Starting phenix.real_space_refine on Thu Sep 26 02:55:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dr6_30824/09_2024/7dr6_30824.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.012 sd= 0.108 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 346 5.16 5 C 38016 2.51 5 N 10246 2.21 5 O 11349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 59957 Number of models: 1 Model: "" Number of chains: 35 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1850 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 8, 'TRANS': 227} Chain: "M" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1763 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "N" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "O" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "P" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "Q" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "R" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "A" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1684 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1720 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Chain: "C" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 11, 'TRANS': 194} Chain breaks: 1 Chain: "D" Number of atoms: 1678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1678 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 8, 'TRANS': 198} Chain breaks: 1 Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1685 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain breaks: 1 Chain: "F" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1695 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain breaks: 1 Chain: "G" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 9, 'TRANS': 195} Chain breaks: 1 Chain: "a" Number of atoms: 1824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1824 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 7, 'TRANS': 224} Chain: "b" Number of atoms: 1790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1790 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain: "c" Number of atoms: 1846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1846 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Chain: "d" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1879 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 5, 'TRANS': 234} Chain: "e" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1856 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "f" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1793 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain: "g" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1936 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 5, 'TRANS': 240} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "I" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1593 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain: "J" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "K" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1685 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "S" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1594 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain: "T" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1584 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "U" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1645 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "V" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1682 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Chain: "W" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "X" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "Y" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Chain: "Z" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1500 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain: "1" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1611 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "2" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1561 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 3, 'TRANS': 197} Time building chain proxies: 29.82, per 1000 atoms: 0.50 Number of scatterers: 59957 At special positions: 0 Unit cell: (239.876, 137.072, 216.152, 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 346 16.00 O 11349 8.00 N 10246 7.00 C 38016 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: 11.61 Conformation dependent library (CDL) restraints added in 6.0 seconds 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14226 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 72 sheets defined 46.1% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 83 through 105 removed outlier: 3.625A pdb=" N SER L 87 " --> pdb=" O MET L 83 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER L 89 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN L 90 " --> pdb=" O ASP L 86 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL L 91 " --> pdb=" O SER L 87 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN L 100 " --> pdb=" O TYR L 96 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS L 102 " --> pdb=" O ALA L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 128 removed outlier: 3.765A pdb=" N TYR L 125 " --> pdb=" O ILE L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 185 removed outlier: 3.707A pdb=" N LYS L 185 " --> pdb=" O LYS L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 207 removed outlier: 3.686A pdb=" N LEU L 202 " --> pdb=" O ALA L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 213 No H-bonds generated for 'chain 'L' and resid 211 through 213' Processing helix chain 'L' and resid 231 through 240 Processing helix chain 'M' and resid 19 through 31 Processing helix chain 'M' and resid 79 through 102 removed outlier: 3.707A pdb=" N TYR M 83 " --> pdb=" O MET M 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG M 84 " --> pdb=" O GLY M 80 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL M 85 " --> pdb=" O PRO M 81 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU M 86 " --> pdb=" O ASP M 82 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS M 88 " --> pdb=" O ARG M 84 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 122 removed outlier: 3.524A pdb=" N ARG M 113 " --> pdb=" O GLN M 109 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET M 118 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 166 through 175 Processing helix chain 'M' and resid 183 through 199 removed outlier: 4.388A pdb=" N GLU M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER M 198 " --> pdb=" O THR M 194 " (cutoff:3.500A) Processing helix chain 'M' and resid 222 through 230 removed outlier: 3.556A pdb=" N ASP M 228 " --> pdb=" O THR M 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 30 removed outlier: 3.764A pdb=" N GLU N 26 " --> pdb=" O GLU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 102 removed outlier: 3.571A pdb=" N ALA N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASN N 84 " --> pdb=" O THR N 80 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN N 100 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 124 removed outlier: 3.563A pdb=" N LEU N 114 " --> pdb=" O LEU N 110 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP N 116 " --> pdb=" O THR N 112 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE N 117 " --> pdb=" O ALA N 113 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR N 122 " --> pdb=" O LYS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 179 removed outlier: 3.530A pdb=" N GLN N 177 " --> pdb=" O SER N 173 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 201 removed outlier: 4.098A pdb=" N ALA N 191 " --> pdb=" O LYS N 187 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA N 193 " --> pdb=" O ALA N 189 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE N 194 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 244 removed outlier: 3.677A pdb=" N HIS N 240 " --> pdb=" O LEU N 236 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU N 244 " --> pdb=" O HIS N 240 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 29 Processing helix chain 'O' and resid 56 through 60 Processing helix chain 'O' and resid 76 through 98 removed outlier: 3.837A pdb=" N ALA O 80 " --> pdb=" O LEU O 76 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL O 83 " --> pdb=" O ASP O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 121 removed outlier: 3.574A pdb=" N TYR O 110 " --> pdb=" O TYR O 106 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS O 115 " --> pdb=" O ILE O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 138 through 140 No H-bonds generated for 'chain 'O' and resid 138 through 140' Processing helix chain 'O' and resid 164 through 176 Processing helix chain 'O' and resid 183 through 195 Processing helix chain 'O' and resid 202 through 206 removed outlier: 3.638A pdb=" N ASN O 205 " --> pdb=" O GLY O 202 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE O 206 " --> pdb=" O GLY O 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 202 through 206' Processing helix chain 'O' and resid 221 through 230 removed outlier: 3.673A pdb=" N TYR O 228 " --> pdb=" O GLU O 224 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 31 Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 81 through 104 removed outlier: 3.886A pdb=" N ALA P 85 " --> pdb=" O LEU P 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS P 91 " --> pdb=" O THR P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 122 Processing helix chain 'P' and resid 173 through 185 removed outlier: 3.939A pdb=" N SER P 179 " --> pdb=" O GLU P 175 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU P 183 " --> pdb=" O SER P 179 " (cutoff:3.500A) Processing helix chain 'P' and resid 190 through 206 removed outlier: 3.656A pdb=" N SER P 197 " --> pdb=" O GLU P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 230 through 240 removed outlier: 3.706A pdb=" N LYS P 239 " --> pdb=" O GLU P 235 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.699A pdb=" N VAL Q 29 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS Q 30 " --> pdb=" O MET Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 99 removed outlier: 4.128A pdb=" N LEU Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU Q 84 " --> pdb=" O ASP Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 122 Proline residue: Q 119 - end of helix removed outlier: 3.950A pdb=" N ARG Q 122 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 175 Processing helix chain 'Q' and resid 175 through 182 removed outlier: 3.896A pdb=" N MET Q 180 " --> pdb=" O MET Q 176 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU Q 181 " --> pdb=" O SER Q 177 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 196 removed outlier: 3.563A pdb=" N LEU Q 195 " --> pdb=" O GLY Q 191 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 199 No H-bonds generated for 'chain 'Q' and resid 197 through 199' Processing helix chain 'Q' and resid 228 through 234 removed outlier: 3.780A pdb=" N PHE Q 232 " --> pdb=" O ASP Q 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 32 Processing helix chain 'R' and resid 81 through 104 Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.629A