 " --> pdb=" O THR Q 72 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE Q 77 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 102 removed outlier: 3.554A pdb=" N MET Q 88 " --> pdb=" O PHE Q 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG Q 90 " --> pdb=" O PRO Q 86 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY Q 92 " --> pdb=" O MET Q 88 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN Q 94 " --> pdb=" O ARG Q 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN Q 95 " --> pdb=" O SER Q 91 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLN Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 31 removed outlier: 3.505A pdb=" N ASP R 9 " --> pdb=" O GLN R 5 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS R 12 " --> pdb=" O LYS R 8 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU R 14 " --> pdb=" O THR R 10 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN R 15 " --> pdb=" O ALA R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 34 through 46 removed outlier: 3.523A pdb=" N THR R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL R 46 " --> pdb=" O HIS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 63 removed outlier: 3.880A pdb=" N LYS R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU R 58 " --> pdb=" O ALA R 54 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU R 62 " --> pdb=" O GLU R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 77 removed outlier: 3.784A pdb=" N ARG R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET R 71 " --> pdb=" O ALA R 67 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL R 73 " --> pdb=" O ARG R 69 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG R 74 " --> pdb=" O ILE R 70 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 100 removed outlier: 4.144A pdb=" N ARG R 90 " --> pdb=" O PRO R 86 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER R 91 " --> pdb=" O GLU R 87 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY R 92 " --> pdb=" O MET R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 112 removed outlier: 3.815A pdb=" N LEU R 105 " --> pdb=" O ARG R 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 4 through 30 removed outlier: 3.514A pdb=" N THR S 13 " --> pdb=" O ASP S 9 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 38 Processing helix chain 'S' and resid 53 through 60 Processing helix chain 'S' and resid 65 through 79 removed outlier: 3.825A pdb=" N ARG S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR S 72 " --> pdb=" O LEU S 68 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG S 74 " --> pdb=" O ILE S 70 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU S 75 " --> pdb=" O MET S 71 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N HIS S 76 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE S 77 " --> pdb=" O VAL S 73 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 102 removed outlier: 3.528A pdb=" N MET S 88 " --> pdb=" O PHE S 84 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG S 90 " --> pdb=" O PRO S 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY S 92 " --> pdb=" O MET S 88 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN S 95 " --> pdb=" O SER S 91 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 34 removed outlier: 3.508A pdb=" N ASP T 9 " --> pdb=" O GLN T 5 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS T 12 " --> pdb=" O LYS T 8 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU T 14 " --> pdb=" O THR T 10 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 34 through 46 removed outlier: 3.520A pdb=" N THR T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL T 46 " --> pdb=" O HIS T 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 63 removed outlier: 3.808A pdb=" N LYS T 57 " --> pdb=" O GLU T 53 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU T 58 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU T 62 " --> pdb=" O GLU T 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 65 through 77 removed outlier: 3.815A pdb=" N ARG T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG T 74 " --> pdb=" O ILE T 70 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU T 75 " --> pdb=" O MET T 71 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS T 76 " --> pdb=" O THR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 100 removed outlier: 4.138A pdb=" N ARG T 90 " --> pdb=" O PRO T 86 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY T 92 " --> pdb=" O MET T 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 101 through 112 removed outlier: 3.799A pdb=" N LEU T 105 " --> pdb=" O ARG T 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 121 removed outlier: 3.914A pdb=" N VAL A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS A 147 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP A 161 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 190 " --> pdb=" O TYR A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG A 195 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE A 219 " --> pdb=" O TRP A 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 215 through 220' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.658A pdb=" N TYR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 280 " --> pdb=" O ALA A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 276 through 280' Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU A 319 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.747A pdb=" N PHE A 346 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 347' Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.950A pdb=" N GLY A 362 " --> pdb=" O LYS A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL A 392 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN A 421 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 423 " --> pdb=" O THR A 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N CYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL A 445 " --> pdb=" O GLU A 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE A 446 " --> pdb=" O GLY A 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 449 " --> pdb=" O VAL A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.752A pdb=" N VAL A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 459 " --> pdb=" O GLU A 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A 462 " --> pdb=" O VAL A 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.743A pdb=" N ALA B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 121 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS B 147 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP B 161 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 190 " --> pdb=" O TYR B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 removed outlier: 4.711A pdb=" N ARG B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY B 197 " --> pdb=" O LEU B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE B 219 " --> pdb=" O TRP B 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 215 through 220' Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR B 257 " --> pdb=" O LYS B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR B 280 " --> pdb=" O ALA B 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 276 through 280' Processing helix chain 'B' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU B 319 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE B 346 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 342 through 347' Processing helix chain 'B' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY B 362 " --> pdb=" O LYS B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL B 392 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 423 " --> pdb=" O THR B 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 424 " --> pdb=" O ALA B 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS B 428 " --> pdb=" O ALA B 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL B 445 " --> pdb=" O GLU B 441 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA B 449 " --> pdb=" O VAL B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL B 458 " --> pdb=" O PRO B 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 459 " --> pdb=" O GLU B 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 25 removed outlier: 3.743A pdb=" N LYS K 25 " --> pdb=" O GLU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 44 removed outlier: 4.730A pdb=" N ALA K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU K 43 " --> pdb=" O ALA K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 56 removed outlier: 3.598A pdb=" N ALA K 56 " --> pdb=" O ILE K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN K 66 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL K 69 " --> pdb=" O ASN K 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER K 76 " --> pdb=" O GLN K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA K 91 " --> pdb=" O LEU K 87 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 101 removed outlier: 4.329A pdb=" N LEU K 98 " --> pdb=" O GLY K 94 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU K 101 " --> pdb=" O VAL K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 104 No H-bonds generated for 'chain 'K' and resid 102 through 104' Processing helix chain 'K' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP K 114 " --> pdb=" O ALA K 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU K 115 " --> pdb=" O ALA K 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N HIS K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 139 removed outlier: 3.528A pdb=" N GLU K 128 " --> pdb=" O ASP K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA K 155 " --> pdb=" O GLY K 151 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP K 159 " --> pdb=" O ALA K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 172 removed outlier: 3.660A pdb=" N ARG K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 167 through 172' Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.046A pdb=" N ARG K 177 " --> pdb=" O ARG K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE K 181 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA K 182 " --> pdb=" O GLY K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 177 through 182' Processing helix chain 'K' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 25 removed outlier: 3.742A pdb=" N LYS L 25 " --> pdb=" O GLU L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 44 removed outlier: 4.729A pdb=" N ALA L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU L 43 " --> pdb=" O ALA L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 56 removed outlier: 3.599A pdb=" N ALA L 56 " --> pdb=" O ILE L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 78 removed outlier: 3.830A pdb=" N GLN L 66 " --> pdb=" O VAL L 62 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL L 67 " --> pdb=" O GLN L 63 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL L 69 " --> pdb=" O ASN L 65 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER L 76 " --> pdb=" O GLN L 72 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 93 removed outlier: 4.207A pdb=" N ALA L 91 " --> pdb=" O LEU L 87 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 101 removed outlier: 4.328A pdb=" N LEU L 98 " --> pdb=" O GLY L 94 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR L 99 " --> pdb=" O SER L 95 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU L 101 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 104 No H-bonds generated for 'chain 'L' and resid 102 through 104' Processing helix chain 'L' and resid 108 through 119 removed outlier: 3.602A pdb=" N ASP L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 117 " --> pdb=" O GLY L 113 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS L 119 " --> pdb=" O LEU L 115 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 139 removed outlier: 3.529A pdb=" N GLU L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 161 removed outlier: 3.673A pdb=" N ALA L 155 " --> pdb=" O GLY L 151 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TRP L 159 " --> pdb=" O ALA L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.659A pdb=" N ARG L 171 " --> pdb=" O ASP L 167 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 167 through 172' Processing helix chain 'L' and resid 172 through 177 removed outlier: 4.045A pdb=" N ARG L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 182 removed outlier: 3.614A pdb=" N PHE L 181 " --> pdb=" O ARG L 177 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA L 182 " --> pdb=" O GLY L 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 177 through 182' Processing helix chain 'L' and resid 185 through 193 removed outlier: 4.120A pdb=" N ILE L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'U' and resid 4 through 30 removed outlier: 3.665A pdb=" N SER U 16 " --> pdb=" O LYS U 12 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN U 29 " --> pdb=" O THR U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 38 Processing helix chain 'U' and resid 53 through 60 Processing helix chain 'U' and resid 65 through 79 removed outlier: 3.847A pdb=" N ARG U 69 " --> pdb=" O ASP U 65 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR U 72 " --> pdb=" O LEU U 68 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG U 74 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU U 75 " --> pdb=" O MET U 71 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N HIS U 76 " --> pdb=" O THR U 72 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE U 77 " --> pdb=" O VAL U 73 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 102 removed outlier: 3.752A pdb=" N ARG U 90 " --> pdb=" O PRO U 86 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY U 92 " --> pdb=" O MET U 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN U 94 " --> pdb=" O ARG U 90 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN U 95 " --> pdb=" O SER U 91 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN U 100 " --> pdb=" O ALA U 96 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 34 removed outlier: 3.503A pdb=" N ASP V 9 " --> pdb=" O GLN V 5 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS V 12 " --> pdb=" O LYS V 8 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU V 14 " --> pdb=" O THR V 10 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN V 15 " --> pdb=" O ALA V 11 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU V 32 " --> pdb=" O ALA V 28 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.505A pdb=" N THR V 43 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL V 46 " --> pdb=" O HIS V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 63 removed outlier: 3.824A pdb=" N LYS V 57 " --> pdb=" O GLU V 53 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU V 62 " --> pdb=" O GLU V 58 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 77 removed outlier: 3.820A pdb=" N ARG V 69 " --> pdb=" O ASP V 65 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET V 71 " --> pdb=" O ALA V 67 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL V 73 " --> pdb=" O ARG V 69 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG V 74 " --> pdb=" O ILE V 70 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU V 75 " --> pdb=" O MET V 71 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS V 76 " --> pdb=" O THR V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 85 through 100 removed outlier: 4.175A pdb=" N ARG V 90 " --> pdb=" O PRO V 86 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER V 91 " --> pdb=" O GLU V 87 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLY V 92 " --> pdb=" O MET V 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 112 removed outlier: 3.818A pdb=" N LEU V 105 " --> pdb=" O ARG V 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 30 removed outlier: 3.527A pdb=" N THR W 13 " --> pdb=" O ASP W 9 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER W 16 " --> pdb=" O LYS W 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 38 Processing helix chain 'W' and resid 53 through 60 Processing helix chain 'W' and resid 65 through 79 removed outlier: 3.809A pdb=" N ARG W 69 " --> pdb=" O ASP W 65 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG W 74 " --> pdb=" O ILE W 70 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU W 75 " --> pdb=" O MET W 71 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS W 76 " --> pdb=" O THR W 72 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE W 77 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 102 removed outlier: 3.524A pdb=" N MET W 88 " --> pdb=" O PHE W 84 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG W 90 " --> pdb=" O PRO W 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY W 92 " --> pdb=" O MET W 88 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN W 94 " --> pdb=" O ARG W 90 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN W 95 " --> pdb=" O SER W 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN W 100 " --> pdb=" O ALA W 96 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 34 removed outlier: 3.507A pdb=" N ASP X 9 " --> pdb=" O GLN X 5 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS X 12 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR X 13 " --> pdb=" O ASP X 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU X 14 " --> pdb=" O THR X 10 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN X 15 " --> pdb=" O ALA X 11 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR X 20 " --> pdb=" O SER X 16 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 34 through 46 removed outlier: 3.502A pdb=" N THR X 43 " --> pdb=" O LEU X 39 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL X 46 " --> pdb=" O HIS X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 63 removed outlier: 3.839A pdb=" N LYS X 57 " --> pdb=" O GLU X 53 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLU X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU X 62 " --> pdb=" O GLU X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 77 removed outlier: 3.800A pdb=" N ARG X 69 " --> pdb=" O ASP X 65 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL X 73 " --> pdb=" O ARG X 69 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG X 74 " --> pdb=" O ILE X 70 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU X 75 " --> pdb=" O MET X 71 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS X 76 " --> pdb=" O THR X 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 85 through 100 removed outlier: 4.147A pdb=" N ARG X 90 " --> pdb=" O PRO X 86 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY X 92 " --> pdb=" O MET X 88 " (cutoff:3.500A) Processing helix chain 'X' and resid 101 through 112 removed outlier: 3.837A pdb=" N LEU X 105 " --> pdb=" O ARG X 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N GLU C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 121 removed outlier: 3.912A pdb=" N VAL C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 121 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS C 147 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.571A pdb=" N ASP C 161 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL C 190 " --> pdb=" O TYR C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE C 219 " --> pdb=" O TRP C 215 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 220 " --> pdb=" O ARG C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 220' Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR C 279 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR C 280 " --> pdb=" O ALA C 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 276 through 280' Processing helix chain 'C' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU C 319 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 347 removed outlier: 3.746A pdb=" N PHE C 346 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 342 through 347' Processing helix chain 'C' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY C 362 " --> pdb=" O LYS C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 396 removed outlier: 3.540A pdb=" N VAL C 392 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 393 " --> pdb=" O PRO C 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 434 removed outlier: 4.715A pdb=" N ASN C 421 " --> pdb=" O GLY C 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 423 " --> pdb=" O THR C 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA C 424 " --> pdb=" O ALA C 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 449 removed outlier: 3.718A pdb=" N VAL C 445 " --> pdb=" O GLU C 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 446 " --> pdb=" O GLY C 442 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C 449 " --> pdb=" O VAL C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA C 459 " --> pdb=" O GLU C 455 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N CYS C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU C 462 " --> pdb=" O VAL C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 3.742A pdb=" N ALA D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLU D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER D 63 " --> pdb=" O ALA D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 121 removed outlier: 3.913A pdb=" N VAL D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 121 " --> pdb=" O VAL D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 147 removed outlier: 3.608A pdb=" N LYS D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 removed outlier: 3.572A pdb=" N ASP D 161 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.615A pdb=" N ALA D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 190 " --> pdb=" O TYR D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.710A pdb=" N ARG D 195 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 220 removed outlier: 3.607A pdb=" N PHE D 219 " --> pdb=" O TRP D 215 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 215 through 220' Processing helix chain 'D' and resid 221 through 223 No H-bonds generated for 'chain 'D' and resid 221 through 223' Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.659A pdb=" N TYR D 257 " --> pdb=" O LYS D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.539A pdb=" N THR D 279 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR D 280 " --> pdb=" O ALA D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 280' Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.613A pdb=" N LEU D 319 " --> pdb=" O LEU D 315 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 347 removed outlier: 3.747A pdb=" N PHE D 346 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N VAL D 347 " --> pdb=" O THR D 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 342 through 347' Processing helix chain 'D' and resid 358 through 362 removed outlier: 3.951A pdb=" N GLY D 362 " --> pdb=" O LYS D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 396 removed outlier: 3.541A pdb=" N VAL D 392 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU D 393 " --> pdb=" O PRO D 389 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D 394 " --> pdb=" O ALA D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 434 removed outlier: 4.714A pdb=" N ASN D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL D 423 " --> pdb=" O THR D 419 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 424 " --> pdb=" O ALA D 420 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS D 428 " --> pdb=" O ALA D 424 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 removed outlier: 3.717A pdb=" N VAL D 445 " --> pdb=" O GLU D 441 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 446 " --> pdb=" O GLY D 442 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 449 " --> pdb=" O VAL D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.753A pdb=" N VAL D 458 " --> pdb=" O PRO D 454 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 459 " --> pdb=" O GLU D 455 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG G 42 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU G 134 " --> pdb=" O ARG G 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR G 44 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR G 101 " --> pdb=" O TYR G 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU G 38 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS G 173 " --> pdb=" O LYS G 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE G 294 " --> pdb=" O HIS G 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA G 377 " --> pdb=" O VAL G 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG H 42 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU H 134 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR H 44 " --> pdb=" O ARG H 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU H 38 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS H 173 " --> pdb=" O LYS H 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'H' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE H 294 " --> pdb=" O HIS H 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA H 377 " --> pdb=" O VAL H 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG E 42 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 134 " --> pdb=" O ARG E 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR E 44 " --> pdb=" O ARG E 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR E 101 " --> pdb=" O TYR E 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 38 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 172 through 174 removed outlier: 6.833A pdb=" N CYS E 173 " --> pdb=" O LYS E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 293 through 294 removed outlier: 3.581A pdb=" N ILE E 294 " --> pdb=" O HIS E 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA E 377 " --> pdb=" O VAL E 400 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG F 42 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU F 134 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR F 44 " --> pdb=" O ARG F 132 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR F 101 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 38 " --> pdb=" O ARG F 140 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 172 through 174 removed outlier: 6.835A pdb=" N CYS F 173 " --> pdb=" O LYS F 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE F 294 " --> pdb=" O HIS F 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA F 377 " --> pdb=" O VAL F 400 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 42 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU A 134 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR A 44 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR A 101 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 38 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS A 173 " --> pdb=" O LYS A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE A 294 " --> pdb=" O HIS A 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 377 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG B 42 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU B 134 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR B 44 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 87 removed outlier: 6.749A pdb=" N TYR B 101 " --> pdb=" O TYR B 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 38 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS B 173 " --> pdb=" O LYS B 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE B 294 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA B 377 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG C 42 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU C 134 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N THR C 44 " --> pdb=" O ARG C 132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR C 101 " --> pdb=" O TYR C 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 38 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 172 through 174 removed outlier: 6.834A pdb=" N CYS C 173 " --> pdb=" O LYS C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 293 through 294 removed outlier: 3.581A pdb=" N ILE C 294 " --> pdb=" O HIS C 326 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA C 377 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG D 42 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU D 134 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR D 44 " --> pdb=" O ARG D 132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 84 through 87 removed outlier: 6.750A pdb=" N TYR D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU D 38 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 172 through 174 removed outlier: 6.833A pdb=" N CYS D 173 " --> pdb=" O LYS D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 293 through 294 removed outlier: 3.582A pdb=" N ILE D 294 " --> pdb=" O HIS D 326 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA D 377 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1637 hydrogen bonds defined for protein. 4623 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: 14.03 Time building geometry restraints manager: 9.99 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: 15616 1.34 - 1.46: 9551 1.46 - 1.58: 25407 1.58 - 1.70: 2 1.70 - 1.82: 280 Bond restraints: 50856 Sorted by residual: bond pdb=" C LEU F 372 " pdb=" N PRO F 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" C LEU B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.82e+01 bond pdb=" C LEU E 372 " pdb=" N PRO E 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.80e+01 bond pdb=" C LEU A 372 " pdb=" N PRO A 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.78e+01 bond pdb=" C LEU G 372 " pdb=" N PRO G 373 " ideal model delta sigma weight residual 1.331 1.382 -0.051 1.20e-02 6.94e+03 1.78e+01 ... (remaining 50851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 67742 4.12 - 8.23: 937 8.23 - 12.35: 112 12.35 - 16.46: 9 16.46 - 20.58: 16 Bond angle restraints: 68816 Sorted by residual: angle pdb=" CA LEU D 291 " pdb=" CB LEU D 291 " pdb=" CG LEU D 291 " ideal model delta sigma weight residual 116.30 136.88 -20.58 3.50e+00 8.16e-02 3.46e+01 angle pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " pdb=" CG LEU B 291 " ideal model delta sigma weight residual 116.30 136.87 -20.57 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU G 291 " pdb=" CB LEU G 291 " pdb=" CG LEU G 291 " ideal model delta sigma weight residual 116.30 136.86 -20.56 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU A 291 " pdb=" CB LEU A 291 " pdb=" CG LEU A 291 " ideal model delta sigma weight residual 116.30 136.86 -20.56 3.50e+00 8.16e-02 3.45e+01 angle pdb=" CA LEU H 291 " pdb=" CB LEU H 291 " pdb=" CG LEU H 291 " ideal model delta sigma weight residual 116.30 136.83 -20.53 3.50e+00 8.16e-02 3.44e+01 ... (remaining 68811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.52: 28528 15.52 - 31.04: 1616 31.04 - 46.56: 312 46.56 - 62.08: 40 62.08 - 77.60: 48 Dihedral angle restraints: 30544 sinusoidal: 12360 harmonic: 18184 Sorted by residual: dihedral pdb=" CA GLU E 260 " pdb=" C GLU E 260 " pdb=" N LEU E 261 " pdb=" CA LEU E 261 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA GLU F 260 " pdb=" C GLU F 260 " pdb=" N LEU F 261 " pdb=" CA LEU F 261 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA GLU H 260 " pdb=" C GLU H 260 " pdb=" N LEU H 261 " pdb=" CA LEU H 261 " ideal model delta harmonic sigma weight residual 180.00 140.50 39.50 0 5.00e+00 4.00e-02 6.24e+01 ... (remaining 30541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 6573 0.089 - 0.177: 928 0.177 - 0.266: 43 0.266 - 0.355: 22 0.355 - 0.444: 10 Chirality restraints: 7576 Sorted by residual: chirality pdb=" CG LEU R 85 " pdb=" CB LEU R 85 " pdb=" CD1 LEU R 85 " pdb=" CD2 LEU R 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CB VAL F 222 " pdb=" CA VAL F 222 " pdb=" CG1 VAL F 222 " pdb=" CG2 VAL F 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.92e+00 chirality pdb=" CB VAL A 222 " pdb=" CA VAL A 222 " pdb=" CG1 VAL A 222 " pdb=" CG2 VAL A 222 " both_signs ideal model delta sigma weight residual False -2.63 -2.23 -0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 7573 not shown) Planarity restraints: 8976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO W 35 " 0.052 5.00e-02 4.00e+02 7.74e-02 9.58e+00 pdb=" N PRO W 36 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO W 36 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO W 36 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO S 35 " -0.051 5.00e-02 4.00e+02 7.64e-02 9.33e+00 pdb=" N PRO S 36 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO S 36 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO S 36 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO 7 35 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO 7 36 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO 7 36 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO 7 36 " -0.043 5.00e-02 4.00e+02 ... (remaining 8973 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 11540 2.78 - 3.31: 43024 3.31 - 3.84: 78113 3.84 - 4.37: 96176 4.37 - 4.90: 155018 Nonbonded interactions: 383871 Sorted by model distance: nonbonded pdb=" O PHE G 275 " pdb=" OG1 THR G 279 " model vdw 2.253 3.040 nonbonded pdb=" O PHE H 275 " pdb=" OG1 THR H 279 " model vdw 2.254 3.040 nonbonded pdb=" O PHE B 275 " pdb=" OG1 THR B 279 " model vdw 2.254 3.040 nonbonded pdb=" O PHE F 275 " pdb=" OG1 THR F 279 " model vdw 2.254 3.040 nonbonded pdb=" O PHE D 275 " pdb=" OG1 THR D 279 " model vdw 2.254 3.040 ... (remaining 383866 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 '1' selection = (chain '2' and resid 2 through 102) selection = chain '3' selection = (chain '4' and resid 2 through 102) selection = chain '5' selection = (chain '6' and resid 2 through 102) selection = chain '7' selection = (chain '8' and resid 2 through 102) selection = chain 'Q' selection = (chain 'R' and resid 2 through 102) selection = chain 'S' selection = (chain 'T' and resid 2 through 102) selection = chain 'U' selection = (chain 'V' and resid 2 through 102) selection = chain 'W' selection = (chain 'X' and resid 2 through 102) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.730 Check model and map are aligned: 0.330 Set scattering table: 0.330 Process input model: 74.810 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5183 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 : 0.009 0.095 50856 Z= 0.572 Angle : 1.336 20.576 68816 Z= 0.733 Chirality : 0.063 0.444 7576 Planarity : 0.009 0.077 8976 Dihedral : 11.072 77.603 18784 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 0.77 % Allowed : 2.88 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -5.61 (0.08), residues: 6128 helix: -4.39 (0.05), residues: 3032 sheet: -4.31 (0.19), residues: 288 loop : -2.70 (0.10), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.005 TRP H 284 HIS 0.016 0.003 HIS E 326 PHE 0.044 0.006 PHE F 219 TYR 0.029 0.004 TYR L 48 ARG 0.020 0.002 ARG W 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1619 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 1579 time to evaluate : 3.983 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: 5 26 VAL cc_start: 0.6945 (t) cc_final: 0.6464 (t) REVERT: 5 44 PHE cc_start: 0.3105 (m-80) cc_final: 0.2478 (m-80) REVERT: 5 68 LEU cc_start: 0.4453 (mt) cc_final: 0.4206 (tp) REVERT: 5 98 MET cc_start: 0.5861 (mmm) cc_final: 0.5259 (mmm) REVERT: 6 13 THR cc_start: 0.4466 (m) cc_final: 0.3683 (p) REVERT: 6 94 GLN cc_start: 0.6359 (mt0) cc_final: 0.5988 (mm110) REVERT: 7 24 MET cc_start: 0.5431 (mmm) cc_final: 0.5152 (tpp) REVERT: 7 25 THR cc_start: 0.5791 (m) cc_final: 0.5563 (m) REVERT: 7 66 LEU cc_start: 0.6407 (mt) cc_final: 0.6152 (tp) REVERT: 7 71 MET cc_start: 0.3875 (mmt) cc_final: 0.3544 (mmt) REVERT: 7 81 VAL cc_start: 0.5706 (t) cc_final: 0.5177 (p) REVERT: 8 3 LEU cc_start: 0.5881 (tp) cc_final: 0.5550 (mt) REVERT: 8 100 GLN cc_start: 0.2575 (mt0) cc_final: 0.1985 (mp10) REVERT: 8 104 HIS cc_start: 0.3313 (t70) cc_final: 0.3046 (m-70) REVERT: O 33 TRP cc_start: 0.5667 (p-90) cc_final: 0.5051 (p-90) REVERT: H 53 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5784 (mm-30) REVERT: 1 18 LEU cc_start: 0.6077 (mt) cc_final: 0.5773 (tt) REVERT: 1 24 MET cc_start: 0.6327 (mmm) cc_final: 0.6015 (ppp) REVERT: 1 26 VAL cc_start: 0.5373 (t) cc_final: 0.4888 (t) REVERT: 2 13 THR cc_start: 0.3526 (m) cc_final: 0.3154 (p) REVERT: 2 105 LEU cc_start: 0.4948 (mm) cc_final: 0.4216 (tp) REVERT: 2 108 MET cc_start: 0.5098 (tpp) cc_final: 0.4352 (ptm) REVERT: 3 97 ASN cc_start: 0.2820 (m-40) cc_final: 0.2494 (t0) REVERT: 4 76 HIS cc_start: 0.5363 (t70) cc_final: 0.5006 (t-90) REVERT: M 26 LEU cc_start: 0.5466 (tt) cc_final: 0.4768 (tt) REVERT: F 327 ILE cc_start: 0.6556 (pt) cc_final: 0.6267 (pt) REVERT: I 27 ARG cc_start: 0.4382 (ptm-80) cc_final: 0.3196 (mtm180) REVERT: Q 68 LEU cc_start: 0.4922 (mt) cc_final: 0.4274 (tp) REVERT: R 95 GLN cc_start: 0.5976 (mt0) cc_final: 0.5758 (mm110) REVERT: S 20 TYR cc_start: 0.5598 (t80) cc_final: 0.5114 (t80) REVERT: S 21 GLN cc_start: 0.5219 (mm110) cc_final: 0.4362 (mm-40) REVERT: S 74 ARG cc_start: 0.3347 (ptt180) cc_final: 0.2983 (ttp-110) REVERT: S 86 PRO cc_start: 0.3700 (Cg_exo) cc_final: 0.3262 (Cg_endo) REVERT: A 421 ASN cc_start: 0.6689 (m-40) cc_final: 0.5976 (t0) REVERT: A 467 LYS cc_start: 0.6455 (mttt) cc_final: 0.5857 (mptt) REVERT: B 387 HIS cc_start: 0.2366 (m-70) cc_final: 0.2051 (m-70) REVERT: K 26 LEU cc_start: 0.4865 (tt) cc_final: 0.4401 (tt) REVERT: K 27 ARG cc_start: 0.4025 (ptm-80) cc_final: 0.3678 (mtm180) REVERT: K 118 THR cc_start: 0.6822 (m) cc_final: 0.6547 (p) REVERT: K 124 ASP cc_start: 0.7242 (m-30) cc_final: 0.6566 (m-30) REVERT: K 135 ASP cc_start: 0.5492 (m-30) cc_final: 0.5047 (m-30) REVERT: L 192 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5275 (mm-30) REVERT: U 4 LYS cc_start: 0.4300 (mtpm) cc_final: 0.3943 (mtpp) REVERT: U 24 MET cc_start: 0.6044 (mmm) cc_final: 0.5836 (tpp) REVERT: U 48 LYS cc_start: 0.4151 (mttt) cc_final: 0.3918 (tppt) REVERT: U 68 LEU cc_start: 0.3517 (mt) cc_final: 0.2983 (tp) REVERT: U 102 ARG cc_start: 0.4329 (ptm-80) cc_final: 0.3952 (ptm-80) REVERT: V 108 MET cc_start: 0.4756 (tpp) cc_final: 0.4474 (ptt) REVERT: W 24 MET cc_start: 0.5917 (mmm) cc_final: 0.5577 (ppp) REVERT: W 66 LEU cc_start: 0.6517 (mt) cc_final: 0.6314 (mp) REVERT: X 100 GLN cc_start: 0.3792 (mt0) cc_final: 0.3512 (mt0) REVERT: X 108 MET cc_start: 0.5451 (tpp) cc_final: 0.4969 (ptt) REVERT: C 215 TRP cc_start: 0.5067 (p-90) cc_final: 0.3868 (p-90) outliers start: 40 outliers final: 7 residues processed: 1598 average time/residue: 0.5539 time to fit residues: 1397.4196 Evaluate side-chains 830 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 823 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain D residue 267 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 9.9990 chunk 466 optimal weight: 8.9990 chunk 259 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 314 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 482 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 293 optimal weight: 0.9990 chunk 359 optimal weight: 9.9990 chunk 559 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 15 GLN 5 21 GLN 5 34 ASN 7 15 GLN 7 21 GLN 7 34 ASN 7 76 HIS 8 21 GLN O 30 GLN O 64 GLN O 65 ASN O 66 GLN P 30 GLN P 64 GLN P 66 GLN G 46 GLN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 HIS G 308 HIS ** G 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 154 HIS H 164 ASN H 206 ASN ** H 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 308 HIS H 326 HIS H 443 ASN 1 15 GLN 1 21 GLN 1 29 GLN 1 34 ASN 2 21 GLN 2 29 GLN 2 97 ASN 3 15 GLN 3 21 GLN 3 34 ASN 4 21 GLN 4 29 GLN M 30 GLN M 64 GLN M 65 ASN M 66 GLN M 106 HIS N 30 GLN N 66 GLN E 116 ASN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 206 ASN E 208 ASN E 242 ASN ** E 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS E 353 ASN F 116 ASN F 164 ASN F 206 ASN F 208 ASN ** F 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 308 HIS F 311 HIS I 30 GLN I 64 GLN I 65 ASN I 66 GLN J 30 GLN J 44 GLN J 64 GLN J 65 ASN J 66 GLN Q 21 GLN Q 34 ASN ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN S 15 GLN S 21 GLN ** S 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 GLN T 29 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN A 206 ASN A 308 HIS A 311 HIS A 353 ASN A 357 GLN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 HIS ** B 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 387 HIS B 443 ASN K 30 GLN K 64 GLN K 65 ASN K 66 GLN L 30 GLN L 65 ASN L 66 GLN U 21 GLN U 34 ASN U 76 HIS U 100 GLN V 15 GLN V 29 GLN W 15 GLN W 21 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 21 GLN X 29 GLN X 103 GLN C 124 ASN ** C 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 206 ASN C 208 ASN C 311 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN D 206 ASN D 208 ASN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 308 HIS ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS D 357 GLN Total number of N/Q/H flips: 114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5657 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 50856 Z= 0.244 Angle : 0.742 13.269 68816 Z= 0.383 Chirality : 0.044 0.259 7576 Planarity : 0.006 0.074 8976 Dihedral : 6.245 37.436 6859 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.25 % Allowed : 11.03 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -4.30 (0.09), residues: 6128 helix: -3.08 (0.07), residues: 3264 sheet: -3.59 (0.21), residues: 328 loop : -2.18 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP K 36 HIS 0.010 0.001 HIS G 239 PHE 0.024 0.002 PHE S 44 TYR 0.034 0.002 TYR S 20 ARG 0.008 0.001 ARG F 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1215 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 1047 time to evaluate : 4.058 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: 5 26 VAL cc_start: 0.6361 (t) cc_final: 0.6151 (t) REVERT: 5 44 PHE cc_start: 0.3058 (m-80) cc_final: 0.2402 (m-80) REVERT: 5 88 MET cc_start: 0.2427 (tpp) cc_final: 0.2102 (mmm) REVERT: 5 98 MET cc_start: 0.5648 (mmm) cc_final: 0.4964 (mmm) REVERT: 6 94 GLN cc_start: 0.6390 (mt0) cc_final: 0.5943 (mm110) REVERT: 6 102 ARG cc_start: 0.4715 (mmt180) cc_final: 0.4128 (mmm-85) REVERT: 7 16 SER cc_start: 0.1599 (m) cc_final: 0.1321 (p) REVERT: 8 3 LEU cc_start: 0.5412 (tp) cc_final: 0.4808 (mt) REVERT: 8 98 MET cc_start: 0.6790 (tpp) cc_final: 0.6095 (mmt) REVERT: O 20 GLN cc_start: 0.5274 (mm-40) cc_final: 0.4954 (mm-40) REVERT: O 120 LYS cc_start: 0.6864 (tptt) cc_final: 0.6358 (mptt) REVERT: O 193 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.4712 (tm-30) REVERT: G 87 ASP cc_start: 0.5340 (t70) cc_final: 0.4000 (t0) REVERT: G 347 VAL cc_start: 0.6938 (p) cc_final: 0.6717 (p) REVERT: H 387 HIS cc_start: 0.2308 (m-70) cc_final: 0.1635 (m-70) REVERT: 1 3 LEU cc_start: 0.3479 (mt) cc_final: 0.2482 (tp) REVERT: 1 24 MET cc_start: 0.6482 (mmm) cc_final: 0.5868 (ptp) REVERT: 2 13 THR cc_start: 0.3316 (m) cc_final: 0.2923 (p) REVERT: 2 83 GLU cc_start: 0.4308 (tp30) cc_final: 0.3608 (tm-30) REVERT: 2 98 MET cc_start: 0.6872 (mpp) cc_final: 0.6357 (mpp) REVERT: 2 105 LEU cc_start: 0.4567 (mm) cc_final: 0.4173 (tp) REVERT: 2 108 MET cc_start: 0.5559 (tpp) cc_final: 0.4680 (ptm) REVERT: 3 17 TYR cc_start: 0.3482 (t80) cc_final: 0.3140 (t80) REVERT: 4 76 HIS cc_start: 0.5151 (t70) cc_final: 0.4721 (t70) REVERT: 4 108 MET cc_start: 0.3784 (mmt) cc_final: 0.3213 (mmm) REVERT: M 26 LEU cc_start: 0.5708 (tt) cc_final: 0.5339 (tt) REVERT: M 120 LYS cc_start: 0.7106 (tptp) cc_final: 0.6810 (mmtm) REVERT: M 179 LEU cc_start: 0.8002 (mt) cc_final: 0.7695 (mp) REVERT: N 129 ILE cc_start: 0.6373 (mm) cc_final: 0.6007 (tt) REVERT: N 140 ARG cc_start: 0.6103 (mpt180) cc_final: 0.5437 (ptt90) REVERT: E 270 TYR cc_start: 0.5790 (p90) cc_final: 0.5504 (p90) REVERT: E 421 ASN cc_start: 0.5948 (m-40) cc_final: 0.5186 (t0) REVERT: E 426 GLU cc_start: 0.5553 (pt0) cc_final: 0.4677 (mt-10) REVERT: I 27 ARG cc_start: 0.4577 (ptm-80) cc_final: 0.3439 (mtp180) REVERT: J 90 TYR cc_start: 0.5866 (m-80) cc_final: 0.5619 (m-80) REVERT: J 106 HIS cc_start: 0.5732 (OUTLIER) cc_final: 0.4734 (m90) REVERT: Q 71 MET cc_start: 0.3547 (mmt) cc_final: 0.1787 (tpt) REVERT: Q 76 HIS cc_start: 0.5731 (t70) cc_final: 0.5492 (t70) REVERT: Q 80 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6385 (mt-10) REVERT: R 24 MET cc_start: 0.1256 (mmm) cc_final: 0.0513 (tpt) REVERT: S 13 THR cc_start: 0.6364 (OUTLIER) cc_final: 0.5633 (t) REVERT: S 16 SER cc_start: 0.3628 (m) cc_final: 0.2944 (p) REVERT: S 24 MET cc_start: 0.6056 (ptp) cc_final: 0.5688 (mmm) REVERT: A 421 ASN cc_start: 0.6393 (m-40) cc_final: 0.6017 (t0) REVERT: B 163 LEU cc_start: 0.5311 (OUTLIER) cc_final: 0.4956 (mp) REVERT: B 365 PHE cc_start: 0.6516 (m-10) cc_final: 0.6303 (m-80) REVERT: B 443 ASN cc_start: 0.6250 (OUTLIER) cc_final: 0.5993 (m-40) REVERT: K 22 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5712 (mt) REVERT: K 26 LEU cc_start: 0.5205 (tt) cc_final: 0.4605 (tt) REVERT: K 27 ARG cc_start: 0.4237 (ptm-80) cc_final: 0.3654 (mtt180) REVERT: K 55 GLU cc_start: 0.5393 (tt0) cc_final: 0.4834 (mm-30) REVERT: L 24 ARG cc_start: 0.4290 (tpt170) cc_final: 0.3944 (tpt90) REVERT: L 32 ASN cc_start: 0.6069 (p0) cc_final: 0.5629 (p0) REVERT: U 24 MET cc_start: 0.5815 (mmm) cc_final: 0.5333 (tpp) REVERT: U 48 LYS cc_start: 0.5105 (mttt) cc_final: 0.4607 (tppt) REVERT: U 68 LEU cc_start: 0.3006 (mt) cc_final: 0.2705 (tp) REVERT: V 83 GLU cc_start: 0.4589 (mm-30) cc_final: 0.3607 (mp0) REVERT: W 24 MET cc_start: 0.6250 (mmm) cc_final: 0.5751 (ppp) REVERT: X 107 ARG cc_start: 0.6238 (mpt180) cc_final: 0.5701 (ptt-90) REVERT: X 108 MET cc_start: 0.5530 (tpp) cc_final: 0.5072 (ptt) REVERT: C 61 GLU cc_start: 0.4489 (mm-30) cc_final: 0.3964 (mm-30) REVERT: C 89 GLU cc_start: 0.6112 (tp30) cc_final: 0.5811 (tp30) REVERT: C 270 TYR cc_start: 0.4645 (p90) cc_final: 0.4313 (p90) REVERT: C 351 ARG cc_start: 0.6778 (mtp180) cc_final: 0.6577 (mtp180) REVERT: D 111 GLU cc_start: 0.5517 (tm-30) cc_final: 0.4644 (mt-10) outliers start: 168 outliers final: 95 residues processed: 1158 average time/residue: 0.5258 time to fit residues: 998.3395 Evaluate side-chains 877 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 776 time to evaluate : 4.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 5 residue 70 ILE Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain O residue 193 GLN Chi-restraints excluded: chain P residue 46 SER Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain G residue 82 LYS Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 263 GLN Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 326 HIS Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 66 GLN Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 44 GLN Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain S residue 13 THR Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain B residue 443 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 283 ARG Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 425 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 465 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 560 optimal weight: 0.5980 chunk 605 optimal weight: 8.9990 chunk 499 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 449 optimal weight: 10.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 29 GLN 7 97 ASN ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS G 116 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 HIS G 387 HIS H 208 ASN H 242 ASN ** H 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 357 GLN H 387 HIS 1 94 GLN 1 100 GLN 3 15 GLN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 44 GLN N 64 GLN ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 HIS E 326 HIS E 421 ASN ** F 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS F 326 HIS I 106 HIS J 30 GLN J 44 GLN J 66 GLN ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 21 GLN R 97 ASN S 34 ASN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN B 308 HIS ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN K 193 GLN L 30 GLN L 66 GLN L 106 HIS U 76 HIS ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN C 357 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN D 421 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 50856 Z= 0.305 Angle : 0.769 12.936 68816 Z= 0.400 Chirality : 0.046 0.255 7576 Planarity : 0.006 0.081 8976 Dihedral : 6.322 34.464 6858 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.48 % Allowed : 13.79 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.62 (0.09), residues: 6128 helix: -2.41 (0.08), residues: 3216 sheet: -3.43 (0.21), residues: 360 loop : -2.00 (0.12), residues: 2552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 36 HIS 0.034 0.002 HIS F 268 PHE 0.033 0.003 PHE H 219 TYR 0.023 0.002 TYR S 20 ARG 0.009 0.001 ARG H 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 954 time to evaluate : 4.112 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: 5 88 MET cc_start: 0.2069 (tpp) cc_final: 0.1771 (mmm) REVERT: 5 93 ILE cc_start: 0.3831 (mt) cc_final: 0.3390 (tp) REVERT: 5 98 MET cc_start: 0.5641 (mmm) cc_final: 0.5306 (mmm) REVERT: 6 94 GLN cc_start: 0.6394 (mt0) cc_final: 0.6097 (mm110) REVERT: 7 16 SER cc_start: 0.2206 (m) cc_final: 0.1956 (p) REVERT: 7 24 MET cc_start: 0.5453 (tpp) cc_final: 0.5077 (tpp) REVERT: 7 66 LEU cc_start: 0.6662 (tp) cc_final: 0.6405 (tt) REVERT: 7 80 GLU cc_start: 0.5076 (mm-30) cc_final: 0.4524 (mt-10) REVERT: 8 98 MET cc_start: 0.6867 (tpp) cc_final: 0.6137 (mmt) REVERT: O 24 ARG cc_start: 0.5505 (ttp80) cc_final: 0.4720 (tpt90) REVERT: O 48 TYR cc_start: 0.5722 (OUTLIER) cc_final: 0.5229 (m-10) REVERT: O 55 GLU cc_start: 0.5966 (tt0) cc_final: 0.5153 (mp0) REVERT: O 120 LYS cc_start: 0.7369 (tptt) cc_final: 0.6878 (mptt) REVERT: P 30 GLN cc_start: 0.4956 (mm110) cc_final: 0.4703 (mm110) REVERT: G 191 TYR cc_start: 0.6616 (t80) cc_final: 0.5064 (t80) REVERT: G 250 GLU cc_start: 0.7528 (tp30) cc_final: 0.7297 (tp30) REVERT: G 388 MET cc_start: 0.6987 (tpp) cc_final: 0.6780 (tpp) REVERT: G 421 ASN cc_start: 0.6300 (m-40) cc_final: 0.6075 (t0) REVERT: G 452 TRP cc_start: 0.5396 (m-90) cc_final: 0.5002 (m-90) REVERT: H 119 THR cc_start: 0.7417 (t) cc_final: 0.7018 (m) REVERT: H 253 LYS cc_start: 0.5390 (OUTLIER) cc_final: 0.5146 (mtpt) REVERT: H 463 TRP cc_start: 0.3930 (m-10) cc_final: 0.3458 (m100) REVERT: 1 20 TYR cc_start: 0.6045 (t80) cc_final: 0.5366 (t80) REVERT: 1 24 MET cc_start: 0.6259 (mmm) cc_final: 0.5348 (mtp) REVERT: 1 37 LEU cc_start: 0.5531 (OUTLIER) cc_final: 0.5221 (mm) REVERT: 2 13 THR cc_start: 0.3556 (m) cc_final: 0.3299 (p) REVERT: 2 88 MET cc_start: 0.4718 (tpt) cc_final: 0.4301 (mtm) REVERT: 2 98 MET cc_start: 0.6697 (mpp) cc_final: 0.6329 (mpp) REVERT: 2 105 LEU cc_start: 0.4697 (mm) cc_final: 0.4201 (tt) REVERT: 2 108 MET cc_start: 0.5618 (tpp) cc_final: 0.4753 (ptm) REVERT: 3 13 THR cc_start: 0.5872 (p) cc_final: 0.5619 (t) REVERT: M 26 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5684 (tt) REVERT: M 120 LYS cc_start: 0.7630 (tptp) cc_final: 0.7410 (mptt) REVERT: M 127 ARG cc_start: 0.6625 (OUTLIER) cc_final: 0.6172 (tpt-90) REVERT: E 270 TYR cc_start: 0.5880 (p90) cc_final: 0.5622 (p90) REVERT: E 354 TYR cc_start: 0.7462 (t80) cc_final: 0.7227 (t80) REVERT: F 421 ASN cc_start: 0.6511 (m-40) cc_final: 0.6176 (t0) REVERT: I 48 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.4249 (m-10) REVERT: Q 80 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6720 (mt-10) REVERT: S 16 SER cc_start: 0.3863 (m) cc_final: 0.3250 (p) REVERT: S 20 TYR cc_start: 0.5019 (t80) cc_final: 0.4775 (t80) REVERT: T 100 GLN cc_start: 0.5924 (mt0) cc_final: 0.5294 (mt0) REVERT: A 421 ASN cc_start: 0.6704 (m-40) cc_final: 0.6207 (t0) REVERT: B 263 GLN cc_start: 0.6852 (OUTLIER) cc_final: 0.6454 (tt0) REVERT: B 352 GLU cc_start: 0.6463 (mp0) cc_final: 0.6049 (mm-30) REVERT: K 26 LEU cc_start: 0.5624 (OUTLIER) cc_final: 0.5100 (tt) REVERT: K 27 ARG cc_start: 0.4496 (ptm-80) cc_final: 0.3532 (mtt180) REVERT: K 55 GLU cc_start: 0.5302 (tt0) cc_final: 0.4943 (mm-30) REVERT: K 156 TYR cc_start: 0.6681 (t80) cc_final: 0.6345 (t80) REVERT: L 66 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.5219 (tt0) REVERT: U 13 THR cc_start: 0.4797 (p) cc_final: 0.4399 (t) REVERT: V 13 THR cc_start: 0.3644 (m) cc_final: 0.3384 (p) REVERT: V 24 MET cc_start: 0.3495 (mmp) cc_final: 0.2271 (tpt) REVERT: V 83 GLU cc_start: 0.4483 (mm-30) cc_final: 0.3523 (mp0) REVERT: W 20 TYR cc_start: 0.5742 (t80) cc_final: 0.5469 (t80) REVERT: W 24 MET cc_start: 0.6612 (mmm) cc_final: 0.5906 (ptm) REVERT: W 71 MET cc_start: 0.5391 (ppp) cc_final: 0.5054 (mmt) REVERT: X 24 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.1740 (tmm) REVERT: X 108 MET cc_start: 0.5398 (tpp) cc_final: 0.4988 (ptt) REVERT: C 61 GLU cc_start: 0.4993 (mm-30) cc_final: 0.4299 (mm-30) REVERT: C 137 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6614 (mm-30) REVERT: C 351 ARG cc_start: 0.7166 (mtp180) cc_final: 0.6963 (mtp180) REVERT: C 421 ASN cc_start: 0.6416 (OUTLIER) cc_final: 0.5799 (m-40) REVERT: D 119 THR cc_start: 0.6865 (m) cc_final: 0.6658 (m) outliers start: 232 outliers final: 134 residues processed: 1093 average time/residue: 0.4870 time to fit residues: 877.0076 Evaluate side-chains 934 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 789 time to evaluate : 4.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 253 LYS Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 1 residue 37 LEU Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 224 ASP Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 310 ILE Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 363 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain F residue 452 TRP Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain X residue 24 MET Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 419 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 8.9990 chunk 421 optimal weight: 8.9990 chunk 290 optimal weight: 5.9990 chunk 62 optimal weight: 0.0570 chunk 267 optimal weight: 5.9990 chunk 376 optimal weight: 8.9990 chunk 562 optimal weight: 5.9990 chunk 595 optimal weight: 10.0000 chunk 293 optimal weight: 3.9990 chunk 533 optimal weight: 0.9990 chunk 160 optimal weight: 20.0000 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 100 GLN 6 15 GLN 7 97 ASN ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 66 GLN G 116 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN G 421 ASN ** H 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS 4 15 GLN 4 110 HIS M 66 GLN E 213 GLN F 268 HIS I 32 ASN I 106 HIS ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 GLN L 66 GLN W 34 ASN W 76 HIS ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 50856 Z= 0.247 Angle : 0.683 14.094 68816 Z= 0.355 Chirality : 0.044 0.237 7576 Planarity : 0.005 0.065 8976 Dihedral : 5.901 33.253 6858 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.22 % Allowed : 15.03 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.08 (0.10), residues: 6128 helix: -1.93 (0.08), residues: 3200 sheet: -3.35 (0.24), residues: 280 loop : -1.87 (0.11), residues: 2648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP K 36 HIS 0.017 0.001 HIS P 106 PHE 0.028 0.002 PHE H 219 TYR 0.029 0.002 TYR C 191 ARG 0.009 0.001 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 270 poor density : 881 time to evaluate : 4.128 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: 5 88 MET cc_start: 0.2137 (tpp) cc_final: 0.1875 (mmm) REVERT: 5 93 ILE cc_start: 0.3843 (mt) cc_final: 0.3118 (tp) REVERT: 5 98 MET cc_start: 0.5372 (mmm) cc_final: 0.4643 (mmm) REVERT: 6 94 GLN cc_start: 0.6608 (mt0) cc_final: 0.6230 (mm110) REVERT: 7 80 GLU cc_start: 0.5395 (mm-30) cc_final: 0.5146 (mt-10) REVERT: 8 98 MET cc_start: 0.6886 (tpp) cc_final: 0.6217 (mmt) REVERT: O 24 ARG cc_start: 0.5417 (ttp80) cc_final: 0.4620 (tpt90) REVERT: O 48 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.5427 (m-10) REVERT: O 55 GLU cc_start: 0.5950 (tt0) cc_final: 0.5194 (mp0) REVERT: O 120 LYS cc_start: 0.7346 (tptt) cc_final: 0.6952 (mptt) REVERT: P 36 TRP cc_start: 0.5349 (m-10) cc_final: 0.5122 (m-90) REVERT: P 48 TYR cc_start: 0.4884 (OUTLIER) cc_final: 0.4563 (m-10) REVERT: P 128 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: G 191 TYR cc_start: 0.6647 (t80) cc_final: 0.5667 (t80) REVERT: G 250 GLU cc_start: 0.7432 (tp30) cc_final: 0.7173 (tp30) REVERT: G 421 ASN cc_start: 0.6401 (m110) cc_final: 0.6098 (t0) REVERT: G 448 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7426 (mt-10) REVERT: G 452 TRP cc_start: 0.5326 (m-90) cc_final: 0.5025 (m-10) REVERT: G 463 TRP cc_start: 0.3658 (m-10) cc_final: 0.3357 (m100) REVERT: H 119 THR cc_start: 0.7583 (t) cc_final: 0.7328 (m) REVERT: 1 24 MET cc_start: 0.6170 (mmm) cc_final: 0.5444 (ptm) REVERT: 2 83 GLU cc_start: 0.4235 (tp30) cc_final: 0.3126 (tm-30) REVERT: 2 88 MET cc_start: 0.4764 (tpt) cc_final: 0.4463 (mtm) REVERT: 2 98 MET cc_start: 0.6795 (mpp) cc_final: 0.6360 (mpp) REVERT: 2 105 LEU cc_start: 0.4955 (mm) cc_final: 0.4376 (tt) REVERT: 2 108 MET cc_start: 0.5449 (tpp) cc_final: 0.4852 (ptm) REVERT: 3 13 THR cc_start: 0.5664 (p) cc_final: 0.5405 (t) REVERT: 3 69 ARG cc_start: 0.6053 (ttt-90) cc_final: 0.5720 (ttt-90) REVERT: M 120 LYS cc_start: 0.7723 (tptp) cc_final: 0.7472 (mptt) REVERT: M 127 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.6033 (tpt-90) REVERT: E 260 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.4995 (mt-10) REVERT: E 365 PHE cc_start: 0.7114 (m-10) cc_final: 0.6686 (m-80) REVERT: E 367 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6065 (pp30) REVERT: F 260 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5374 (mt-10) REVERT: F 421 ASN cc_start: 0.6498 (m-40) cc_final: 0.6099 (t0) REVERT: I 26 LEU cc_start: 0.4592 (OUTLIER) cc_final: 0.4187 (tt) REVERT: J 36 TRP cc_start: 0.5059 (m-90) cc_final: 0.4754 (m-90) REVERT: J 64 GLN cc_start: 0.4533 (mt0) cc_final: 0.4325 (mt0) REVERT: J 127 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4447 (ttt180) REVERT: Q 24 MET cc_start: 0.5575 (mmm) cc_final: 0.5279 (tpp) REVERT: Q 80 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6753 (mt-10) REVERT: R 95 GLN cc_start: 0.5125 (mt0) cc_final: 0.4831 (mm-40) REVERT: R 98 MET cc_start: 0.6926 (ttt) cc_final: 0.6203 (mmm) REVERT: S 16 SER cc_start: 0.3936 (m) cc_final: 0.3427 (p) REVERT: S 80 GLU cc_start: 0.6008 (mp0) cc_final: 0.5747 (mp0) REVERT: T 83 GLU cc_start: 0.3290 (tp30) cc_final: 0.1946 (tm-30) REVERT: A 260 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5163 (mt-10) REVERT: A 421 ASN cc_start: 0.6636 (m-40) cc_final: 0.6183 (t0) REVERT: B 147 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7155 (ttmm) REVERT: K 22 LEU cc_start: 0.5292 (OUTLIER) cc_final: 0.4992 (mm) REVERT: K 26 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5517 (tt) REVERT: K 27 ARG cc_start: 0.4611 (ptm-80) cc_final: 0.3948 (mmm-85) REVERT: K 140 ARG cc_start: 0.4925 (mpt180) cc_final: 0.4361 (mpt180) REVERT: L 120 LYS cc_start: 0.7023 (tppt) cc_final: 0.6641 (mmtm) REVERT: U 13 THR cc_start: 0.4910 (p) cc_final: 0.4524 (t) REVERT: V 9 ASP cc_start: 0.4122 (m-30) cc_final: 0.3891 (p0) REVERT: V 13 THR cc_start: 0.3768 (m) cc_final: 0.3481 (p) REVERT: V 88 MET cc_start: 0.3703 (mtm) cc_final: 0.3468 (ptp) REVERT: V 98 MET cc_start: 0.6968 (mpp) cc_final: 0.6394 (mpp) REVERT: W 20 TYR cc_start: 0.5908 (t80) cc_final: 0.5640 (t80) REVERT: W 24 MET cc_start: 0.6312 (mmm) cc_final: 0.5547 (ppp) REVERT: X 108 MET cc_start: 0.5612 (tpp) cc_final: 0.5195 (ptt) REVERT: C 137 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6741 (mm-30) REVERT: C 260 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5364 (mt-10) REVERT: C 421 ASN cc_start: 0.6344 (OUTLIER) cc_final: 0.5746 (m-40) REVERT: D 200 PHE cc_start: 0.5574 (OUTLIER) cc_final: 0.4912 (p90) REVERT: D 365 PHE cc_start: 0.6976 (m-10) cc_final: 0.6671 (m-80) outliers start: 270 outliers final: 186 residues processed: 1045 average time/residue: 0.4795 time to fit residues: 832.1530 Evaluate side-chains 990 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 788 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 27 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 280 THR Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 1 residue 23 LEU Chi-restraints excluded: chain 1 residue 70 ILE Chi-restraints excluded: chain 3 residue 25 THR Chi-restraints excluded: chain 3 residue 30 LEU Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 193 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 222 VAL Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 267 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 365 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain T residue 14 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 6.9990 chunk 337 optimal weight: 3.9990 chunk 8 optimal weight: 9.9990 chunk 443 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 508 optimal weight: 5.9990 chunk 411 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 304 optimal weight: 8.9990 chunk 534 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 42 HIS 7 76 HIS 7 100 GLN ** 8 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 106 HIS ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN H 295 HIS H 311 HIS H 326 HIS 3 76 HIS 4 104 HIS ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 HIS F 353 ASN I 66 GLN I 106 HIS ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 183 HIS Q 76 HIS ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN S 76 HIS A 116 ASN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN W 76 HIS C 326 HIS C 357 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.7659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 50856 Z= 0.302 Angle : 0.733 14.322 68816 Z= 0.382 Chirality : 0.045 0.269 7576 Planarity : 0.006 0.058 8976 Dihedral : 6.157 37.103 6858 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.91 % Allowed : 15.73 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.05 (0.10), residues: 6128 helix: -1.87 (0.08), residues: 3232 sheet: -3.22 (0.22), residues: 360 loop : -1.84 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP K 36 HIS 0.012 0.002 HIS F 268 PHE 0.030 0.003 PHE H 219 TYR 0.031 0.002 TYR E 191 ARG 0.008 0.001 ARG F 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 867 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 98 MET cc_start: 0.4943 (mmm) cc_final: 0.4516 (mmm) REVERT: 6 88 MET cc_start: 0.3927 (ptp) cc_final: 0.3692 (ptp) REVERT: 6 94 GLN cc_start: 0.6403 (mt0) cc_final: 0.6120 (mm110) REVERT: 7 24 MET cc_start: 0.5740 (tpp) cc_final: 0.5230 (tpp) REVERT: 8 3 LEU cc_start: 0.5648 (tp) cc_final: 0.5284 (mt) REVERT: 8 98 MET cc_start: 0.6805 (tpp) cc_final: 0.6194 (mmt) REVERT: O 20 GLN cc_start: 0.5218 (mm-40) cc_final: 0.4862 (mm110) REVERT: O 24 ARG cc_start: 0.5501 (ttp80) cc_final: 0.4604 (tpt90) REVERT: O 48 TYR cc_start: 0.5996 (OUTLIER) cc_final: 0.5601 (m-10) REVERT: O 55 GLU cc_start: 0.5817 (tt0) cc_final: 0.5189 (mp0) REVERT: O 136 PHE cc_start: 0.6851 (t80) cc_final: 0.6609 (t80) REVERT: O 160 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.7090 (ptpp) REVERT: G 191 TYR cc_start: 0.6762 (t80) cc_final: 0.5760 (t80) REVERT: G 200 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.5207 (p90) REVERT: G 260 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5221 (mt-10) REVERT: G 313 ARG cc_start: 0.8039 (ptp90) cc_final: 0.7670 (ptp90) REVERT: G 391 LEU cc_start: 0.7799 (mt) cc_final: 0.7582 (mt) REVERT: G 421 ASN cc_start: 0.6753 (m110) cc_final: 0.6186 (t0) REVERT: G 448 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7417 (mt-10) REVERT: G 463 TRP cc_start: 0.3643 (m100) cc_final: 0.3150 (m100) REVERT: H 119 THR cc_start: 0.7810 (t) cc_final: 0.7536 (m) REVERT: H 120 SER cc_start: 0.7220 (OUTLIER) cc_final: 0.6771 (m) REVERT: H 200 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5260 (p90) REVERT: H 260 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5560 (mt-10) REVERT: H 401 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6895 (mt) REVERT: H 425 LEU cc_start: 0.6499 (tt) cc_final: 0.6042 (tt) REVERT: 1 23 LEU cc_start: 0.4346 (OUTLIER) cc_final: 0.4141 (tt) REVERT: 1 24 MET cc_start: 0.6216 (mmm) cc_final: 0.5336 (ptp) REVERT: 2 88 MET cc_start: 0.5040 (tpt) cc_final: 0.4747 (mtp) REVERT: 2 98 MET cc_start: 0.6769 (mpp) cc_final: 0.6413 (mpp) REVERT: 2 103 GLN cc_start: 0.3727 (mt0) cc_final: 0.3439 (mp10) REVERT: 2 105 LEU cc_start: 0.4765 (mm) cc_final: 0.4275 (tt) REVERT: 2 108 MET cc_start: 0.5178 (tpp) cc_final: 0.4628 (ptm) REVERT: 3 13 THR cc_start: 0.5588 (p) cc_final: 0.5292 (t) REVERT: 3 69 ARG cc_start: 0.6161 (ttt-90) cc_final: 0.5871 (ttt-90) REVERT: 4 94 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: 4 98 MET cc_start: 0.6519 (ttt) cc_final: 0.6309 (mmt) REVERT: 4 108 MET cc_start: 0.3575 (mmt) cc_final: 0.3161 (mmp) REVERT: M 134 LYS cc_start: 0.7492 (tptp) cc_final: 0.7139 (tttt) REVERT: E 200 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.5381 (p90) REVERT: E 260 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5265 (mt-10) REVERT: E 365 PHE cc_start: 0.7111 (m-10) cc_final: 0.6648 (m-80) REVERT: E 367 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6293 (pp30) REVERT: F 260 GLU cc_start: 0.6186 (OUTLIER) cc_final: 0.5481 (mt-10) REVERT: F 263 GLN cc_start: 0.5393 (tp-100) cc_final: 0.5103 (tp-100) REVERT: F 421 ASN cc_start: 0.6496 (m-40) cc_final: 0.6021 (t0) REVERT: I 26 LEU cc_start: 0.5173 (OUTLIER) cc_final: 0.4880 (tt) REVERT: I 48 TYR cc_start: 0.5379 (OUTLIER) cc_final: 0.5123 (m-10) REVERT: J 36 TRP cc_start: 0.5090 (m-90) cc_final: 0.4833 (m-90) REVERT: Q 24 MET cc_start: 0.5567 (mmm) cc_final: 0.5240 (tpp) REVERT: Q 80 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6875 (mt-10) REVERT: R 95 GLN cc_start: 0.5149 (mt0) cc_final: 0.4805 (mm-40) REVERT: R 98 MET cc_start: 0.6856 (ttt) cc_final: 0.6183 (mmm) REVERT: S 16 SER cc_start: 0.4209 (m) cc_final: 0.3566 (p) REVERT: S 44 PHE cc_start: 0.2899 (m-80) cc_final: 0.2598 (m-80) REVERT: A 46 GLN cc_start: 0.3799 (OUTLIER) cc_final: 0.2781 (mp10) REVERT: A 200 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.5006 (p90) REVERT: A 260 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5109 (mt-10) REVERT: A 421 ASN cc_start: 0.6515 (m-40) cc_final: 0.6031 (t0) REVERT: A 463 TRP cc_start: 0.3990 (m-10) cc_final: 0.3170 (m100) REVERT: B 147 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7336 (ttmm) REVERT: B 200 PHE cc_start: 0.5801 (OUTLIER) cc_final: 0.5217 (p90) REVERT: K 27 ARG cc_start: 0.5117 (ptm-80) cc_final: 0.4122 (mmm-85) REVERT: K 129 ILE cc_start: 0.6452 (mm) cc_final: 0.6240 (tt) REVERT: K 140 ARG cc_start: 0.5185 (mpt180) cc_final: 0.4432 (mpt180) REVERT: L 120 LYS cc_start: 0.7264 (tppt) cc_final: 0.6797 (mmtm) REVERT: U 13 THR cc_start: 0.4959 (p) cc_final: 0.4572 (t) REVERT: V 24 MET cc_start: 0.3735 (mmp) cc_final: 0.2527 (tpt) REVERT: V 98 MET cc_start: 0.6991 (mpp) cc_final: 0.6543 (mpp) REVERT: V 100 GLN cc_start: 0.3958 (mt0) cc_final: 0.3654 (mp10) REVERT: V 108 MET cc_start: 0.4401 (mmm) cc_final: 0.3911 (mtm) REVERT: W 20 TYR cc_start: 0.5940 (t80) cc_final: 0.4923 (t80) REVERT: W 24 MET cc_start: 0.6237 (mmm) cc_final: 0.4997 (ptp) REVERT: W 71 MET cc_start: 0.5068 (ppp) cc_final: 0.4756 (mmt) REVERT: X 108 MET cc_start: 0.5464 (tpp) cc_final: 0.4971 (ptt) REVERT: C 137 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6600 (mm-30) REVERT: C 260 GLU cc_start: 0.5969 (OUTLIER) cc_final: 0.5483 (mt-10) REVERT: C 421 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.5945 (t0) REVERT: D 195 ARG cc_start: 0.5745 (OUTLIER) cc_final: 0.5209 (mtt-85) REVERT: D 200 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.5206 (p90) REVERT: D 260 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5072 (mt-10) REVERT: D 313 ARG cc_start: 0.7988 (ptp90) cc_final: 0.7462 (ptp90) outliers start: 306 outliers final: 222 residues processed: 1056 average time/residue: 0.4739 time to fit residues: 831.0137 Evaluate side-chains 1036 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 248 poor density : 788 time to evaluate : 4.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 13 THR Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 160 LYS Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 106 HIS Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 166 SER Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 267 MET Chi-restraints excluded: chain G residue 268 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 1 residue 23 LEU Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain 4 residue 94 GLN Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 365 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 97 ASN Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 154 VAL Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain U residue 88 MET Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 343 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 9.9990 chunk 536 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 349 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 596 optimal weight: 3.9990 chunk 494 optimal weight: 0.2980 chunk 275 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 HIS O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN 1 100 GLN 3 76 HIS ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 GLN E 293 HIS E 326 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 ASN F 357 GLN I 106 HIS I 119 HIS J 44 GLN ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 HIS A 46 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.7999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 50856 Z= 0.261 Angle : 0.697 13.732 68816 Z= 0.362 Chirality : 0.044 0.235 7576 Planarity : 0.006 0.077 8976 Dihedral : 5.941 35.653 6855 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 5.93 % Allowed : 16.77 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.85 (0.10), residues: 6128 helix: -1.66 (0.09), residues: 3272 sheet: -3.19 (0.23), residues: 360 loop : -1.78 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP 3 40 HIS 0.020 0.001 HIS P 106 PHE 0.026 0.002 PHE J 146 TYR 0.034 0.002 TYR 3 20 ARG 0.007 0.001 ARG P 171 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 307 poor density : 831 time to evaluate : 4.712 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: 5 98 MET cc_start: 0.5063 (mmm) cc_final: 0.4615 (mmm) REVERT: 6 94 GLN cc_start: 0.6433 (mt0) cc_final: 0.6190 (mm110) REVERT: 7 24 MET cc_start: 0.5781 (tpp) cc_final: 0.5322 (tpp) REVERT: 8 3 LEU cc_start: 0.5854 (tp) cc_final: 0.5372 (mt) REVERT: 8 98 MET cc_start: 0.6716 (tpp) cc_final: 0.6145 (mmt) REVERT: O 24 ARG cc_start: 0.5548 (ttp80) cc_final: 0.4633 (tpt90) REVERT: O 48 TYR cc_start: 0.5878 (OUTLIER) cc_final: 