pdb=" N TYR R 123 " --> pdb=" O TYR R 119 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR R 124 " --> pdb=" O VAL R 120 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 179 Processing helix chain 'R' and resid 186 through 202 removed outlier: 4.403A pdb=" N LYS R 192 " --> pdb=" O ARG R 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU R 193 " --> pdb=" O ASP R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 245 removed outlier: 3.558A pdb=" N GLU R 242 " --> pdb=" O LYS R 238 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER R 243 " --> pdb=" O TYR R 239 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU R 244 " --> pdb=" O ALA R 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 34 removed outlier: 3.699A pdb=" N ARG A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 20 " --> pdb=" O GLN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.850A pdb=" N ILE A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 128 removed outlier: 3.707A pdb=" N ALA A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Proline residue: A 109 - end of helix removed outlier: 3.509A pdb=" N LEU A 128 " --> pdb=" O TRP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 181 removed outlier: 3.800A pdb=" N GLN A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE A 168 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 229 removed outlier: 3.821A pdb=" N ALA A 189 " --> pdb=" O MET A 185 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N GLU A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LYS A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.769A pdb=" N VAL B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.563A pdb=" N SER B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.683A pdb=" N LEU B 57 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 138 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 147 through 191 removed outlier: 3.544A pdb=" N SER B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B 179 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 239 removed outlier: 4.376A pdb=" N ARG B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN B 233 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N GLU B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 236 " --> pdb=" O LYS B 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 31 Processing helix chain 'C' and resid 31 through 45 Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 107 through 137 removed outlier: 3.684A pdb=" N ARG C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Proline residue: C 119 - end of helix Processing helix chain 'C' and resid 150 through 191 removed outlier: 3.761A pdb=" N GLU C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 178 " --> pdb=" O ILE C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 239 removed outlier: 3.900A pdb=" N GLN C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LYS C 236 " --> pdb=" O LYS C 232 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 16 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 22 through 34 removed outlier: 3.675A pdb=" N PHE D 31 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 33 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 48 removed outlier: 3.511A pdb=" N ILE D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 53 Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 98 through 127 removed outlier: 3.553A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Proline residue: D 109 - end of helix removed outlier: 3.651A pdb=" N LYS D 115 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 180 removed outlier: 4.409A pdb=" N PHE D 168 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER D 169 " --> pdb=" O SER D 165 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 4.088A pdb=" N ARG D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 229 removed outlier: 4.167A pdb=" N ARG D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 31 removed outlier: 3.808A pdb=" N VAL E 14 " --> pdb=" O ALA E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.514A pdb=" N SER E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 138 Proline residue: E 119 - end of helix Processing helix chain 'E' and resid 147 through 191 removed outlier: 3.724A pdb=" N MET E 160 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N THR E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N HIS E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 233 removed outlier: 3.527A pdb=" N TYR E 209 " --> pdb=" O ASP E 205 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 34 removed outlier: 3.569A pdb=" N LYS F 15 " --> pdb=" O GLY F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 48 removed outlier: 3.671A pdb=" N GLN F 38 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 41 " --> pdb=" O PRO F 37 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 128 removed outlier: 3.624A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) Proline residue: F 109 - end of helix removed outlier: 3.561A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 181 removed outlier: 3.569A pdb=" N GLN F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE F 168 " --> pdb=" O ILE F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'F' and resid 192 through 223 removed outlier: 4.105A pdb=" N TYR F 213 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN F 223 " --> pdb=" O ILE F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 228 removed outlier: 3.877A pdb=" N VAL F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 31 Processing helix chain 'G' and resid 31 through 46 Processing helix chain 'G' and resid 107 through 139 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 147 through 191 removed outlier: 3.745A pdb=" N ALA G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL G 152 " --> pdb=" O PHE G 148 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 233 removed outlier: 3.607A pdb=" N LEU G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 28 removed outlier: 3.804A pdb=" N VAL a 26 " --> pdb=" O ALA a 22 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS a 27 " --> pdb=" O GLN a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 98 removed outlier: 4.194A pdb=" N ALA a 80 " --> pdb=" O LEU a 76 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG a 81 " --> pdb=" O THR a 77 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE a 82 " --> pdb=" O ALA a 78 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL a 83 " --> pdb=" O ASP a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 103 through 121 removed outlier: 3.729A pdb=" N THR a 108 " --> pdb=" O VAL a 104 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 176 removed outlier: 3.793A pdb=" N LYS a 174 " --> pdb=" O GLU a 170 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 196 Processing helix chain 'a' and resid 221 through 230 removed outlier: 3.674A pdb=" N TYR a 228 " --> pdb=" O GLU a 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 21 through 32 removed outlier: 3.749A pdb=" N ILE b 28 " --> pdb=" O VAL b 24 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU b 29 " --> pdb=" O GLU b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 104 removed outlier: 4.149A pdb=" N LYS b 86 " --> pdb=" O ILE b 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU b 88 " --> pdb=" O ASP b 84 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP b 90 " --> pdb=" O LYS b 86 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS b 91 " --> pdb=" O THR b 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 121 removed outlier: 3.783A pdb=" N THR b 113 " --> pdb=" O VAL b 109 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN b 114 " --> pdb=" O GLU b 110 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL b 116 " --> pdb=" O VAL b 112 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN b 118 " --> pdb=" O GLN b 114 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU b 119 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU b 121 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 173 through 185 removed outlier: 3.540A pdb=" N SER b 180 " --> pdb=" O GLY b 176 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU b 183 " --> pdb=" O SER b 179 " (cutoff:3.500A) Processing helix chain 'b' and resid 190 through 206 removed outlier: 3.508A pdb=" N LYS b 196 " --> pdb=" O LYS b 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE b 201 " --> pdb=" O SER b 197 " (cutoff:3.500A) Processing helix chain 'b' and resid 230 through 240 removed outlier: 4.025A pdb=" N GLU b 236 " --> pdb=" O GLU b 232 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP b 240 " --> pdb=" O GLU b 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 19 through 31 removed outlier: 4.274A pdb=" N VAL c 29 " --> pdb=" O ALA c 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS c 30 " --> pdb=" O MET c 26 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 99 removed outlier: 3.928A pdb=" N LEU c 83 " --> pdb=" O ALA c 79 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE c 87 " --> pdb=" O LEU c 83 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG c 96 " --> pdb=" O CYS c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 104 through 118 removed outlier: 3.517A pdb=" N LEU c 111 " --> pdb=" O ARG c 107 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS c 115 " --> pdb=" O LEU c 111 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR c 116 " --> pdb=" O ILE c 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 164 through 175 removed outlier: 3.860A pdb=" N ALA c 168 " --> pdb=" O ARG c 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG c 169 " --> pdb=" O SER c 165 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR c 170 " --> pdb=" O GLN c 166 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR c 171 " --> pdb=" O SER c 167 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU c 172 " --> pdb=" O ALA c 168 " (cutoff:3.500A) Processing helix chain 'c' and resid 175 through 182 removed outlier: 4.080A pdb=" N MET c 180 " --> pdb=" O MET c 176 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU c 181 " --> pdb=" O SER c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 183 through 197 removed outlier: 3.506A pdb=" N ARG c 193 " --> pdb=" O LYS c 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'c' and resid 229 through 234 Processing helix chain 'd' and resid 21 through 33 removed outlier: 3.530A pdb=" N VAL d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 103 removed outlier: 3.532A pdb=" N LEU d 88 " --> pdb=" O ASP d 84 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASP d 90 " --> pdb=" O ARG d 86 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG d 100 " --> pdb=" O ALA d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 123 removed outlier: 3.640A pdb=" N ARG d 115 " --> pdb=" O HIS d 111 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR d 123 " --> pdb=" O TYR d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 180 removed outlier: 3.975A pdb=" N GLU d 176 " --> pdb=" O ALA d 172 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 202 removed outlier: 4.739A pdb=" N LYS d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA d 195 " --> pdb=" O VAL d 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS d 196 " --> pdb=" O LYS d 192 " (cutoff:3.500A) Processing helix chain 'd' and resid 229 through 243 removed outlier: 3.501A pdb=" N ALA d 236 " --> pdb=" O VAL d 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 12 removed outlier: 3.643A pdb=" N ASP e 10 " --> pdb=" O ALA e 7 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG e 11 " --> pdb=" O GLY e 8 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 31 Processing helix chain 'e' and resid 32 through 36 removed outlier: 3.708A pdb=" N GLY e 36 " --> pdb=" O ASN e 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 83 through 105 removed outlier: 3.763A pdb=" N GLN e 92 " --> pdb=" O ARG e 88 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG e 93 " --> pdb=" O SER e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 127 removed outlier: 3.575A pdb=" N LYS e 116 " --> pdb=" O ASP e 112 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE e 121 " --> pdb=" O ARG e 117 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL e 124 " --> pdb=" O ASP e 120 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR e 125 " --> pdb=" O ILE e 121 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR e 126 " --> pdb=" O SER e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 172 through 185 removed outlier: 4.569A pdb=" N LYS e 181 " --> pdb=" O SER e 177 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS e 182 " --> pdb=" O PHE e 178 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS e 185 " --> pdb=" O LYS e 181 " (cutoff:3.500A) Processing helix chain 'e' and resid 190 through 207 removed outlier: 3.572A pdb=" N CYS e 201 " --> pdb=" O THR e 197 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU e 202 " --> pdb=" O ALA e 198 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL e 205 " --> pdb=" O CYS e 201 " (cutoff:3.500A) Processing helix chain 'e' and resid 231 through 240 removed outlier: 3.645A pdb=" N ASP e 236 " --> pdb=" O GLU e 232 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA e 237 " --> pdb=" O ALA e 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 19 through 31 removed outlier: 3.819A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 102 removed outlier: 4.385A pdb=" N LEU f 86 " --> pdb=" O ASP f 82 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 121 removed outlier: 3.511A pdb=" N VAL f 111 " --> pdb=" O THR f 107 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN f 112 " --> pdb=" O ALA f 108 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL f 117 " --> pdb=" O ARG f 113 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR f 121 " --> pdb=" O VAL f 117 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 178 Processing helix chain 'f' and resid 183 through 199 removed outlier: 3.557A pdb=" N HIS f 189 " --> pdb=" O GLU f 185 " (cutoff:3.500A) Processing helix chain 'f' and resid 222 through 228 removed outlier: 3.552A pdb=" N VAL f 226 " --> pdb=" O THR f 222 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS f 227 " --> pdb=" O PRO f 223 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASP f 228 " --> pdb=" O THR f 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 222 through 228' Processing helix chain 'g' and resid 18 through 28 Processing helix chain 'g' and resid 29 through 31 No H-bonds generated for 'chain 'g' and resid 29 through 31' Processing helix chain 'g' and resid 79 through 102 removed outlier: 4.014A pdb=" N ALA g 83 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN g 84 " --> pdb=" O THR g 80 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL g 85 " --> pdb=" O SER g 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN g 88 " --> pdb=" O ASN g 84 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 123 removed outlier: 3.838A pdb=" N ASP g 116 " --> pdb=" O THR g 112 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ILE g 117 " --> pdb=" O ALA g 113 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR g 121 " --> pdb=" O ILE g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 167 through 178 removed outlier: 3.565A pdb=" N SER g 173 " --> pdb=" O ALA g 169 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET g 174 " --> pdb=" O ALA g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 185 through 201 removed outlier: 4.016A pdb=" N ALA g 191 " --> pdb=" O LYS g 187 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS g 199 " --> pdb=" O LYS g 195 " (cutoff:3.500A) Processing helix chain 'g' and resid 229 through 244 Processing helix chain 'H' and resid 56 through 78 removed outlier: 3.701A pdb=" N VAL H 60 " --> pdb=" O LEU H 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN H 61 " --> pdb=" O ALA H 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 62 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 97 removed outlier: 4.077A pdb=" N SER H 89 " --> pdb=" O TYR H 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET H 90 " --> pdb=" O THR H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 154 removed outlier: 4.146A pdb=" N GLY H 148 " --> pdb=" O GLU H 144 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET H 149 " --> pdb=" O GLN H 145 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS H 150 " --> pdb=" O MET H 146 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 178 removed outlier: 3.908A pdb=" N ASP H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASP H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 72 removed outlier: 3.613A pdb=" N GLU I 58 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR I 59 " --> pdb=" O GLN I 55 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 60 " --> pdb=" O PHE I 56 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL I 64 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN I 65 " --> pdb=" O GLN I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 91 removed outlier: 3.553A pdb=" N ASN I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN I 87 " --> pdb=" O PHE I 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR I 91 " --> pdb=" O ASN I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 139 removed outlier: 4.032A pdb=" N LEU I 138 " --> pdb=" O TYR I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 147 removed outlier: 3.794A pdb=" N LEU I 143 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP I 144 " --> pdb=" O LEU I 140 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG I 145 " --> pdb=" O SER I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 165 Processing helix chain 'I' and resid 165 through 170 Processing helix chain 'J' and resid 85 through 107 removed outlier: 3.518A pdb=" N CYS J 89 " --> pdb=" O PHE J 85 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU J 90 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 99 " --> pdb=" O ILE J 95 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS J 101 " --> pdb=" O GLU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 removed outlier: 4.193A pdb=" N ALA J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA J 118 " --> pdb=" O GLY J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 169 through 181 Proline residue: J 175 - end of helix removed outlier: 3.526A pdb=" N ASP J 178 " --> pdb=" O GLN J 174 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN J 179 " --> pdb=" O PRO J 175 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN J 180 " --> pdb=" O LEU J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 214 removed outlier: 3.830A pdb=" N MET J 200 " --> pdb=" O LEU J 196 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU J 212 " --> pdb=" O ILE J 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 123 removed outlier: 3.709A pdb=" N PHE K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU K 119 " --> pdb=" O MET K 115 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU K 120 " --> pdb=" O VAL K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 146 removed outlier: 3.836A pdb=" N ARG K 144 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG K 145 " --> pdb=" O MET K 141 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER K 146 " --> pdb=" O TYR K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 188 removed outlier: 3.828A pdb=" N ALA K 188 " --> pdb=" O GLY K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 191 through 202 removed outlier: 3.996A pdb=" N GLU K 200 " --> pdb=" O ARG K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 225 Processing helix chain 'K' and resid 254 through 259 removed outlier: 3.940A pdb=" N HIS K 258 " --> pdb=" O TRP K 254 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 Processing helix chain 'S' and resid 56 through 78 removed outlier: 3.648A pdb=" N ALA S 64 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN S 65 " --> pdb=" O GLN S 61 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS S 68 " --> pdb=" O ALA S 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE S 69 " --> pdb=" O GLN S 65 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU S 73 " --> pdb=" O PHE S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 98 removed outlier: 3.914A pdb=" N SER S 89 " --> pdb=" O TYR S 85 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS S 98 " --> pdb=" O LEU S 94 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 154 removed outlier: 4.564A pdb=" N GLY S 148 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET S 149 " --> pdb=" O GLN S 145 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 177 removed outlier: 3.746A pdb=" N GLU S 165 " --> pdb=" O GLU S 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN S 173 " --> pdb=" O GLN S 169 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG S 177 " --> pdb=" O ASN S 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.789A pdb=" N VAL T 54 " --> pdb=" O ALA T 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU T 58 " --> pdb=" O VAL T 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE T 60 " --> pdb=" O PHE T 56 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET T 69 " --> pdb=" O GLN T 65 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG T 70 " --> pdb=" O LEU T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 91 removed outlier: 3.616A pdb=" N ASN T 87 " --> pdb=" O PHE T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 135 through 147 removed outlier: 4.442A pdb=" N SER T 141 " --> pdb=" O PHE T 137 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ILE T 142 " --> pdb=" O LEU T 138 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG T 145 " --> pdb=" O SER T 141 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 170 removed outlier: 3.730A pdb=" N VAL T 157 " --> pdb=" O ARG T 153 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS T 162 " --> pdb=" O GLU T 158 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS T 163 " --> pdb=" O LEU T 159 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU T 166 " --> pdb=" O LYS T 162 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU T 167 " --> pdb=" O CYS T 163 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN T 168 " --> pdb=" O LEU T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 108 removed outlier: 3.586A pdb=" N CYS U 89 " --> pdb=" O PHE U 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU U 90 " --> pdb=" O HIS U 86 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR U 91 " --> pdb=" O GLY U 87 " (cutoff:3.500A) Processing helix chain 'U' and resid 112 through 127 removed outlier: 3.804A pdb=" N ALA U 117 " --> pdb=" O THR U 113 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA U 118 " --> pdb=" O GLY U 114 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG U 127 " --> pdb=" O ILE U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 169 through 181 removed outlier: 3.882A pdb=" N GLN U 174 " --> pdb=" O SER U 170 " (cutoff:3.500A) Proline residue: U 175 - end of helix Processing helix chain 'U' and resid 195 through 214 removed outlier: 3.576A pdb=" N LYS U 204 " --> pdb=" O MET U 200 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG U 213 " --> pdb=" O SER U 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 101 through 123 removed outlier: 3.509A pdb=" N PHE V 105 " --> pdb=" O ASP V 101 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR V 107 " --> pdb=" O ALA V 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY V 113 " --> pdb=" O LYS V 109 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP V 118 " --> pdb=" O GLN V 114 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU V 119 " --> pdb=" O MET V 115 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU V 122 " --> pdb=" O ASP V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 147 removed outlier: 3.930A pdb=" N ARG V 144 " --> pdb=" O ALA V 140 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG V 145 " --> pdb=" O MET V 141 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER V 146 " --> pdb=" O TYR V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 184 through 189 Processing helix chain 'V' and resid 190 through 202 removed outlier: 3.795A pdb=" N LEU V 194 " --> pdb=" O LEU V 190 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS V 201 " --> pdb=" O GLU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 224 removed outlier: 3.660A pdb=" N VAL V 220 " --> pdb=" O ARG V 216 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU V 221 " --> pdb=" O CYS V 217 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR V 223 " --> pdb=" O ARG V 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 91 removed outlier: 3.702A pdb=" N LEU W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU W 91 " --> pdb=" O GLY W 87 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 111 removed outlier: 3.501A pdb=" N LYS W 109 " --> pdb=" O ASN W 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 135 through 138 removed outlier: 3.501A pdb=" N MET W 138 " --> pdb=" O MET W 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 135 through 138' Processing helix chain 'W' and resid 154 through 162 removed outlier: 3.593A pdb=" N ALA W 161 " --> pdb=" O TYR W 157 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 186 removed outlier: 3.526A pdb=" N LYS W 184 " --> pdb=" O ALA W 180 " (cutoff:3.500A) Processing helix chain 'W' and resid 209 through 213 removed outlier: 3.557A pdb=" N LEU W 213 " --> pdb=" O GLY W 210 " (cutoff:3.500A) Processing helix chain 'X' and resid 87 through 110 removed outlier: 3.624A pdb=" N ALA X 91 " --> pdb=" O VAL X 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR X 94 " --> pdb=" O ASP X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 114 through 128 removed outlier: 3.608A pdb=" N VAL X 118 " --> pdb=" O ARG X 114 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG X 128 " --> pdb=" O GLN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 180 removed outlier: 3.927A pdb=" N VAL X 176 " --> pdb=" O ALA X 172 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU X 177 " --> pdb=" O ALA X 173 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP X 179 " --> pdb=" O ALA X 175 " (cutoff:3.500A) Processing helix chain 'X' and resid 186 through 205 removed outlier: 3.730A pdb=" N ALA X 200 " --> pdb=" O GLU X 196 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY X 201 " --> pdb=" O ALA X 197 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 140 removed outlier: 3.665A pdb=" N CYS Y 124 " --> pdb=" O CYS Y 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU Y 134 " --> pdb=" O LEU Y 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 162 removed outlier: 3.525A pdb=" N MET Y 158 " --> pdb=" O LEU Y 154 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN Y 161 " --> pdb=" O ASN Y 157 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR Y 162 " --> pdb=" O MET Y 158 " (cutoff:3.500A) Processing helix chain 'Y' and resid 203 through 213 removed outlier: 4.468A pdb=" N GLY Y 209 " --> pdb=" O SER Y 205 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL Y 210 " --> pdb=" O HIS Y 206 " (cutoff:3.500A) Processing helix chain 'Y' and resid 220 through 238 removed outlier: 3.552A pdb=" N ILE Y 232 " --> pdb=" O GLY Y 228 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL Y 233 " --> pdb=" O ARG Y 229 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS Y 234 " --> pdb=" O ARG Y 230 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG Y 238 " --> pdb=" O HIS Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 264 through 273 removed outlier: 3.660A pdb=" N HIS Y 269 " --> pdb=" O SER Y 265 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU Y 273 " --> pdb=" O HIS Y 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 68 through 91 removed outlier: 3.569A pdb=" N ALA Z 74 " --> pdb=" O ALA Z 70 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE Z 75 " --> pdb=" O ASP Z 71 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU Z 90 " --> pdb=" O HIS Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 95 through 111 Processing helix chain 'Z' and resid 135 through 138 Processing helix chain 'Z' and resid 150 through 153 removed outlier: 3.683A pdb=" N TYR Z 153 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 150 through 153' Processing helix chain 'Z' and resid 154 through 162 removed outlier: 3.837A pdb=" N ASP Z 159 " --> pdb=" O TYR Z 155 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA Z 160 " --> pdb=" O GLY Z 156 " (cutoff:3.500A) Processing helix chain 'Z' and resid 167 through 186 removed outlier: 4.114A pdb=" N LYS Z 184 " --> pdb=" O ALA Z 180 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG Z 185 " --> pdb=" O LEU Z 181 " (cutoff:3.500A) Processing helix chain '1' and resid 87 through 110 removed outlier: 3.556A pdb=" N THR 1 94 " --> pdb=" O ASP 1 90 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN 1 101 " --> pdb=" O MET 1 97 " (cutoff:3.500A) Processing helix chain '1' and resid 114 through 129 removed outlier: 3.908A pdb=" N VAL 1 118 " --> pdb=" O ARG 1 114 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR 1 119 " --> pdb=" O VAL 1 115 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG 1 120 " --> pdb=" O ALA 1 116 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET 1 121 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN 1 124 " --> pdb=" O ARG 1 120 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR 1 129 " --> pdb=" O THR 1 125 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 181 removed outlier: 4.128A pdb=" N VAL 1 176 " --> pdb=" O ALA 1 172 " (cutoff:3.500A) Processing helix chain '1' and resid 186 through 205 removed outlier: 3.769A pdb=" N LEU 1 203 " --> pdb=" O THR 1 199 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY 1 204 " --> pdb=" O ALA 1 200 " (cutoff:3.500A) Processing helix chain '2' and resid 120 through 142 removed outlier: 3.630A pdb=" N CYS 2 124 " --> pdb=" O CYS 2 120 " (cutoff:3.500A) Processing helix chain '2' and resid 147 through 162 removed outlier: 4.200A pdb=" N TYR 2 162 " --> pdb=" O MET 2 158 " (cutoff:3.500A) Processing helix chain '2' and resid 204 through 212 removed outlier: 4.083A pdb=" N GLY 2 209 " --> pdb=" O SER 2 205 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL 2 210 " --> pdb=" O HIS 2 206 " (cutoff:3.500A) Processing helix chain '2' and resid 220 through 239 Processing helix chain '2' and resid 267 through 273 removed outlier: 3.672A pdb=" N TYR 2 271 " --> pdb=" O LEU 2 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 165 through 168 Processing sheet with id=AA2, first strand: chain 'L' and resid 69 through 71 removed outlier: 3.895A pdb=" N GLY L 77 " --> pdb=" O ILE L 141 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS L 153 " --> pdb=" O CYS L 161 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N CYS L 161 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'M' and resid 160 through 163 Processing sheet with id=AA4, first strand: chain 'M' and resid 66 through 69 removed outlier: 6.646A pdb=" N ILE M 72 " --> pdb=" O ILE M 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL M 75 " --> pdb=" O LEU M 135 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER M 133 " --> pdb=" O SER M 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 161 through 164 removed outlier: 3.696A pdb=" N LEU N 216 " --> pdb=" O VAL N 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'N' and resid 65 through 66 removed outlier: 4.052A pdb=" N LEU N 134 " --> pdb=" O SER N 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY N 138 " --> pdb=" O GLN N 146 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LEU N 147 " --> pdb=" O TRP N 159 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY N 158 " --> pdb=" O ASP O 55 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 158 through 161 removed outlier: 3.668A pdb=" N VAL O 42 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL O 45 " --> pdb=" O GLU O 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU O 207 " --> pdb=" O VAL O 45 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'P' and resid 169 through 170 removed outlier: 3.838A pdb=" N THR P 219 " --> pdb=" O HIS P 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 141 through 147 removed outlier: 3.556A pdb=" N VAL P 163 " --> pdb=" O HIS P 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 158 through 161 Processing sheet with id=AB3, first strand: chain 'Q' and resid 63 through 65 removed outlier: 3.587A pdb=" N ILE Q 72 " --> pdb=" O LEU Q 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 163 through 166 removed outlier: 4.792A pdb=" N ALA R 209 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AB6, first strand: chain 'a' and resid 158 through 161 removed outlier: 3.953A pdb=" N THR a 31 " --> pdb=" O GLU a 46 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL a 42 " --> pdb=" O VAL a 35 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET a 211 " --> pdb=" O VAL a 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'a' and resid 54 through 55 removed outlier: 4.244A pdb=" N GLY g 158 " --> pdb=" O ASP a 55 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LEU g 147 " --> pdb=" O TRP g 159 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU g 135 " --> pdb=" O SER g 75 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE g 137 " --> pdb=" O ALA g 73 