0.5516 (m-10) REVERT: O 55 GLU cc_start: 0.5842 (tt0) cc_final: 0.5211 (mp0) REVERT: O 120 LYS cc_start: 0.7650 (tptp) cc_final: 0.7240 (mptt) REVERT: G 191 TYR cc_start: 0.6675 (t80) cc_final: 0.5700 (t80) REVERT: G 200 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.4939 (p90) REVERT: G 260 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5025 (mt-10) REVERT: H 119 THR cc_start: 0.7845 (t) cc_final: 0.7592 (m) REVERT: H 120 SER cc_start: 0.7208 (OUTLIER) cc_final: 0.6806 (m) REVERT: H 200 PHE cc_start: 0.5949 (OUTLIER) cc_final: 0.4903 (p90) REVERT: H 260 GLU cc_start: 0.6367 (OUTLIER) cc_final: 0.5656 (mt-10) REVERT: H 425 LEU cc_start: 0.6541 (tt) cc_final: 0.6117 (tt) REVERT: 1 23 LEU cc_start: 0.4366 (OUTLIER) cc_final: 0.4158 (tt) REVERT: 1 24 MET cc_start: 0.6186 (mmm) cc_final: 0.5242 (ptp) REVERT: 2 13 THR cc_start: 0.3911 (m) cc_final: 0.3647 (p) REVERT: 2 71 MET cc_start: 0.0899 (tpt) cc_final: 0.0595 (mmm) REVERT: 2 88 MET cc_start: 0.5018 (tpt) cc_final: 0.4767 (mtp) REVERT: 2 98 MET cc_start: 0.6778 (mpp) cc_final: 0.6437 (mpp) REVERT: 2 103 GLN cc_start: 0.3612 (mt0) cc_final: 0.3336 (mp10) REVERT: 2 105 LEU cc_start: 0.4514 (mm) cc_final: 0.3835 (tp) REVERT: 2 108 MET cc_start: 0.5030 (tpp) cc_final: 0.4434 (ptm) REVERT: 3 13 THR cc_start: 0.5554 (p) cc_final: 0.5242 (t) REVERT: 4 108 MET cc_start: 0.3081 (mmt) cc_final: 0.2868 (mmp) REVERT: M 134 LYS cc_start: 0.7412 (tptp) cc_final: 0.7207 (tttt) REVERT: N 55 GLU cc_start: 0.6196 (tt0) cc_final: 0.5687 (mp0) REVERT: E 200 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.5437 (p90) REVERT: E 260 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5230 (mt-10) REVERT: E 365 PHE cc_start: 0.7109 (m-10) cc_final: 0.6753 (m-80) REVERT: E 367 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6299 (pp30) REVERT: F 260 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5642 (mt-10) REVERT: F 263 GLN cc_start: 0.5389 (tp-100) cc_final: 0.5093 (tp-100) REVERT: F 421 ASN cc_start: 0.6381 (m-40) cc_final: 0.5995 (t0) REVERT: I 26 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4818 (tt) REVERT: I 48 TYR cc_start: 0.5426 (OUTLIER) cc_final: 0.5019 (m-10) REVERT: J 36 TRP cc_start: 0.5089 (m-90) cc_final: 0.4837 (m-90) REVERT: R 83 GLU cc_start: 0.3620 (tt0) cc_final: 0.3211 (tt0) REVERT: R 95 GLN cc_start: 0.5191 (mt0) cc_final: 0.4915 (mm-40) REVERT: S 16 SER cc_start: 0.4167 (m) cc_final: 0.3529 (p) REVERT: S 44 PHE cc_start: 0.3053 (m-80) cc_final: 0.2806 (m-80) REVERT: T 83 GLU cc_start: 0.3221 (tp30) cc_final: 0.2985 (tp30) REVERT: A 200 PHE cc_start: 0.5800 (OUTLIER) cc_final: 0.5108 (p90) REVERT: A 260 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5158 (mt-10) REVERT: A 421 ASN cc_start: 0.6476 (m-40) cc_final: 0.6031 (t0) REVERT: A 434 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6336 (pt0) REVERT: B 147 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7220 (ttmm) REVERT: B 200 PHE cc_start: 0.5746 (OUTLIER) cc_final: 0.5041 (p90) REVERT: B 260 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5388 (mt-10) REVERT: B 270 TYR cc_start: 0.5808 (p90) cc_final: 0.5319 (p90) REVERT: K 27 ARG cc_start: 0.5187 (ptm-80) cc_final: 0.4247 (mmm-85) REVERT: K 140 ARG cc_start: 0.5136 (mpt180) cc_final: 0.4423 (mpt180) REVERT: L 189 LYS cc_start: 0.5961 (mmpt) cc_final: 0.5722 (mmtt) REVERT: U 13 THR cc_start: 0.4970 (p) cc_final: 0.4604 (t) REVERT: V 24 MET cc_start: 0.3822 (mmp) cc_final: 0.2740 (tpt) REVERT: V 83 GLU cc_start: 0.3520 (tm-30) cc_final: 0.3045 (tp30) REVERT: V 108 MET cc_start: 0.4341 (mmm) cc_final: 0.4060 (mmp) REVERT: W 24 MET cc_start: 0.6267 (mmm) cc_final: 0.5067 (ptp) REVERT: W 44 PHE cc_start: 0.2191 (m-80) cc_final: 0.1681 (m-80) REVERT: W 66 LEU cc_start: 0.5136 (mp) cc_final: 0.4792 (tt) REVERT: W 71 MET cc_start: 0.5173 (ppp) cc_final: 0.4860 (mmt) REVERT: X 108 MET cc_start: 0.5250 (tpp) cc_final: 0.4802 (ptt) REVERT: C 137 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6559 (mm-30) REVERT: C 260 GLU cc_start: 0.5990 (OUTLIER) cc_final: 0.5491 (mt-10) REVERT: C 421 ASN cc_start: 0.6388 (OUTLIER) cc_final: 0.5767 (m-40) REVERT: D 195 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5253 (mtt-85) REVERT: D 200 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5305 (p90) REVERT: D 260 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.4954 (mt-10) REVERT: D 313 ARG cc_start: 0.7982 (ptp90) cc_final: 0.7503 (ptp90) REVERT: D 348 ASP cc_start: 0.6822 (m-30) cc_final: 0.6538 (m-30) REVERT: D 365 PHE cc_start: 0.7098 (m-10) cc_final: 0.6673 (m-80) outliers start: 307 outliers final: 238 residues processed: 1025 average time/residue: 0.5125 time to fit residues: 882.7211 Evaluate side-chains 1032 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 770 time to evaluate : 4.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 14 LEU Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 119 HIS Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 173 CYS Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 268 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 310 ILE Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 348 ASP Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain 1 residue 23 LEU Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 30 LEU Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 268 HIS Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 365 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain Q residue 44 PHE Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 98 MET Chi-restraints excluded: chain S residue 14 LEU Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 76 HIS Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 242 ASN Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 326 HIS Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 339 optimal weight: 10.0000 chunk 435 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 501 optimal weight: 4.9990 chunk 332 optimal weight: 8.9990 chunk 593 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 361 optimal weight: 30.0000 chunk 274 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 104 HIS ** 7 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 21 GLN 8 21 GLN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 106 HIS O 148 ASN P 106 HIS ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS ** 3 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 295 HIS E 326 HIS E 357 GLN ** E 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN I 106 HIS I 119 HIS ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 GLN ** A 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 HIS A 421 ASN ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN U 100 GLN W 76 HIS ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 293 HIS D 295 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.8539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 50856 Z= 0.409 Angle : 0.866 15.754 68816 Z= 0.451 Chirality : 0.050 0.248 7576 Planarity : 0.007 0.066 8976 Dihedral : 6.770 41.117 6852 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 6.65 % Allowed : 17.14 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.27 (0.10), residues: 6128 helix: -1.97 (0.08), residues: 3344 sheet: -3.37 (0.24), residues: 312 loop : -2.07 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP 3 40 HIS 0.020 0.002 HIS S 76 PHE 0.040 0.003 PHE B 219 TYR 0.033 0.003 TYR O 156 ARG 0.009 0.001 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1161 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 344 poor density : 817 time to evaluate : 5.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 37 LEU cc_start: 0.5755 (mt) cc_final: 0.5275 (mp) REVERT: 5 93 ILE cc_start: 0.2619 (mt) cc_final: 0.2086 (tp) REVERT: 8 98 MET cc_start: 0.6714 (tpp) cc_final: 0.6142 (mmt) REVERT: O 20 GLN cc_start: 0.4973 (mm-40) cc_final: 0.4710 (mm110) REVERT: O 30 GLN cc_start: 0.5295 (mm110) cc_final: 0.5095 (mm110) REVERT: O 48 TYR cc_start: 0.6113 (OUTLIER) cc_final: 0.5676 (m-10) REVERT: O 55 GLU cc_start: 0.5745 (tt0) cc_final: 0.5265 (mp0) REVERT: O 120 LYS cc_start: 0.7798 (tptp) cc_final: 0.7414 (mptt) REVERT: G 200 PHE cc_start: 0.5737 (OUTLIER) cc_final: 0.4861 (p90) REVERT: G 260 GLU cc_start: 0.6395 (OUTLIER) cc_final: 0.5669 (mt-10) REVERT: H 119 THR cc_start: 0.8033 (t) cc_final: 0.7770 (m) REVERT: H 120 SER cc_start: 0.7076 (OUTLIER) cc_final: 0.6779 (m) REVERT: H 200 PHE cc_start: 0.6022 (OUTLIER) cc_final: 0.5341 (p90) REVERT: H 260 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5898 (mt-10) REVERT: H 425 LEU cc_start: 0.6609 (tt) cc_final: 0.6288 (tt) REVERT: 1 23 LEU cc_start: 0.4433 (OUTLIER) cc_final: 0.4199 (tt) REVERT: 1 24 MET cc_start: 0.6372 (mmm) cc_final: 0.5329 (ptp) REVERT: 2 13 THR cc_start: 0.4079 (m) cc_final: 0.3757 (p) REVERT: 2 83 GLU cc_start: 0.3454 (tp30) cc_final: 0.2307 (tm-30) REVERT: 2 88 MET cc_start: 0.4900 (tpt) cc_final: 0.4517 (mtp) REVERT: 2 98 MET cc_start: 0.6901 (mpp) cc_final: 0.6552 (mpp) REVERT: 2 103 GLN cc_start: 0.4032 (mt0) cc_final: 0.3366 (mp10) REVERT: 2 108 MET cc_start: 0.4971 (tpp) cc_final: 0.4378 (ptm) REVERT: 3 13 THR cc_start: 0.5720 (p) cc_final: 0.5398 (t) REVERT: 3 69 ARG cc_start: 0.6018 (ttt-90) cc_final: 0.5655 (ttt-90) REVERT: N 55 GLU cc_start: 0.6064 (tt0) cc_final: 0.5607 (mp0) REVERT: N 120 LYS cc_start: 0.7204 (mmtm) cc_final: 0.6886 (mttp) REVERT: E 200 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5507 (p90) REVERT: E 260 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5666 (mt-10) REVERT: E 367 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6589 (pp30) REVERT: F 200 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.5221 (p90) REVERT: F 260 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5963 (mt-10) REVERT: F 421 ASN cc_start: 0.6409 (m-40) cc_final: 0.5871 (t0) REVERT: F 426 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5328 (mt-10) REVERT: I 29 LYS cc_start: 0.5643 (OUTLIER) cc_final: 0.5181 (mmmt) REVERT: J 20 GLN cc_start: 0.5306 (mm-40) cc_final: 0.4955 (mm-40) REVERT: J 36 TRP cc_start: 0.5164 (m-90) cc_final: 0.4908 (m-90) REVERT: J 48 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5965 (m-10) REVERT: J 127 ARG cc_start: 0.5577 (OUTLIER) cc_final: 0.4954 (ttt180) REVERT: Q 75 GLU cc_start: 0.6440 (tp30) cc_final: 0.5982 (tm-30) REVERT: Q 79 GLU cc_start: 0.4503 (mm-30) cc_final: 0.4235 (mm-30) REVERT: R 3 LEU cc_start: 0.5273 (tp) cc_final: 0.4655 (mt) REVERT: R 46 VAL cc_start: 0.3271 (OUTLIER) cc_final: 0.3070 (t) REVERT: R 83 GLU cc_start: 0.3761 (tt0) cc_final: 0.3393 (tt0) REVERT: R 95 GLN cc_start: 0.5257 (mt0) cc_final: 0.4904 (mm-40) REVERT: R 98 MET cc_start: 0.6781 (ttt) cc_final: 0.5965 (mmt) REVERT: R 102 ARG cc_start: 0.5453 (mtt180) cc_final: 0.5132 (ttt-90) REVERT: S 76 HIS cc_start: 0.5347 (m170) cc_final: 0.4651 (t-170) REVERT: A 200 PHE cc_start: 0.5841 (OUTLIER) cc_final: 0.5020 (p90) REVERT: A 260 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5768 (mt-10) REVERT: A 463 TRP cc_start: 0.4073 (m100) cc_final: 0.3212 (m100) REVERT: B 200 PHE cc_start: 0.5712 (OUTLIER) cc_final: 0.5084 (p90) REVERT: B 260 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5767 (mt-10) REVERT: B 351 ARG cc_start: 0.7338 (OUTLIER) cc_final: 0.6754 (mtt180) REVERT: L 146 PHE cc_start: 0.5293 (m-80) cc_final: 0.5005 (m-80) REVERT: U 13 THR cc_start: 0.4915 (p) cc_final: 0.4539 (t) REVERT: V 13 THR cc_start: 0.3844 (m) cc_final: 0.3542 (p) REVERT: V 24 MET cc_start: 0.3315 (mmp) cc_final: 0.2500 (mmm) REVERT: V 108 MET cc_start: 0.4331 (mmm) cc_final: 0.4098 (mmp) REVERT: W 24 MET cc_start: 0.6156 (mmm) cc_final: 0.4966 (ptp) REVERT: W 44 PHE cc_start: 0.2094 (m-80) cc_final: 0.1547 (m-80) REVERT: W 66 LEU cc_start: 0.4764 (mp) cc_final: 0.4542 (tt) REVERT: X 83 GLU cc_start: 0.3391 (tp30) cc_final: 0.2446 (tp30) REVERT: C 137 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6675 (mm-30) REVERT: C 200 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5350 (p90) REVERT: C 260 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5888 (mt-10) REVERT: C 421 ASN cc_start: 0.6506 (OUTLIER) cc_final: 0.5894 (m-40) REVERT: D 195 ARG cc_start: 0.5847 (OUTLIER) cc_final: 0.5367 (mtt-85) REVERT: D 200 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5115 (p90) REVERT: D 260 GLU cc_start: 0.6315 (OUTLIER) cc_final: 0.5638 (mt-10) REVERT: D 313 ARG cc_start: 0.8155 (ptp90) cc_final: 0.7695 (ptp90) REVERT: D 348 ASP cc_start: 0.6789 (m-30) cc_final: 0.6457 (m-30) outliers start: 344 outliers final: 254 residues processed: 1040 average time/residue: 0.4900 time to fit residues: 858.3042 Evaluate side-chains 1044 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 281 poor density : 763 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 21 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain 7 residue 70 ILE Chi-restraints excluded: chain 7 residue 73 VAL Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 48 TYR Chi-restraints excluded: chain O residue 154 VAL Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain P residue 186 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 268 HIS Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 385 VAL Chi-restraints excluded: chain G residue 386 TRP Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 268 HIS Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 343 THR Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain H residue 445 VAL Chi-restraints excluded: chain H residue 458 VAL Chi-restraints excluded: chain H residue 470 PHE Chi-restraints excluded: chain 1 residue 23 LEU Chi-restraints excluded: chain 1 residue 33 THR Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 65 ASP Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain M residue 154 VAL Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 154 VAL Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 326 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 397 ASP Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 429 VAL Chi-restraints excluded: chain E residue 445 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 392 VAL Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain I residue 29 LYS Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 106 HIS Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 133 ILE Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain R residue 27 LEU Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 351 ARG Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 122 ASP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain K residue 175 ILE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 GLN Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 268 HIS Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 421 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 354 optimal weight: 7.9990 chunk 178 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 377 optimal weight: 2.9990 chunk 404 optimal weight: 8.9990 chunk 293 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 466 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 21 GLN ** 6 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN H 242 ASN H 353 ASN 1 94 GLN 3 76 HIS 3 94 GLN M 66 GLN M 106 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 HIS ** J 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 GLN R 110 HIS S 76 HIS A 154 HIS ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.8662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 50856 Z= 0.209 Angle : 0.667 13.922 68816 Z= 0.345 Chirality : 0.043 0.249 7576 Planarity : 0.005 0.057 8976 Dihedral : 5.822 36.291 6849 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 5.33 % Allowed : 18.70 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.68 (0.10), residues: 6128 helix: -1.45 (0.09), residues: 3296 sheet: -3.14 (0.23), residues: 360 loop : -1.82 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP 3 40 HIS 0.012 0.001 HIS E 239 PHE 0.025 0.002 PHE M 59 TYR 0.036 0.002 TYR 3 20 ARG 0.012 0.000 ARG 6 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 276 poor density : 818 time to evaluate : 4.