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS g 74 " --> pdb=" O TYR g 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 63 through 64 removed outlier: 3.837A pdb=" N THR a 141 " --> pdb=" O ASP a 137 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 167 through 170 removed outlier: 3.667A pdb=" N ALA b 49 " --> pdb=" O ILE b 38 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL b 46 " --> pdb=" O VAL b 220 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL b 220 " --> pdb=" O VAL b 46 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA b 218 " --> pdb=" O LEU b 48 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL b 50 " --> pdb=" O GLU b 216 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU b 217 " --> pdb=" O PHE b 229 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR b 219 " --> pdb=" O HIS b 227 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN b 221 " --> pdb=" O ASN b 225 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASN b 225 " --> pdb=" O GLN b 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 67 through 69 Processing sheet with id=AC2, first strand: chain 'b' and resid 79 through 80 removed outlier: 4.104A pdb=" N LEU b 141 " --> pdb=" O MET b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'c' and resid 158 through 161 removed outlier: 3.783A pdb=" N SER c 211 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 63 through 65 Processing sheet with id=AC5, first strand: chain 'd' and resid 163 through 166 removed outlier: 4.005A pdb=" N CYS d 164 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY d 39 " --> pdb=" O CYS d 164 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE d 38 " --> pdb=" O GLY d 49 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE d 48 " --> pdb=" O SER d 215 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'd' and resid 68 through 69 removed outlier: 4.313A pdb=" N GLY d 75 " --> pdb=" O GLY d 139 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY d 139 " --> pdb=" O GLY d 75 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA d 77 " --> pdb=" O MET d 137 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER d 140 " --> pdb=" O GLN d 148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN d 148 " --> pdb=" O SER d 140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET d 151 " --> pdb=" O TYR d 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR d 159 " --> pdb=" O MET d 151 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 168 through 169 removed outlier: 3.539A pdb=" N SER e 39 " --> pdb=" O ALA e 168 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR e 38 " --> pdb=" O GLN e 53 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL e 220 " --> pdb=" O ALA e 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'e' and resid 70 through 71 removed outlier: 4.150A pdb=" N GLY e 77 " --> pdb=" O ILE e 141 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE e 141 " --> pdb=" O GLY e 77 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY e 142 " --> pdb=" O GLN e 150 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN e 150 " --> pdb=" O GLY e 142 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'f' and resid 160 through 163 removed outlier: 3.669A pdb=" N GLY f 37 " --> pdb=" O THR f 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL f 44 " --> pdb=" O CYS f 213 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'f' and resid 66 through 67 removed outlier: 3.550A pdb=" N VAL f 75 " --> pdb=" O LEU f 135 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER f 77 " --> pdb=" O SER f 133 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN f 140 " --> pdb=" O ARG f 143 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'g' and resid 161 through 164 removed outlier: 3.501A pdb=" N ILE g 37 " --> pdb=" O LEU g 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU g 44 " --> pdb=" O ILE g 37 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL g 43 " --> pdb=" O LEU g 216 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA g 47 " --> pdb=" O GLU g 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 136 through 140 removed outlier: 5.549A pdb=" N ALA H 10 " --> pdb=" O ASP H 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL H 20 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL H 185 " --> pdb=" O LEU H 200 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 28 through 30 removed outlier: 6.751A pdb=" N PHE H 28 " --> pdb=" O VAL H 35 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 42 through 44 removed outlier: 3.620A pdb=" N ILE H 51 " --> pdb=" O PHE H 43 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 129 through 131 Processing sheet with id=AD7, first strand: chain 'I' and resid 21 through 23 removed outlier: 6.613A pdb=" N SER I 23 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N GLN I 27 " --> pdb=" O SER I 23 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 36 through 37 removed outlier: 3.516A pdb=" N LEU I 102 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N MET I 118 " --> pdb=" O LEU I 102 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 163 through 167 removed outlier: 6.018A pdb=" N THR J 39 " --> pdb=" O ASP J 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP J 54 " --> pdb=" O THR J 39 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 57 through 59 removed outlier: 3.681A pdb=" N LEU J 57 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR J 65 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLU J 59 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 72 through 75 removed outlier: 6.597A pdb=" N THR J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY J 139 " --> pdb=" O VAL J 79 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE J 137 " --> pdb=" O GLY J 81 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL J 149 " --> pdb=" O ASP J 161 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER J 151 " --> pdb=" O GLN J 159 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN J 159 " --> pdb=" O SER J 151 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 181 through 183 removed outlier: 6.394A pdb=" N PHE K 232 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE K 234 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR K 238 " --> pdb=" O GLY K 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 73 through 75 removed outlier: 6.108A pdb=" N TYR K 75 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA K 79 " --> pdb=" O TYR K 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 87 through 90 removed outlier: 4.157A pdb=" N MET K 155 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL K 170 " --> pdb=" O MET K 155 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 136 through 140 removed outlier: 5.408A pdb=" N ALA S 10 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL S 185 " --> pdb=" O LEU S 200 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER 1 252 " --> pdb=" O THR S 199 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 28 through 30 removed outlier: 5.761A pdb=" N ILE S 30 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 42 through 44 removed outlier: 3.601A pdb=" N ILE S 51 " --> pdb=" O PHE S 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA S 110 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 129 through 131 Processing sheet with id=AF1, first strand: chain 'T' and resid 21 through 23 removed outlier: 6.169A pdb=" N SER T 23 " --> pdb=" O GLN T 27 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN T 27 " --> pdb=" O SER T 23 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 35 through 37 removed outlier: 3.713A pdb=" N ALA T 105 " --> pdb=" O LEU T 43 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 163 through 164 removed outlier: 4.214A pdb=" N SER U 49 " --> pdb=" O VAL U 226 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL U 226 " --> pdb=" O SER U 49 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 57 through 59 removed outlier: 7.102A pdb=" N LEU U 57 " --> pdb=" O HIS U 64 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 72 through 73 removed outlier: 3.670A pdb=" N GLY U 81 " --> pdb=" O ILE U 137 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASN U 136 " --> pdb=" O PHE U 152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 181 through 182 removed outlier: 3.534A pdb=" N GLY V 64 " --> pdb=" O PHE V 61 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'V' and resid 88 through 90 removed outlier: 3.546A pdb=" N GLY V 158 " --> pdb=" O MET V 95 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 144 through 148 removed outlier: 5.821A pdb=" N THR W 22 " --> pdb=" O ASP W 37 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL W 32 " --> pdb=" O ILE W 198 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE W 198 " --> pdb=" O VAL W 32 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 40 through 42 removed outlier: 6.992A pdb=" N VAL W 40 " --> pdb=" O VAL W 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 54 through 56 removed outlier: 3.682A pdb=" N SER W 55 " --> pdb=" O CYS W 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 164 through 167 removed outlier: 3.618A pdb=" N THR X 164 " --> pdb=" O GLY X 44 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE X 42 " --> pdb=" O LEU X 166 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS X 215 " --> pdb=" O LEU X 53 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL X 216 " --> pdb=" O LYS X 223 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR X 218 " --> pdb=" O GLY X 221 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY X 221 " --> pdb=" O THR X 218 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 59 through 60 removed outlier: 6.742A pdb=" N ALA X 59 " --> pdb=" O ALA X 66 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 74 through 77 removed outlier: 3.991A pdb=" N CYS X 82 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE X 76 " --> pdb=" O ILE X 80 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE X 80 " --> pdb=" O ILE X 76 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 197 through 200 removed outlier: 3.683A pdb=" N VAL Y 84 " --> pdb=" O MET Y 251 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N HIS Y 250 " --> pdb=" O LYS Y 258 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LYS Y 258 " --> pdb=" O HIS Y 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 92 through 94 removed outlier: 7.220A pdb=" N ALA Y 92 " --> pdb=" O ALA Y 99 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 114 through 115 removed outlier: 3.670A pdb=" N LEU Y 114 " --> pdb=" O CYS Y 174 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS Y 174 " --> pdb=" O LEU Y 114 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 144 through 147 removed outlier: 3.784A pdb=" N VAL Z 32 " --> pdb=" O ILE Z 198 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE Z 198 " --> pdb=" O VAL Z 32 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 40 through 41 Processing sheet with id=AH2, first strand: chain 'Z' and resid 54 through 56 removed outlier: 3.522A pdb=" N SER Z 55 " --> pdb=" O CYS Z 63 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS Z 117 " --> pdb=" O SER Z 66 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '1' and resid 164 through 167 removed outlier: 6.639A pdb=" N THR 1 41 " --> pdb=" O ASP 1 56 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP 1 56 " --> pdb=" O THR 1 41 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA 1 214 " --> pdb=" O ALA 1 227 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA 1 227 " --> pdb=" O ALA 1 214 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL 1 216 " --> pdb=" O LEU 1 225 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU 1 225 " --> pdb=" O VAL 1 216 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 1 218 " --> pdb=" O LYS 1 223 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LYS 1 223 " --> pdb=" O THR 1 218 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '1' and resid 59 through 60 Processing sheet with id=AH5, first strand: chain '1' and resid 73 through 77 removed outlier: 6.587A pdb=" N ILE 1 80 " --> pdb=" O ILE 1 76 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR 1 81 " --> pdb=" O GLY 1 140 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY 1 140 " --> pdb=" O TYR 1 81 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain '2' and resid 200 through 201 removed outlier: 5.976A pdb=" N THR 2 74 " --> pdb=" O ASP 2 89 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP 2 89 " --> pdb=" O THR 2 74 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE 2 78 " --> pdb=" O ILE 2 85 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU 2 260 " --> pdb=" O MET 2 248 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS 2 250 " --> pdb=" O LYS 2 258 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS 2 258 " --> pdb=" O HIS 2 250 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '2' and resid 92 through 94 removed outlier: 7.580A pdb=" N ALA 2 92 " --> pdb=" O ALA 2 99 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 2 99 " --> pdb=" O ALA 2 92 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain '2' and resid 107 through 110 removed outlier: 6.423A pdb=" N LEU 2 113 " --> pdb=" O ILE 2 109 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY 2 170 " --> pdb=" O SER 2 118 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain '2' and resid 107 through 110 removed outlier: 6.423A pdb=" N LEU 2 113 " --> pdb=" O ILE 2 109 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER 2 171 " --> pdb=" O VAL 2 186 " (cutoff:3.500A) 3138 hydrogen bonds defined for protein. 9033 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: 25.85 Time building geometry restraints manager: 13.93 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: 19668 1.34 - 1.46: 8870 1.46 - 1.58: 31935 1.58 - 1.70: 0 1.70 - 1.82: 569 Bond restraints: 61042 Sorted by residual: bond pdb=" C GLY Y 180 " pdb=" N PRO Y 181 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.41e+00 bond pdb=" C GLN B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.78e+00 bond pdb=" C GLN E 191 " pdb=" N PRO E 192 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.15e+00 bond pdb=" CA SER X 63 " pdb=" C SER X 63 " ideal model delta sigma weight residual 1.523 1.496 0.027 1.34e-02 5.57e+03 4.06e+00 bond pdb=" N GLY F 232 " pdb=" CA GLY F 232 " ideal model delta sigma weight residual 1.449 1.474 -0.025 1.45e-02 4.76e+03 3.02e+00 ... (remaining 61037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 81140 1.66 - 3.32: 1144 3.32 - 4.99: 158 4.99 - 6.65: 29 6.65 - 8.31: 9 Bond angle restraints: 82480 Sorted by residual: angle pdb=" N THR c 78 " pdb=" CA THR c 78 " pdb=" C THR c 78 " ideal model delta sigma weight residual 111.82 120.13 -8.31 1.16e+00 7.43e-01 5.13e+01 angle pdb=" C LYS b 187 " pdb=" CA LYS b 187 " pdb=" CB LYS b 187 " ideal model delta sigma weight residual 116.54 109.13 7.41 1.15e+00 7.56e-01 4.15e+01 angle pdb=" C ARG a 213 " pdb=" CA ARG a 213 " pdb=" CB ARG a 213 " ideal model delta sigma weight residual 116.54 110.17 6.37 1.15e+00 7.56e-01 3.07e+01 angle pdb=" C ALA f 41 " pdb=" CA ALA f 41 " pdb=" CB ALA f 41 " ideal model delta sigma weight residual 117.23 109.79 7.44 1.36e+00 5.41e-01 3.00e+01 angle pdb=" C ASN I 24 " pdb=" CA ASN I 24 " pdb=" CB ASN I 24 " ideal model delta sigma weight residual 116.63 110.52 6.11 1.16e+00 7.43e-01 2.77e+01 ... (remaining 82475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 36229 16.80 - 33.59: 515 33.59 - 50.39: 201 50.39 - 67.18: 39 67.18 - 83.98: 12 Dihedral angle restraints: 36996 sinusoidal: 14812 harmonic: 22184 Sorted by residual: dihedral pdb=" CA GLY S 101 " pdb=" C GLY S 101 " pdb=" N PRO S 102 " pdb=" CA PRO S 102 " ideal model delta harmonic sigma weight residual 180.00 -150.11 -29.89 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA GLN a 200 " pdb=" C GLN a 200 " pdb=" N SER a 201 " pdb=" CA SER a 201 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLY H 101 " pdb=" C GLY H 101 " pdb=" N PRO H 102 " pdb=" CA PRO H 102 " ideal model delta harmonic sigma weight residual -180.00 -154.41 -25.59 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 36993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 7813 0.055 - 0.110: 1295 0.110 - 0.164: 170 0.164 - 0.219: 6 0.219 - 0.274: 5 Chirality restraints: 9289 Sorted by residual: chirality pdb=" CA VAL V 51 " pdb=" N VAL V 51 " pdb=" C VAL V 51 " pdb=" CB VAL V 51 " both_signs ideal model delta sigma weight residual False 2.44 2.17 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA THR c 78 " pdb=" N THR c 78 " pdb=" C THR c 78 " pdb=" CB THR c 78 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA ASP 1 62 " pdb=" N ASP 1 62 " pdb=" C ASP 1 62 " pdb=" CB ASP 1 62 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 9286 not shown) Planarity restraints: 10629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 235 " 0.061 5.00e-02 4.00e+02 9.38e-02 1.41e+01 pdb=" N PRO D 236 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 231 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.04e+01 pdb=" C LYS F 231 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS F 231 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY F 232 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR 1 232 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.12e+00 pdb=" C THR 1 232 " 0.049 2.00e-02 2.50e+03 pdb=" O THR 1 232 " -0.019 2.00e-02 2.50e+03 pdb=" N LYS 1 233 " -0.017 2.00e-02 2.50e+03 ... (remaining 10626 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4148 2.74 - 3.28: 60683 3.28 - 3.82: 96288 3.82 - 4.36: 118302 4.36 - 4.90: 200658 Nonbonded interactions: 480079 Sorted by model distance: nonbonded pdb=" OG SER N 62 " pdb=" O ILE N 65 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR b 161 " pdb=" OG1 THR c 78 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS U 164 " pdb=" OG1 THR 2 100 " model vdw 2.208 3.120 nonbonded pdb=" O LEU C 49 " pdb=" OH TYR C 209 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR O 31 " pdb=" O ARG O 163 " model vdw 2.215 3.040 ... (remaining 480074 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 'X' } ncs_group { reference = chain '2' selection = chain 'Y' } ncs_group { reference = (chain 'A' and (resid 7 through 67 or resid 94 through 237)) selection = (chain 'D' and (resid 7 through 200 or (resid 201 and (name N or name CA or name \ C or name O or name CB )) or resid 202 through 237)) selection = (chain 'F' and (resid 7 through 67 or resid 94 through 200 or (resid 201 and (na \ me N or name CA or name C or name O or name CB )) or resid 202 through 237)) } ncs_group { reference = (chain 'B' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'C' and (resid 4 through 63 or resid 102 through 242)) selection = (chain 'E' and resid 4 through 242) selection = (chain 'G' and (resid 4 through 63 or resid 102 through 242)) } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = (chain 'I' and resid 1 through 197) selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = (chain 'K' and resid 47 through 261) selection = (chain 'V' and resid 47 through 261) } ncs_group { reference = (chain 'L' and resid 9 through 243) selection = (chain 'e' and resid 9 through 243) } ncs_group { reference = chain 'M' selection = (chain 'f' and resid 7 through 232) } ncs_group { reference = chain 'N' selection = chain 'g' } ncs_group { reference = chain 'O' selection = chain 'a' } ncs_group { reference = chain 'P' selection = chain 'b' } ncs_group { reference = chain 'Q' selection = chain 'c' } ncs_group { reference = chain 'R' selection = chain 'd' } ncs_group { reference = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.060 Extract box with map and model: 1.880 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 113.830 Find NCS groups from input model: 4.200 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 61042 Z= 0.127 Angle : 0.548 8.309 82480 Z= 0.349 Chirality : 0.041 0.274 9289 Planarity : 0.004 0.094 10629 Dihedral : 7.814 83.979 22770 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.91 % Favored : 94.95 % Rotamer: Outliers : 0.12 % Allowed : 0.19 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.08), residues: 7577 helix: -2.80 (0.06), residues: 3115 sheet: -0.71 (0.13), residues: 1293 loop : -0.99 (0.10), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP V 152 HIS 0.007 0.001 HIS J 105 PHE 0.017 0.001 PHE T 171 TYR 0.019 0.001 TYR K 229 ARG 0.005 0.000 ARG 2 238 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3302 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 3294 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.8783 (mttt) cc_final: 0.8476 (ttmm) REVERT: L 33 ASN cc_start: 0.7064 (t0) cc_final: 0.6584 (t0) REVERT: L 65 THR cc_start: 0.7958 (p) cc_final: 0.7677 (p) REVERT: L 139 ILE cc_start: 0.8510 (mt) cc_final: 0.8210 (mt) REVERT: L 230 LEU cc_start: 0.7646 (tp) cc_final: 0.6052 (tp) REVERT: L 235 ILE cc_start: 0.8056 (mt) cc_final: 0.7667 (mt) REVERT: M 63 HIS cc_start: 0.4281 (m-70) cc_final: 0.3692 (m170) REVERT: M 163 MET cc_start: 0.7367 (ptm) cc_final: 0.7084 (ptm) REVERT: M 171 LYS cc_start: 0.7511 (mttt) cc_final: 0.7269 (mttt) REVERT: N 98 LEU cc_start: 0.8259 (tp) cc_final: 0.8042 (tt) REVERT: N 172 VAL cc_start: 0.8660 (t) cc_final: 0.8399 (p) REVERT: N 240 HIS cc_start: 0.4217 (t70) cc_final: 0.3958 (t70) REVERT: O 21 TYR cc_start: 0.8786 (m-10) cc_final: 0.8377 (m-10) REVERT: O 77 THR cc_start: 0.8034 (m) cc_final: 0.7823 (p) REVERT: O 110 TYR cc_start: 0.6941 (t80) cc_final: 0.6574 (t80) REVERT: O 115 LYS cc_start: 0.8666 (mttt) cc_final: 0.8414 (mtmt) REVERT: O 136 PHE cc_start: 0.2896 (m-10) cc_final: 0.2003 (m-10) REVERT: O 141 THR cc_start: 0.5437 (m) cc_final: 0.4695 (p) REVERT: O 185 ASP cc_start: 0.7332 (m-30) cc_final: 0.6850 (p0) REVERT: P 53 ARG cc_start: 0.7658 (ttt90) cc_final: 0.7287 (ptm160) REVERT: P 67 ILE cc_start: 0.6607 (mt) cc_final: 0.6282 (mt) REVERT: P 161 THR cc_start: 0.8093 (t) cc_final: 0.7878 (p) REVERT: Q 70 ILE cc_start: 0.8535 (mt) cc_final: 0.7840 (mt) REVERT: Q 90 GLN cc_start: 0.8464 (tp40) cc_final: 0.7808 (tp-100) REVERT: Q 103 LEU cc_start: 0.8057 (tp) cc_final: 0.7515 (tp) REVERT: Q 137 TYR cc_start: 0.6613 (t80) cc_final: 0.6017 (t80) REVERT: Q 174 ARG