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 37 LEU cc_start: 0.6021 (mt) cc_final: 0.5536 (mp) REVERT: 5 93 ILE cc_start: 0.2638 (mt) cc_final: 0.2164 (tp) REVERT: 5 98 MET cc_start: 0.4835 (mmm) cc_final: 0.4314 (mmm) REVERT: 6 98 MET cc_start: 0.6631 (mmt) cc_final: 0.5903 (mpp) REVERT: 7 76 HIS cc_start: 0.6087 (t-90) cc_final: 0.5761 (t-90) REVERT: 8 3 LEU cc_start: 0.5859 (tp) cc_final: 0.5418 (mt) REVERT: 8 98 MET cc_start: 0.6583 (tpp) cc_final: 0.6026 (mpp) REVERT: O 24 ARG cc_start: 0.5633 (ttp80) cc_final: 0.4663 (tpt90) REVERT: O 55 GLU cc_start: 0.5799 (tt0) cc_final: 0.5077 (mm-30) REVERT: O 120 LYS cc_start: 0.7722 (tptp) cc_final: 0.7405 (mptt) REVERT: P 30 GLN cc_start: 0.5302 (mm110) cc_final: 0.5050 (mm110) REVERT: G 200 PHE cc_start: 0.5597 (OUTLIER) cc_final: 0.4906 (p90) REVERT: G 244 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8136 (m) REVERT: G 260 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5082 (mt-10) REVERT: H 200 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.4897 (p90) REVERT: H 260 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5629 (mt-10) REVERT: H 425 LEU cc_start: 0.6503 (tt) cc_final: 0.6134 (tt) REVERT: 1 24 MET cc_start: 0.6443 (mmm) cc_final: 0.5435 (ptp) REVERT: 2 13 THR cc_start: 0.4115 (m) cc_final: 0.3821 (p) REVERT: 2 83 GLU cc_start: 0.3213 (tp30) cc_final: 0.2151 (tm-30) REVERT: 2 88 MET cc_start: 0.4829 (tpt) cc_final: 0.4458 (mtm) REVERT: 2 98 MET cc_start: 0.6943 (mpp) cc_final: 0.6586 (mpp) REVERT: 3 13 THR cc_start: 0.5620 (p) cc_final: 0.5305 (t) REVERT: 3 40 TRP cc_start: 0.5183 (t60) cc_final: 0.4784 (t-100) REVERT: 4 108 MET cc_start: 0.2962 (mmt) cc_final: 0.2752 (mmp) REVERT: N 55 GLU cc_start: 0.5522 (tt0) cc_final: 0.5177 (mm-30) REVERT: N 120 LYS cc_start: 0.7194 (mmtm) cc_final: 0.6914 (mttp) REVERT: E 200 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5540 (p90) REVERT: E 260 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5267 (mt-10) REVERT: E 266 ILE cc_start: 0.5734 (OUTLIER) cc_final: 0.5438 (mm) REVERT: F 200 PHE cc_start: 0.5913 (OUTLIER) cc_final: 0.5357 (p90) REVERT: F 260 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.5650 (mt-10) REVERT: F 421 ASN cc_start: 0.6311 (m-40) cc_final: 0.5883 (t0) REVERT: I 48 TYR cc_start: 0.4728 (OUTLIER) cc_final: 0.3938 (m-10) REVERT: I 160 LYS cc_start: 0.7755 (pttm) cc_final: 0.6898 (pttm) REVERT: J 20 GLN cc_start: 0.5271 (mm-40) cc_final: 0.4922 (mm-40) REVERT: J 48 TYR cc_start: 0.6278 (OUTLIER) cc_final: 0.6002 (m-10) REVERT: J 127 ARG cc_start: 0.5566 (OUTLIER) cc_final: 0.4843 (ttt180) REVERT: Q 75 GLU cc_start: 0.6459 (tp30) cc_final: 0.6021 (tm-30) REVERT: Q 79 GLU cc_start: 0.4611 (mm-30) cc_final: 0.4300 (mm-30) REVERT: R 95 GLN cc_start: 0.5058 (mt0) cc_final: 0.4808 (mm-40) REVERT: R 98 MET cc_start: 0.6732 (ttt) cc_final: 0.5945 (mmt) REVERT: R 102 ARG cc_start: 0.5345 (mtt180) cc_final: 0.5085 (ttt-90) REVERT: S 76 HIS cc_start: 0.5475 (m-70) cc_final: 0.4798 (t-170) REVERT: T 3 LEU cc_start: 0.4914 (OUTLIER) cc_final: 0.4633 (tp) REVERT: T 83 GLU cc_start: 0.3299 (tp30) cc_final: 0.1421 (tm-30) REVERT: T 98 MET cc_start: 0.6602 (ttt) cc_final: 0.6200 (mmt) REVERT: A 200 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.4953 (p90) REVERT: A 260 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5141 (mt-10) REVERT: A 463 TRP cc_start: 0.3927 (m100) cc_final: 0.3120 (m100) REVERT: B 88 ILE cc_start: 0.7454 (mm) cc_final: 0.7191 (mm) REVERT: B 147 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.7036 (ttmm) REVERT: B 200 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5029 (p90) REVERT: B 260 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5486 (mt-10) REVERT: B 270 TYR cc_start: 0.5829 (p90) cc_final: 0.5435 (p90) REVERT: B 351 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6538 (mtt180) REVERT: K 140 ARG cc_start: 0.4995 (mpt180) cc_final: 0.4479 (mpt180) REVERT: L 128 GLU cc_start: 0.6705 (mm-30) cc_final: 0.6497 (mp0) REVERT: U 13 THR cc_start: 0.4850 (p) cc_final: 0.4461 (t) REVERT: V 13 THR cc_start: 0.4014 (m) cc_final: 0.3677 (p) REVERT: V 24 MET cc_start: 0.3981 (mmp) cc_final: 0.3189 (mmm) REVERT: V 108 MET cc_start: 0.4284 (mmm) cc_final: 0.3810 (mtm) REVERT: W 24 MET cc_start: 0.6385 (mmm) cc_final: 0.5202 (ptp) REVERT: W 66 LEU cc_start: 0.4825 (mp) cc_final: 0.4573 (tt) REVERT: X 83 GLU cc_start: 0.3164 (tp30) cc_final: 0.2498 (tp30) REVERT: C 118 LEU cc_start: 0.7618 (mt) cc_final: 0.7358 (mt) REVERT: C 200 PHE cc_start: 0.5733 (OUTLIER) cc_final: 0.5223 (p90) REVERT: C 260 GLU cc_start: 0.6059 (OUTLIER) cc_final: 0.5471 (mt-10) REVERT: D 200 PHE cc_start: 0.5744 (OUTLIER) cc_final: 0.5193 (p90) REVERT: D 260 GLU cc_start: 0.6135 (OUTLIER) cc_final: 0.5300 (mt-10) REVERT: D 313 ARG cc_start: 0.7984 (ptp90) cc_final: 0.7519 (ptp90) outliers start: 276 outliers final: 190 residues processed: 999 average time/residue: 0.4709 time to fit residues: 784.4902 Evaluate side-chains 970 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 756 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 5 residue 91 SER Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 21 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 65 ASP Chi-restraints excluded: chain O residue 179 LEU Chi-restraints excluded: chain P residue 36 TRP Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 244 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 265 ILE Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 96 ASN Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 287 ASP Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 392 VAL Chi-restraints excluded: chain H residue 419 THR Chi-restraints excluded: chain H residue 428 CYS Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 34 VAL Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 397 ASP Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 175 ILE Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 147 LYS Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 268 HIS Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 114 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 147 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 351 ARG Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 343 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 397 ASP Chi-restraints excluded: chain D residue 419 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 445 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 20.0000 chunk 568 optimal weight: 4.9990 chunk 518 optimal weight: 9.9990 chunk 553 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 241 optimal weight: 0.7980 chunk 434 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 499 optimal weight: 0.9990 chunk 523 optimal weight: 7.9990 chunk 551 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 21 GLN 7 100 GLN O 66 GLN O 148 ASN ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN 3 76 HIS M 66 GLN ** M 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 183 HIS ** E 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 HIS F 288 ASN ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 GLN I 106 HIS J 106 HIS Q 76 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN ** C 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.8793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 50856 Z= 0.177 Angle : 0.624 12.045 68816 Z= 0.322 Chirality : 0.042 0.251 7576 Planarity : 0.005 0.058 8976 Dihedral : 5.366 40.413 6849 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.86 % Allowed : 20.48 % Favored : 75.66 % 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: -2.29 (0.10), residues: 6128 helix: -1.09 (0.09), residues: 3352 sheet: -2.49 (0.29), residues: 232 loop : -1.88 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP P 36 HIS 0.018 0.001 HIS 3 76 PHE 0.025 0.002 PHE M 59 TYR 0.027 0.001 TYR O 156 ARG 0.010 0.000 ARG J 140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 836 time to evaluate : 4.140 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: 5 37 LEU cc_start: 0.5952 (mt) cc_final: 0.5495 (mp) REVERT: 5 93 ILE cc_start: 0.2645 (mt) cc_final: 0.2197 (tp) REVERT: 5 98 MET cc_start: 0.5036 (mmm) cc_final: 0.4826 (mmm) REVERT: 8 3 LEU cc_start: 0.6015 (tp) cc_final: 0.5449 (mt) REVERT: 8 98 MET cc_start: 0.6554 (tpp) cc_final: 0.6032 (mpp) REVERT: O 24 ARG cc_start: 0.5752 (ttp80) cc_final: 0.4649 (tpt90) REVERT: O 55 GLU cc_start: 0.5702 (tt0) cc_final: 0.5031 (mm-30) REVERT: O 120 LYS cc_start: 0.7648 (tptp) cc_final: 0.7288 (mptt) REVERT: P 30 GLN cc_start: 0.4898 (mm110) cc_final: 0.4687 (mm110) REVERT: G 191 TYR cc_start: 0.6697 (t80) cc_final: 0.5639 (t80) REVERT: G 200 PHE cc_start: 0.5653 (OUTLIER) cc_final: 0.5088 (p90) REVERT: G 244 THR cc_start: 0.8434 (t) cc_final: 0.8192 (m) REVERT: G 260 GLU cc_start: 0.6208 (OUTLIER) cc_final: 0.4752 (mt-10) REVERT: G 367 GLN cc_start: 0.6977 (pp30) cc_final: 0.6680 (pp30) REVERT: H 200 PHE cc_start: 0.5888 (OUTLIER) cc_final: 0.5109 (p90) REVERT: H 260 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5474 (mt-10) REVERT: H 425 LEU cc_start: 0.6500 (tt) cc_final: 0.6156 (tt) REVERT: 1 24 MET cc_start: 0.6484 (mmm) cc_final: 0.5382 (ptp) REVERT: 2 13 THR cc_start: 0.4115 (m) cc_final: 0.3829 (p) REVERT: 2 83 GLU cc_start: 0.3259 (tp30) cc_final: 0.2181 (tm-30) REVERT: 2 88 MET cc_start: 0.4922 (tpt) cc_final: 0.4471 (mtm) REVERT: 2 98 MET cc_start: 0.6779 (mpp) cc_final: 0.6403 (mpp) REVERT: 3 13 THR cc_start: 0.5692 (p) cc_final: 0.5391 (t) REVERT: 3 24 MET cc_start: 0.5867 (tpp) cc_final: 0.5476 (tpp) REVERT: 3 40 TRP cc_start: 0.5478 (t60) cc_final: 0.5066 (t-100) REVERT: 3 71 MET cc_start: 0.4360 (mtt) cc_final: 0.3770 (mtt) REVERT: 3 102 ARG cc_start: 0.4723 (ttp-110) cc_final: 0.4448 (ptm-80) REVERT: 4 100 GLN cc_start: 0.3686 (mt0) cc_final: 0.3477 (mp10) REVERT: N 55 GLU cc_start: 0.5406 (tt0) cc_final: 0.5082 (mm-30) REVERT: E 200 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5292 (p90) REVERT: E 260 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.4853 (mt-10) REVERT: F 200 PHE cc_start: 0.5849 (OUTLIER) cc_final: 0.5231 (p90) REVERT: F 260 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5493 (mt-10) REVERT: F 452 TRP cc_start: 0.5004 (m-90) cc_final: 0.4538 (m-90) REVERT: I 30 GLN cc_start: 0.5213 (mm110) cc_final: 0.5010 (tp40) REVERT: I 48 TYR cc_start: 0.4584 (OUTLIER) cc_final: 0.3833 (m-80) REVERT: I 189 LYS cc_start: 0.5694 (mmmt) cc_final: 0.4997 (mmtt) REVERT: J 127 ARG cc_start: 0.5690 (OUTLIER) cc_final: 0.4947 (ttt180) REVERT: J 140 ARG cc_start: 0.4868 (mmt-90) cc_final: 0.4602 (mmp80) REVERT: Q 75 GLU cc_start: 0.6407 (tp30) cc_final: 0.5899 (tm-30) REVERT: Q 79 GLU cc_start: 0.4831 (mm-30) cc_final: 0.4544 (mm-30) REVERT: R 83 GLU cc_start: 0.4402 (tp30) cc_final: 0.2798 (mm-30) REVERT: R 95 GLN cc_start: 0.5398 (mt0) cc_final: 0.5071 (mm-40) REVERT: R 98 MET cc_start: 0.6660 (ttt) cc_final: 0.5864 (mmt) REVERT: R 102 ARG cc_start: 0.5375 (mtt180) cc_final: 0.5040 (ttt90) REVERT: S 16 SER cc_start: 0.4703 (m) cc_final: 0.4230 (p) REVERT: S 21 GLN cc_start: 0.4771 (mm-40) cc_final: 0.4500 (mm-40) REVERT: S 66 LEU cc_start: 0.5593 (mp) cc_final: 0.5091 (tt) REVERT: S 76 HIS cc_start: 0.5345 (m-70) cc_final: 0.4854 (t-170) REVERT: T 3 LEU cc_start: 0.4810 (OUTLIER) cc_final: 0.4353 (tp) REVERT: T 83 GLU cc_start: 0.3122 (tp30) cc_final: 0.1483 (tm-30) REVERT: T 108 MET cc_start: 0.3443 (mmp) cc_final: 0.3170 (mmp) REVERT: A 200 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5125 (p90) REVERT: B 147 LYS cc_start: 0.6830 (ptmt) cc_final: 0.6610 (ptmm) REVERT: B 200 PHE cc_start: 0.5691 (OUTLIER) cc_final: 0.5093 (p90) REVERT: B 260 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5372 (mt-10) REVERT: B 270 TYR cc_start: 0.5672 (p90) cc_final: 0.5373 (p90) REVERT: B 313 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7431 (ptp90) REVERT: K 140 ARG cc_start: 0.4903 (mpt180) cc_final: 0.4440 (mpt180) REVERT: L 42 SER cc_start: 0.5099 (t) cc_final: 0.4642 (m) REVERT: L 128 GLU cc_start: 0.6570 (mm-30) cc_final: 0.6288 (mp0) REVERT: U 13 THR cc_start: 0.4802 (p) cc_final: 0.4491 (t) REVERT: V 13 THR cc_start: 0.4168 (m) cc_final: 0.3866 (p) REVERT: V 24 MET cc_start: 0.4132 (mmp) cc_final: 0.3469 (mmm) REVERT: V 108 MET cc_start: 0.4298 (mmm) cc_final: 0.3822 (mtm) REVERT: W 24 MET cc_start: 0.6367 (mmm) cc_final: 0.5212 (ptp) REVERT: W 66 LEU cc_start: 0.4944 (mp) cc_final: 0.4743 (tt) REVERT: X 83 GLU cc_start: 0.3067 (tp30) cc_final: 0.1371 (tm-30) REVERT: X 108 MET cc_start: 0.4905 (tpp) cc_final: 0.4290 (ptt) REVERT: C 118 LEU cc_start: 0.7667 (mt) cc_final: 0.7410 (mt) REVERT: C 200 PHE cc_start: 0.5566 (OUTLIER) cc_final: 0.4901 (p90) REVERT: C 260 GLU cc_start: 0.5961 (OUTLIER) cc_final: 0.5502 (mt-10) REVERT: D 174 THR cc_start: 0.6843 (t) cc_final: 0.6615 (m) REVERT: D 195 ARG cc_start: 0.5698 (OUTLIER) cc_final: 0.5164 (mtt-85) REVERT: D 200 PHE cc_start: 0.5661 (OUTLIER) cc_final: 0.5179 (p90) REVERT: D 313 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7392 (ptp90) REVERT: D 352 GLU cc_start: 0.5462 (mp0) cc_final: 0.5032 (tp30) outliers start: 200 outliers final: 149 residues processed: 965 average time/residue: 0.4772 time to fit residues: 767.7479 Evaluate side-chains 921 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 754 time to evaluate : 4.