cc_start: 0.7158 (mtt180) cc_final: 0.6920 (tpt90) REVERT: Q 237 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7138 (tm-30) REVERT: R 14 THR cc_start: 0.8975 (m) cc_final: 0.8520 (p) REVERT: R 141 TYR cc_start: 0.6774 (t80) cc_final: 0.6565 (t80) REVERT: R 168 LYS cc_start: 0.7260 (tttt) cc_final: 0.6021 (ptpt) REVERT: A 25 PHE cc_start: 0.7103 (t80) cc_final: 0.6491 (m-80) REVERT: A 31 PHE cc_start: 0.7088 (t80) cc_final: 0.6772 (t80) REVERT: A 39 LYS cc_start: 0.5695 (mmtt) cc_final: 0.5432 (mmmm) REVERT: A 40 ILE cc_start: 0.7404 (mt) cc_final: 0.6841 (pt) REVERT: A 58 THR cc_start: 0.5675 (p) cc_final: 0.4922 (p) REVERT: A 65 ASP cc_start: 0.2301 (m-30) cc_final: 0.1989 (p0) REVERT: A 112 TRP cc_start: 0.5822 (m100) cc_final: 0.5615 (m100) REVERT: A 120 LEU cc_start: 0.7766 (mt) cc_final: 0.7382 (mp) REVERT: A 157 VAL cc_start: 0.8151 (t) cc_final: 0.7687 (t) REVERT: A 186 ASP cc_start: 0.8018 (p0) cc_final: 0.7340 (t0) REVERT: A 192 HIS cc_start: 0.7416 (m170) cc_final: 0.7145 (m-70) REVERT: A 193 GLU cc_start: 0.8202 (tp30) cc_final: 0.7742 (mt-10) REVERT: A 203 ARG cc_start: 0.6173 (ttt90) cc_final: 0.5302 (ppt170) REVERT: A 217 TYR cc_start: 0.5421 (t80) cc_final: 0.5086 (t80) REVERT: A 221 SER cc_start: 0.6770 (t) cc_final: 0.6453 (m) REVERT: B 5 ARG cc_start: 0.5393 (mtt180) cc_final: 0.3798 (mmp-170) REVERT: B 105 ASN cc_start: 0.5682 (p0) cc_final: 0.5436 (p0) REVERT: B 107 ASN cc_start: 0.3847 (t0) cc_final: 0.2306 (t0) REVERT: B 109 LYS cc_start: 0.5890 (ttmt) cc_final: 0.5551 (mmtt) REVERT: B 138 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8316 (mm110) REVERT: B 174 ILE cc_start: 0.8213 (mt) cc_final: 0.7942 (pt) REVERT: B 192 PRO cc_start: 0.6960 (Cg_endo) cc_final: 0.6546 (Cg_exo) REVERT: C 14 VAL cc_start: 0.7825 (t) cc_final: 0.7612 (t) REVERT: C 33 PHE cc_start: 0.6315 (m-10) cc_final: 0.5352 (m-80) REVERT: C 49 LEU cc_start: 0.5304 (tp) cc_final: 0.5008 (tt) REVERT: C 108 GLU cc_start: 0.7505 (tt0) cc_final: 0.7246 (pp20) REVERT: C 114 LEU cc_start: 0.7482 (mt) cc_final: 0.6998 (mm) REVERT: C 117 LEU cc_start: 0.6161 (tp) cc_final: 0.5269 (tp) REVERT: C 121 ILE cc_start: 0.8754 (mt) cc_final: 0.8419 (mt) REVERT: C 138 GLN cc_start: 0.6852 (mm110) cc_final: 0.6262 (mt0) REVERT: C 160 MET cc_start: 0.9058 (mtm) cc_final: 0.8846 (mmt) REVERT: C 166 LYS cc_start: 0.5750 (mttt) cc_final: 0.5460 (ptmm) REVERT: C 211 ASP cc_start: 0.6512 (m-30) cc_final: 0.6083 (m-30) REVERT: C 218 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 219 ILE cc_start: 0.6913 (mt) cc_final: 0.6271 (mt) REVERT: D 7 VAL cc_start: 0.5395 (m) cc_final: 0.4738 (p) REVERT: D 40 ILE cc_start: 0.6790 (mt) cc_final: 0.6442 (mt) REVERT: D 57 LEU cc_start: 0.7207 (tp) cc_final: 0.6792 (tp) REVERT: D 153 VAL cc_start: 0.8934 (t) cc_final: 0.8498 (t) REVERT: D 163 THR cc_start: 0.8062 (m) cc_final: 0.7634 (p) REVERT: D 164 ILE cc_start: 0.8294 (mt) cc_final: 0.7784 (mm) REVERT: E 110 ILE cc_start: 0.7003 (mt) cc_final: 0.6303 (pt) REVERT: E 127 GLN cc_start: 0.6184 (mm-40) cc_final: 0.5965 (tp40) REVERT: E 132 THR cc_start: 0.7924 (m) cc_final: 0.7478 (p) REVERT: E 158 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8020 (tp30) REVERT: E 178 PHE cc_start: 0.5303 (m-10) cc_final: 0.4809 (m-80) REVERT: E 183 ASP cc_start: 0.8203 (m-30) cc_final: 0.7959 (t70) REVERT: E 223 TYR cc_start: 0.7375 (m-80) cc_final: 0.6958 (m-10) REVERT: F 8 ARG cc_start: 0.6465 (mtt-85) cc_final: 0.6195 (mmm160) REVERT: F 64 LEU cc_start: 0.4058 (mt) cc_final: 0.3825 (mt) REVERT: F 110 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6849 (tp30) REVERT: F 121 VAL cc_start: 0.6271 (t) cc_final: 0.5767 (t) REVERT: F 130 PRO cc_start: 0.6598 (Cg_endo) cc_final: 0.6169 (Cg_exo) REVERT: F 171 ARG cc_start: 0.5064 (mtp85) cc_final: 0.4406 (mmp80) REVERT: F 219 ILE cc_start: 0.8073 (mt) cc_final: 0.7599 (tp) REVERT: G 128 LEU cc_start: 0.8063 (mt) cc_final: 0.7671 (pp) REVERT: G 134 TRP cc_start: 0.7294 (t60) cc_final: 0.7009 (t60) REVERT: G 139 ILE cc_start: 0.5565 (mt) cc_final: 0.5351 (mt) REVERT: G 187 LYS cc_start: 0.6716 (mttt) cc_final: 0.6479 (mttt) REVERT: a 127 PHE cc_start: 0.8216 (m-10) cc_final: 0.7953 (m-10) REVERT: a 166 LYS cc_start: 0.7266 (mttt) cc_final: 0.6778 (tptm) REVERT: a 207 GLU cc_start: 0.6488 (tt0) cc_final: 0.6197 (tp30) REVERT: b 74 ILE cc_start: 0.7695 (mt) cc_final: 0.7144 (mt) REVERT: b 213 THR cc_start: 0.7502 (p) cc_final: 0.7288 (m) REVERT: c 23 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7542 (mm-30) REVERT: c 63 ILE cc_start: 0.7164 (mt) cc_final: 0.6909 (mt) REVERT: c 137 TYR cc_start: 0.6147 (t80) cc_final: 0.5761 (t80) REVERT: c 140 MET cc_start: 0.8669 (mtp) cc_final: 0.8305 (mtt) REVERT: c 185 ASN cc_start: 0.8789 (m-40) cc_final: 0.8426 (t0) REVERT: c 186 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7457 (mm-30) REVERT: c 228 ASP cc_start: 0.7221 (m-30) cc_final: 0.6962 (t0) REVERT: c 233 LEU cc_start: 0.8114 (mt) cc_final: 0.7452 (tp) REVERT: d 26 TYR cc_start: 0.7607 (m-10) cc_final: 0.7343 (m-10) REVERT: d 31 VAL cc_start: 0.5272 (t) cc_final: 0.4882 (t) REVERT: d 59 TYR cc_start: 0.7987 (m-80) cc_final: 0.7592 (m-10) REVERT: d 138 LEU cc_start: 0.7178 (mt) cc_final: 0.6839 (mt) REVERT: d 145 ASP cc_start: 0.8495 (m-30) cc_final: 0.8177 (m-30) REVERT: d 154 PRO cc_start: 0.5914 (Cg_exo) cc_final: 0.5507 (Cg_endo) REVERT: d 199 TYR cc_start: 0.5137 (m-10) cc_final: 0.4413 (m-80) REVERT: e 80 MET cc_start: 0.7994 (mmm) cc_final: 0.7576 (mmt) REVERT: e 101 TRP cc_start: 0.8864 (t-100) cc_final: 0.8099 (t-100) REVERT: e 196 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7581 (pt0) REVERT: f 124 SER cc_start: 0.8270 (t) cc_final: 0.7333 (t) REVERT: g 28 ILE cc_start: 0.9114 (pt) cc_final: 0.8853 (pt) REVERT: g 159 TRP cc_start: 0.8092 (m100) cc_final: 0.7883 (m-10) REVERT: H 71 LEU cc_start: 0.8814 (tp) cc_final: 0.8478 (tp) REVERT: H 129 CYS cc_start: 0.8405 (t) cc_final: 0.8098 (p) REVERT: H 146 MET cc_start: 0.7855 (mtm) cc_final: 0.7535 (mpp) REVERT: H 157 ASN cc_start: 0.7111 (m-40) cc_final: 0.6755 (p0) REVERT: H 168 SER cc_start: 0.8314 (p) cc_final: 0.8039 (p) REVERT: H 173 ASN cc_start: 0.7929 (m-40) cc_final: 0.7710 (m-40) REVERT: H 175 VAL cc_start: 0.8214 (t) cc_final: 0.7943 (p) REVERT: I 43 LEU cc_start: 0.7740 (tt) cc_final: 0.7493 (tp) REVERT: I 45 LEU cc_start: 0.8729 (mp) cc_final: 0.6661 (mp) REVERT: I 119 ASP cc_start: 0.7563 (p0) cc_final: 0.7358 (p0) REVERT: I 170 ARG cc_start: 0.8867 (tpp-160) cc_final: 0.8582 (mmm-85) REVERT: J 54 ASP cc_start: 0.7065 (p0) cc_final: 0.6441 (p0) REVERT: J 123 ILE cc_start: 0.9046 (mt) cc_final: 0.8363 (mt) REVERT: J 128 ARG cc_start: 0.9035 (tpt90) cc_final: 0.8753 (tpt170) REVERT: K 94 THR cc_start: 0.7021 (OUTLIER) cc_final: 0.6755 (t) REVERT: K 142 TYR cc_start: 0.7835 (t80) cc_final: 0.6862 (t80) REVERT: S 61 GLN cc_start: 0.7387 (mt0) cc_final: 0.7161 (mt0) REVERT: S 88 MET cc_start: 0.6835 (ttp) cc_final: 0.6624 (ttp) REVERT: S 89 SER cc_start: 0.9428 (p) cc_final: 0.9142 (p) REVERT: S 169 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7177 (mm-40) REVERT: S 181 SER cc_start: 0.8015 (m) cc_final: 0.7220 (t) REVERT: S 185 VAL cc_start: 0.5451 (t) cc_final: 0.4873 (t) REVERT: S 201 LYS cc_start: 0.7771 (tttt) cc_final: 0.7249 (tmtt) REVERT: U 129 PHE cc_start: 0.6677 (m-10) cc_final: 0.6013 (m-10) REVERT: U 239 ARG cc_start: 0.6391 (ptm160) cc_final: 0.6083 (ptm-80) REVERT: U 241 ASP cc_start: 0.5933 (p0) cc_final: 0.5598 (p0) REVERT: V 90 VAL cc_start: 0.7477 (t) cc_final: 0.6937 (t) REVERT: V 96 LEU cc_start: 0.8837 (tp) cc_final: 0.8355 (tp) REVERT: V 99 SER cc_start: 0.9265 (t) cc_final: 0.8945 (t) REVERT: V 192 GLN cc_start: 0.6897 (tt0) cc_final: 0.6570 (tm-30) REVERT: V 201 LYS cc_start: 0.5066 (mttt) cc_final: 0.4637 (tptt) REVERT: V 237 VAL cc_start: 0.8225 (t) cc_final: 0.7909 (t) REVERT: W 66 SER cc_start: 0.7531 (t) cc_final: 0.7307 (t) REVERT: W 88 MET cc_start: 0.8158 (mmm) cc_final: 0.7866 (tpp) REVERT: W 132 TYR cc_start: 0.6966 (m-80) cc_final: 0.5761 (m-80) REVERT: W 176 THR cc_start: 0.7995 (m) cc_final: 0.7414 (p) REVERT: W 177 ASN cc_start: 0.8013 (m-40) cc_final: 0.7784 (t0) REVERT: W 198 ILE cc_start: 0.6784 (mt) cc_final: 0.6379 (mp) REVERT: X 102 MET cc_start: 0.7858 (mmm) cc_final: 0.7564 (mmm) REVERT: X 104 LEU cc_start: 0.9114 (mt) cc_final: 0.8820 (mt) REVERT: X 178 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6243 (mm-30) REVERT: Y 84 VAL cc_start: 0.9312 (t) cc_final: 0.8876 (p) REVERT: Y 116 THR cc_start: 0.8117 (p) cc_final: 0.7414 (p) REVERT: Y 123 ASP cc_start: 0.7747 (m-30) cc_final: 0.7411 (m-30) REVERT: Y 138 TYR cc_start: 0.8646 (t80) cc_final: 0.8394 (t80) REVERT: Y 204 ASN cc_start: 0.8781 (p0) cc_final: 0.8420 (p0) REVERT: Z 163 LYS cc_start: 0.5382 (mttt) cc_final: 0.5082 (mttp) REVERT: Z 171 CYS cc_start: 0.7590 (m) cc_final: 0.7152 (t) REVERT: 1 215 CYS cc_start: 0.7018 (t) cc_final: 0.6782 (t) REVERT: 2 181 PRO cc_start: 0.4897 (Cg_endo) cc_final: 0.4620 (Cg_exo) outliers start: 8 outliers final: 2 residues processed: 3299 average time/residue: 0.6262 time to fit residues: 3353.0805 Evaluate side-chains 1863 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1860 time to evaluate : 5.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 632 optimal weight: 9.9990 chunk 567 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 382 optimal weight: 7.9990 chunk 303 optimal weight: 0.4980 chunk 587 optimal weight: 9.9990 chunk 227 optimal weight: 0.3980 chunk 356 optimal weight: 1.9990 chunk 436 optimal weight: 10.0000 chunk 680 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 140 ASN M 148 GLN M 179 ASN N 100 GLN ** N 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 GLN ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 205 ASN ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN P 99 HIS Q 143 HIS ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN D 136 ASN E 27 ASN E 164 HIS E 233 ASN F 218 HIS G 7 GLN G 115 GLN a 94 HIS ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN b 41 GLN b 99 HIS c 143 HIS d 144 ASN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 238 HIS g 102 GLN g 146 GLN H 7 ASN ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 71 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 ASN J 105 HIS J 107 ASN J 136 ASN J 179 ASN K 114 GLN K 126 HIS ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 207 GLN S 7 ASN S 65 GLN S 145 GLN S 173 ASN T 82 ASN ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 189 HIS T 193 ASN U 64 HIS U 107 ASN ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS W 82 GLN ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 177 ASN X 61 ASN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 HIS Y 269 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 82 HIS 2 142 ASN 2 206 HIS 2 234 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 61042 Z= 0.246 Angle : 0.696 10.715 82480 Z= 0.369 Chirality : 0.046 0.257 9289 Planarity : 0.005 0.086 10629 Dihedral : 4.819 53.152 8371 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.24 % Favored : 97.74 % Rotamer: Outliers : 0.16 % Allowed : 2.86 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % Twisted General : 0.01 % 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: -1.05 (0.09), residues: 7577 helix: -0.58 (0.08), residues: 3200 sheet: -0.32 (0.13), residues: 1361 loop : -0.80 (0.10), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 152 HIS 0.013 0.001 HIS e 238 PHE 0.051 0.002 PHE F 138 TYR 0.040 0.002 TYR S 96 ARG 0.009 0.001 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2330 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2320 time to evaluate : 5.