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 21 GLN Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 48 TYR Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 386 TRP Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 346 PHE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 30.0000 chunk 585 optimal weight: 10.0000 chunk 357 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 chunk 613 optimal weight: 10.0000 chunk 564 optimal weight: 7.9990 chunk 488 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 377 optimal weight: 2.9990 chunk 299 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 104 HIS 7 76 HIS O 66 GLN P 106 HIS P 119 HIS ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 76 HIS 3 94 GLN 4 104 HIS ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 HIS J 106 HIS Q 76 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 50856 Z= 0.220 Angle : 0.658 13.701 68816 Z= 0.341 Chirality : 0.044 0.252 7576 Planarity : 0.005 0.055 8976 Dihedral : 5.520 40.929 6849 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.86 % Allowed : 20.69 % Favored : 75.44 % 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: -2.26 (0.10), residues: 6128 helix: -1.05 (0.09), residues: 3352 sheet: -2.76 (0.24), residues: 360 loop : -1.77 (0.12), residues: 2416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 36 HIS 0.011 0.001 HIS F 387 PHE 0.029 0.002 PHE M 59 TYR 0.028 0.002 TYR I 156 ARG 0.010 0.000 ARG J 140 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12256 Ramachandran restraints generated. 6128 Oldfield, 0 Emsley, 6128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 774 time to evaluate : 4.103 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: 5 37 LEU cc_start: 0.5970 (mt) cc_final: 0.5383 (mp) REVERT: 5 93 ILE cc_start: 0.2763 (mt) cc_final: 0.2293 (tp) REVERT: 5 98 MET cc_start: 0.4898 (mmm) cc_final: 0.4671 (mmm) REVERT: 8 3 LEU cc_start: 0.6039 (tp) cc_final: 0.5472 (mt) REVERT: 8 98 MET cc_start: 0.6556 (tpp) cc_final: 0.6027 (mmt) REVERT: O 24 ARG cc_start: 0.5775 (ttp80) cc_final: 0.4640 (tpt90) REVERT: O 55 GLU cc_start: 0.5772 (tt0) cc_final: 0.5075 (mm-30) REVERT: O 120 LYS cc_start: 0.7678 (tptp) cc_final: 0.7282 (mptt) REVERT: P 30 GLN cc_start: 0.4875 (mm110) cc_final: 0.4642 (mm110) REVERT: G 191 TYR cc_start: 0.6672 (t80) cc_final: 0.5638 (t80) REVERT: G 200 PHE cc_start: 0.5657 (OUTLIER) cc_final: 0.5079 (p90) REVERT: G 260 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.4922 (mt-10) REVERT: H 200 PHE cc_start: 0.5844 (OUTLIER) cc_final: 0.5148 (p90) REVERT: H 260 GLU cc_start: 0.6338 (OUTLIER) cc_final: 0.5219 (mt-10) REVERT: H 425 LEU cc_start: 0.6503 (tt) cc_final: 0.6146 (tt) REVERT: 1 24 MET cc_start: 0.6438 (mmm) cc_final: 0.4994 (ptp) REVERT: 2 13 THR cc_start: 0.4128 (m) cc_final: 0.3806 (p) REVERT: 2 83 GLU cc_start: 0.3671 (tp30) cc_final: 0.2334 (tm-30) REVERT: 2 88 MET cc_start: 0.5096 (tpt) cc_final: 0.4510 (mtm) REVERT: 2 98 MET cc_start: 0.6796 (mpp) cc_final: 0.6442 (mpp) REVERT: 3 13 THR cc_start: 0.5702 (p) cc_final: 0.5401 (t) REVERT: 3 24 MET cc_start: 0.5890 (tpp) cc_final: 0.5389 (tpp) REVERT: 3 40 TRP cc_start: 0.5443 (t60) cc_final: 0.5016 (t-100) REVERT: 3 71 MET cc_start: 0.4225 (mtt) cc_final: 0.3763 (mtt) REVERT: 4 100 GLN cc_start: 0.3643 (mt0) cc_final: 0.3396 (mp10) REVERT: N 55 GLU cc_start: 0.5393 (tt0) cc_final: 0.5086 (mm-30) REVERT: E 200 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5420 (p90) REVERT: E 260 GLU cc_start: 0.6319 (OUTLIER) cc_final: 0.5318 (mt-10) REVERT: F 200 PHE cc_start: 0.5783 (OUTLIER) cc_final: 0.5284 (p90) REVERT: F 260 GLU cc_start: 0.6247 (OUTLIER) cc_final: 0.5339 (mt-10) REVERT: F 421 ASN cc_start: 0.6302 (OUTLIER) cc_final: 0.5883 (t0) REVERT: F 426 GLU cc_start: 0.5568 (mt-10) cc_final: 0.5211 (mt-10) REVERT: F 452 TRP cc_start: 0.5029 (m-90) cc_final: 0.4618 (m-90) REVERT: I 48 TYR cc_start: 0.4673 (OUTLIER) cc_final: 0.3977 (m-80) REVERT: I 189 LYS cc_start: 0.5658 (mmmt) cc_final: 0.4994 (mmtt) REVERT: J 127 ARG cc_start: 0.5670 (OUTLIER) cc_final: 0.4930 (ttt180) REVERT: J 140 ARG cc_start: 0.4826 (mmt-90) cc_final: 0.4590 (mmp80) REVERT: Q 13 THR cc_start: 0.4811 (p) cc_final: 0.4391 (t) REVERT: Q 69 ARG cc_start: 0.4809 (ttt180) cc_final: 0.4456 (ttt-90) REVERT: R 95 GLN cc_start: 0.5323 (mt0) cc_final: 0.4989 (mm-40) REVERT: R 98 MET cc_start: 0.6774 (ttt) cc_final: 0.5970 (mmt) REVERT: R 102 ARG cc_start: 0.5395 (mtt180) cc_final: 0.5061 (ttt90) REVERT: S 76 HIS cc_start: 0.5395 (m-70) cc_final: 0.4828 (t-170) REVERT: T 3 LEU cc_start: 0.5061 (OUTLIER) cc_final: 0.4570 (tp) REVERT: T 83 GLU cc_start: 0.3396 (tp30) cc_final: 0.1850 (tm-30) REVERT: T 98 MET cc_start: 0.6815 (ttt) cc_final: 0.6319 (tpp) REVERT: T 108 MET cc_start: 0.3603 (mmp) cc_final: 0.3363 (mmp) REVERT: A 200 PHE cc_start: 0.5568 (OUTLIER) cc_final: 0.5022 (p90) REVERT: A 313 ARG cc_start: 0.7789 (ptp90) cc_final: 0.7472 (ptp90) REVERT: B 200 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.5112 (p90) REVERT: B 260 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5604 (mt-10) REVERT: B 270 TYR cc_start: 0.5799 (p90) cc_final: 0.5355 (p90) REVERT: B 313 ARG cc_start: 0.7823 (ptp90) cc_final: 0.7415 (ptp90) REVERT: K 140 ARG cc_start: 0.4840 (mpt180) cc_final: 0.4348 (mpt180) REVERT: V 9 ASP cc_start: 0.3994 (p0) cc_final: 0.3656 (p0) REVERT: V 13 THR cc_start: 0.4053 (m) cc_final: 0.3741 (p) REVERT: V 24 MET cc_start: 0.4120 (mmp) cc_final: 0.3480 (mmm) REVERT: V 108 MET cc_start: 0.4272 (mmm) cc_final: 0.3769 (mtm) REVERT: W 24 MET cc_start: 0.6357 (mmm) cc_final: 0.5153 (ptp) REVERT: X 83 GLU cc_start: 0.3075 (tp30) cc_final: 0.2639 (tp30) REVERT: X 102 ARG cc_start: 0.4390 (mmt180) cc_final: 0.3679 (ttt180) REVERT: C 200 PHE cc_start: 0.5734 (OUTLIER) cc_final: 0.5041 (p90) REVERT: C 260 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5495 (mt-10) REVERT: D 174 THR cc_start: 0.6806 (t) cc_final: 0.6569 (m) REVERT: D 195 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5163 (mtt-85) REVERT: D 200 PHE cc_start: 0.5711 (OUTLIER) cc_final: 0.5187 (p90) REVERT: D 313 ARG cc_start: 0.7952 (ptp90) cc_final: 0.7504 (ptp90) REVERT: D 365 PHE cc_start: 0.7010 (m-10) cc_final: 0.6725 (m-80) outliers start: 200 outliers final: 160 residues processed: 907 average time/residue: 0.4669 time to fit residues: 709.9348 Evaluate side-chains 925 residues out of total 5192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 746 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 LEU Chi-restraints excluded: chain 5 residue 16 SER Chi-restraints excluded: chain 5 residue 23 LEU Chi-restraints excluded: chain 6 residue 46 VAL Chi-restraints excluded: chain 7 residue 30 LEU Chi-restraints excluded: chain 7 residue 56 VAL Chi-restraints excluded: chain 7 residue 93 ILE Chi-restraints excluded: chain P residue 48 TYR Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 128 GLU Chi-restraints excluded: chain P residue 141 ILE Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 ASN Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 200 PHE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 233 THR Chi-restraints excluded: chain G residue 236 ILE Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 279 THR Chi-restraints excluded: chain G residue 280 THR Chi-restraints excluded: chain G residue 346 PHE Chi-restraints excluded: chain G residue 366 THR Chi-restraints excluded: chain G residue 419 THR Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 200 PHE Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 260 GLU Chi-restraints excluded: chain H residue 265 ILE Chi-restraints excluded: chain H residue 267 MET Chi-restraints excluded: chain H residue 279 THR Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 342 ILE Chi-restraints excluded: chain H residue 346 PHE Chi-restraints excluded: chain H residue 366 THR Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain 2 residue 9 ASP Chi-restraints excluded: chain 3 residue 73 VAL Chi-restraints excluded: chain 3 residue 76 HIS Chi-restraints excluded: chain 4 residue 91 SER Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain N residue 25 LYS Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 141 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 43 VAL Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 PHE Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 233 THR Chi-restraints excluded: chain E residue 260 GLU Chi-restraints excluded: chain E residue 266 ILE Chi-restraints excluded: chain E residue 270 TYR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 280 THR Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 387 HIS Chi-restraints excluded: chain E residue 419 THR Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 434 GLU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 107 ASP Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 200 PHE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 260 GLU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 268 HIS Chi-restraints excluded: chain F residue 270 TYR Chi-restraints excluded: chain F residue 279 THR Chi-restraints excluded: chain F residue 287 ASP Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain F residue 419 THR Chi-restraints excluded: chain F residue 421 ASN Chi-restraints excluded: chain F residue 428 CYS Chi-restraints excluded: chain I residue 48 TYR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 30 GLN Chi-restraints excluded: chain J residue 48 TYR Chi-restraints excluded: chain J residue 127 ARG Chi-restraints excluded: chain J residue 183 HIS Chi-restraints excluded: chain Q residue 76 HIS Chi-restraints excluded: chain S residue 93 ILE Chi-restraints excluded: chain T residue 3 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 96 ASN Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 200 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 419 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 263 GLN Chi-restraints excluded: chain B residue 268 HIS Chi-restraints excluded: chain B residue 280 THR Chi-restraints excluded: chain B residue 346 PHE Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain K residue 36 TRP Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain L residue 25 LYS Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 48 TYR Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 175 ILE Chi-restraints excluded: chain U residue 39 LEU Chi-restraints excluded: chain V residue 98 MET Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain W residue 76 HIS Chi-restraints excluded: chain X residue 13 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 200 PHE Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain D residue 29 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 195 ARG Chi-restraints excluded: chain D residue 200 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 233 THR Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 267 MET Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 287 ASP Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 425 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 8.9990 chunk 520 optimal weight: 9.9990 chunk 149 optimal weight: 0.9990 chunk 450 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 135 optimal weight: 0.7980 chunk 489 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 chunk 502 optimal weight: 20.0000 chunk 61 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 104 HIS P 106 HIS P 119 HIS ** G 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 242 ASN ** 1 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 104 HIS ** M 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 HIS J 106 HIS Q 76 HIS ** S 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 357 GLN ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 HIS ** C 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 353 ASN ** D 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.243997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.217271 restraints weight = 78295.065| |-----------------------------------------------------------------------------| r_work (start): 0.4634 rms_B_bonded: 1.62 r_work: 0.4536 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.4451 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.4451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.8958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 50856 Z= 0.177 Angle : 0.626 12.911 68816 Z= 0.323 Chirality : 0.043 0.265 7576 Planarity : 0.005 0.059 8976 Dihedral : 5.248 46.806 6849 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.61 % Allowed : 21.12 % Favored : 75.27 % 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: -1.86 (0.11), residues: 6128 helix: -0.75 (0.09), residues: 3256 sheet: -2.07 (0.30), residues: 232 loop : -1.67 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP P 36 HIS 0.020 0.001 HIS W 76 PHE 0.020 0.002 PHE D 109 TYR 0.029 0.001 TYR D 191 ARG 0.009 0.000 ARG J 140 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13080.07 seconds wall clock time: 227 minutes 57.18 seconds (13677.18 seconds total)