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 29 PHE cc_start: 0.7730 (m-10) cc_final: 0.7482 (m-10) REVERT: L 30 LYS cc_start: 0.8924 (mttt) cc_final: 0.8704 (ttmm) REVERT: L 33 ASN cc_start: 0.7277 (t0) cc_final: 0.6817 (t0) REVERT: L 61 LEU cc_start: 0.7769 (mp) cc_final: 0.7553 (mp) REVERT: L 71 LYS cc_start: 0.8216 (mttm) cc_final: 0.7893 (mttm) REVERT: L 108 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7394 (tm-30) REVERT: L 109 ILE cc_start: 0.8931 (tt) cc_final: 0.7710 (tt) REVERT: L 123 GLN cc_start: 0.9230 (tp40) cc_final: 0.8309 (tp40) REVERT: M 38 ILE cc_start: 0.7191 (mm) cc_final: 0.6923 (mm) REVERT: M 63 HIS cc_start: 0.4422 (m-70) cc_final: 0.3282 (m170) REVERT: M 75 VAL cc_start: 0.8522 (m) cc_final: 0.8294 (m) REVERT: M 96 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7833 (tm-30) REVERT: M 188 ILE cc_start: 0.9048 (mt) cc_final: 0.8829 (mt) REVERT: N 33 THR cc_start: 0.7175 (p) cc_final: 0.6964 (p) REVERT: N 143 TYR cc_start: 0.7471 (m-80) cc_final: 0.6695 (m-80) REVERT: N 179 TYR cc_start: 0.6368 (t80) cc_final: 0.6039 (t80) REVERT: O 21 TYR cc_start: 0.8785 (m-10) cc_final: 0.8506 (m-10) REVERT: O 73 PHE cc_start: 0.7309 (p90) cc_final: 0.6914 (p90) REVERT: O 90 GLU cc_start: 0.8445 (tp30) cc_final: 0.8061 (tp30) REVERT: O 115 LYS cc_start: 0.8829 (mttt) cc_final: 0.8539 (mtmt) REVERT: O 116 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8344 (tm-30) REVERT: O 211 MET cc_start: 0.5416 (tmm) cc_final: 0.5141 (tmm) REVERT: P 35 SER cc_start: 0.5320 (t) cc_final: 0.5113 (p) REVERT: P 53 ARG cc_start: 0.7689 (ttt90) cc_final: 0.7122 (ptm160) REVERT: P 87 THR cc_start: 0.8662 (p) cc_final: 0.8320 (t) REVERT: P 156 MET cc_start: 0.6034 (tmm) cc_final: 0.5630 (tmm) REVERT: Q 90 GLN cc_start: 0.8281 (tp40) cc_final: 0.7835 (tp40) REVERT: Q 103 LEU cc_start: 0.8232 (tp) cc_final: 0.7906 (tp) REVERT: Q 117 GLN cc_start: 0.7972 (tm-30) cc_final: 0.7734 (tm-30) REVERT: Q 173 GLU cc_start: 0.6867 (pp20) cc_final: 0.5946 (tm-30) REVERT: Q 176 MET cc_start: 0.6682 (tmm) cc_final: 0.6052 (tmm) REVERT: Q 234 GLU cc_start: 0.5624 (mm-30) cc_final: 0.5375 (mm-30) REVERT: Q 237 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7016 (tm-30) REVERT: R 14 THR cc_start: 0.8933 (m) cc_final: 0.8654 (p) REVERT: R 22 PHE cc_start: 0.6919 (m-10) cc_final: 0.6709 (m-10) REVERT: R 66 ARG cc_start: 0.7415 (mtm180) cc_final: 0.7045 (tpp80) REVERT: R 135 SER cc_start: 0.9339 (t) cc_final: 0.8965 (p) REVERT: R 168 LYS cc_start: 0.7553 (tttt) cc_final: 0.6144 (ptpt) REVERT: R 175 THR cc_start: 0.7958 (p) cc_final: 0.6882 (p) REVERT: A 25 PHE cc_start: 0.7199 (t80) cc_final: 0.6625 (m-80) REVERT: A 26 GLN cc_start: 0.7324 (mt0) cc_final: 0.6383 (pp30) REVERT: A 40 ILE cc_start: 0.7172 (mt) cc_final: 0.6956 (pt) REVERT: A 112 TRP cc_start: 0.6148 (m100) cc_final: 0.5914 (m100) REVERT: A 185 MET cc_start: 0.7219 (mmp) cc_final: 0.6623 (mmm) REVERT: A 203 ARG cc_start: 0.6829 (ttt90) cc_final: 0.5854 (ppt170) REVERT: A 217 TYR cc_start: 0.5288 (t80) cc_final: 0.4962 (t80) REVERT: B 5 ARG cc_start: 0.5628 (mtt180) cc_final: 0.3832 (mmp-170) REVERT: B 28 LEU cc_start: 0.4254 (mt) cc_final: 0.3789 (mt) REVERT: B 35 LYS cc_start: 0.7805 (tttt) cc_final: 0.7461 (pttt) REVERT: B 109 LYS cc_start: 0.5946 (ttmt) cc_final: 0.5488 (mmtt) REVERT: B 138 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8212 (mm110) REVERT: B 170 PHE cc_start: 0.6947 (m-80) cc_final: 0.6529 (m-80) REVERT: B 174 ILE cc_start: 0.8534 (mt) cc_final: 0.8138 (pt) REVERT: B 192 PRO cc_start: 0.6241 (Cg_endo) cc_final: 0.5829 (Cg_exo) REVERT: B 215 MET cc_start: 0.6081 (mtm) cc_final: 0.4430 (tpt) REVERT: C 14 VAL cc_start: 0.7868 (t) cc_final: 0.7563 (t) REVERT: C 33 PHE cc_start: 0.5900 (m-10) cc_final: 0.5638 (m-80) REVERT: C 37 ILE cc_start: 0.5401 (pt) cc_final: 0.5135 (pt) REVERT: C 108 GLU cc_start: 0.7524 (tt0) cc_final: 0.7145 (pp20) REVERT: C 114 LEU cc_start: 0.7472 (mt) cc_final: 0.7172 (mm) REVERT: C 138 GLN cc_start: 0.6692 (mm110) cc_final: 0.6141 (mt0) REVERT: C 166 LYS cc_start: 0.5829 (mttt) cc_final: 0.5465 (ptmm) REVERT: C 174 ILE cc_start: 0.8173 (mt) cc_final: 0.7788 (mt) REVERT: C 227 TYR cc_start: 0.7044 (t80) cc_final: 0.6812 (t80) REVERT: C 233 ASN cc_start: 0.7305 (m-40) cc_final: 0.6737 (p0) REVERT: D 20 PHE cc_start: 0.6267 (m-10) cc_final: 0.6054 (m-80) REVERT: D 21 ARG cc_start: 0.7371 (ptm-80) cc_final: 0.6852 (ptm160) REVERT: D 227 ILE cc_start: 0.7521 (tp) cc_final: 0.7242 (tp) REVERT: E 127 GLN cc_start: 0.6037 (mm-40) cc_final: 0.5809 (tp40) REVERT: E 132 THR cc_start: 0.7672 (m) cc_final: 0.7270 (p) REVERT: E 136 GLN cc_start: 0.7034 (mt0) cc_final: 0.6437 (mt0) REVERT: E 228 ASP cc_start: 0.8128 (m-30) cc_final: 0.7873 (m-30) REVERT: E 241 ARG cc_start: 0.6473 (ptp-110) cc_final: 0.6227 (ptp-110) REVERT: F 32 LEU cc_start: 0.7457 (mt) cc_final: 0.7141 (tp) REVERT: F 122 ILE cc_start: 0.6375 (mm) cc_final: 0.6130 (mm) REVERT: F 124 TRP cc_start: 0.5672 (t60) cc_final: 0.5400 (t60) REVERT: F 130 PRO cc_start: 0.6696 (Cg_endo) cc_final: 0.6202 (Cg_exo) REVERT: F 171 ARG cc_start: 0.5304 (mtp85) cc_final: 0.4467 (mmp80) REVERT: F 219 ILE cc_start: 0.8198 (mt) cc_final: 0.7903 (tp) REVERT: G 40 LEU cc_start: 0.7468 (mt) cc_final: 0.7242 (mp) REVERT: G 138 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6447 (mm110) REVERT: G 163 LEU cc_start: 0.8549 (tp) cc_final: 0.8129 (mt) REVERT: G 164 HIS cc_start: 0.7395 (m170) cc_final: 0.7128 (m-70) REVERT: G 168 GLU cc_start: 0.6948 (mp0) cc_final: 0.6563 (mp0) REVERT: G 183 ASP cc_start: 0.6691 (m-30) cc_final: 0.6374 (m-30) REVERT: G 199 GLN cc_start: 0.7733 (pt0) cc_final: 0.7487 (pt0) REVERT: G 214 LEU cc_start: 0.6572 (mp) cc_final: 0.6190 (pp) REVERT: a 65 LEU cc_start: 0.8402 (mp) cc_final: 0.8163 (mp) REVERT: a 102 VAL cc_start: 0.8876 (t) cc_final: 0.8621 (t) REVERT: a 127 PHE cc_start: 0.8607 (m-10) cc_final: 0.8136 (m-10) REVERT: a 143 ARG cc_start: 0.6927 (mmm160) cc_final: 0.6366 (mmm160) REVERT: a 196 LEU cc_start: 0.7525 (mt) cc_final: 0.7231 (mt) REVERT: b 73 HIS cc_start: 0.6319 (p90) cc_final: 0.6000 (p90) REVERT: b 74 ILE cc_start: 0.7081 (mt) cc_final: 0.6572 (mt) REVERT: b 103 TYR cc_start: 0.8423 (m-80) cc_final: 0.8194 (m-80) REVERT: b 147 ASP cc_start: 0.4661 (m-30) cc_final: 0.4237 (m-30) REVERT: c 23 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7760 (mt-10) REVERT: c 31 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7443 (tp40) REVERT: c 137 TYR cc_start: 0.6447 (t80) cc_final: 0.6130 (t80) REVERT: c 164 ARG cc_start: 0.5998 (ptm160) cc_final: 0.4178 (ptt180) REVERT: c 185 ASN cc_start: 0.8335 (m-40) cc_final: 0.7795 (t0) REVERT: c 186 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7700 (mm-30) REVERT: d 8 TYR cc_start: 0.8427 (m-80) cc_final: 0.8184 (m-80) REVERT: d 38 ILE cc_start: 0.6560 (pt) cc_final: 0.6356 (pt) REVERT: d 59 TYR cc_start: 0.8128 (m-80) cc_final: 0.7637 (m-10) REVERT: d 145 ASP cc_start: 0.8442 (m-30) cc_final: 0.8222 (m-30) REVERT: e 101 TRP cc_start: 0.8496 (t-100) cc_final: 0.8101 (t-100) REVERT: e 138 MET cc_start: 0.8215 (tmm) cc_final: 0.7966 (tmm) REVERT: f 136 ILE cc_start: 0.8838 (mt) cc_final: 0.8602 (mt) REVERT: f 147 PHE cc_start: 0.8540 (m-10) cc_final: 0.8284 (m-10) REVERT: g 108 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7579 (mm-30) REVERT: g 148 TYR cc_start: 0.7305 (m-10) cc_final: 0.7035 (m-80) REVERT: g 159 TRP cc_start: 0.7714 (m100) cc_final: 0.7304 (m-10) REVERT: g 213 ILE cc_start: 0.8624 (mt) cc_final: 0.8419 (mt) REVERT: g 239 LYS cc_start: 0.6302 (tttt) cc_final: 0.6082 (mmtt) REVERT: H 69 PHE cc_start: 0.8856 (t80) cc_final: 0.8489 (t80) REVERT: H 90 MET cc_start: 0.8979 (mmm) cc_final: 0.8742 (tpt) REVERT: H 144 GLU cc_start: 0.8559 (mp0) cc_final: 0.7999 (mp0) REVERT: H 149 MET cc_start: 0.7050 (tpp) cc_final: 0.6698 (tpp) REVERT: H 155 GLU cc_start: 0.6860 (tt0) cc_final: 0.6636 (tt0) REVERT: H 157 ASN cc_start: 0.7207 (m-40) cc_final: 0.6976 (p0) REVERT: H 161 GLU cc_start: 0.6949 (mp0) cc_final: 0.6649 (mp0) REVERT: H 178 ASP cc_start: 0.7777 (t0) cc_final: 0.7503 (t0) REVERT: H 204 MET cc_start: 0.4847 (mmm) cc_final: 0.4411 (mmm) REVERT: I 43 LEU cc_start: 0.7951 (tt) cc_final: 0.7280 (tp) REVERT: I 55 GLN cc_start: 0.8432 (tt0) cc_final: 0.8230 (tt0) REVERT: I 85 ARG cc_start: 0.8956 (ttp80) cc_final: 0.8695 (ttp80) REVERT: I 103 LEU cc_start: 0.9125 (mt) cc_final: 0.8785 (mt) REVERT: J 32 PRO cc_start: 0.7611 (Cg_endo) cc_final: 0.7268 (Cg_exo) REVERT: J 54 ASP cc_start: 0.7039 (p0) cc_final: 0.6467 (p0) REVERT: J 153 ASP cc_start: 0.8282 (p0) cc_final: 0.7752 (p0) REVERT: K 71 MET cc_start: 0.6004 (mtt) cc_final: 0.5775 (mmm) REVERT: K 95 MET cc_start: 0.8147 (tmm) cc_final: 0.7944 (tmm) REVERT: K 142 TYR cc_start: 0.8217 (t80) cc_final: 0.7070 (t80) REVERT: K 233 GLN cc_start: 0.7121 (mt0) cc_final: 0.6707 (mt0) REVERT: S 12 MET cc_start: 0.6916 (ttm) cc_final: 0.6614 (ttt) REVERT: S 61 GLN cc_start: 0.7723 (mt0) cc_final: 0.7397 (mt0) REVERT: S 88 MET cc_start: 0.6854 (ttp) cc_final: 0.6620 (ttp) REVERT: S 145 GLN cc_start: 0.7621 (mt0) cc_final: 0.7218 (mp10) REVERT: S 201 LYS cc_start: 0.7660 (tttt) cc_final: 0.7336 (tmtt) REVERT: T 52 ASP cc_start: 0.7904 (m-30) cc_final: 0.7619 (m-30) REVERT: T 65 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7124 (mp10) REVERT: T 85 ARG cc_start: 0.7600 (tmm160) cc_final: 0.7273 (tmm-80) REVERT: T 99 HIS cc_start: 0.7339 (m-70) cc_final: 0.7086 (t-170) REVERT: T 140 LEU cc_start: 0.8072 (mt) cc_final: 0.7856 (mt) REVERT: T 168 GLN cc_start: 0.7286 (tt0) cc_final: 0.6746 (tp-100) REVERT: T 183 ILE cc_start: 0.7549 (tp) cc_final: 0.7139 (mm) REVERT: U 103 TYR cc_start: 0.5758 (t80) cc_final: 0.5492 (t80) REVERT: U 105 HIS cc_start: 0.7851 (m-70) cc_final: 0.7553 (m170) REVERT: U 129 PHE cc_start: 0.6423 (m-10) cc_final: 0.6083 (m-10) REVERT: U 130 PHE cc_start: 0.6090 (t80) cc_final: 0.5837 (t80) REVERT: U 238 LEU cc_start: 0.6834 (mt) cc_final: 0.6606 (mt) REVERT: V 57 LEU cc_start: 0.8406 (mt) cc_final: 0.8147 (mt) REVERT: V 117 ILE cc_start: 0.7825 (mm) cc_final: 0.7563 (mm) REVERT: V 201 LYS cc_start: 0.4916 (mttt) cc_final: 0.4427 (tptt) REVERT: V 217 CYS cc_start: 0.8430 (m) cc_final: 0.8001 (m) REVERT: W 21 THR cc_start: 0.7952 (m) cc_final: 0.7507 (p) REVERT: W 105 ASN cc_start: 0.8633 (t0) cc_final: 0.8379 (t0) REVERT: W 198 ILE cc_start: 0.6797 (mt) cc_final: 0.6592 (mm) REVERT: X 58 ARG cc_start: 0.8534 (ttm170) cc_final: 0.8331 (ttm110) REVERT: X 93 MET cc_start: 0.7062 (mmp) cc_final: 0.6771 (mmm) REVERT: Y 84 VAL cc_start: 0.9214 (t) cc_final: 0.8901 (p) REVERT: Y 153 LYS cc_start: 0.8289 (tttt) cc_final: 0.7548 (tppt) REVERT: Y 160 CYS cc_start: 0.6283 (p) cc_final: 0.5975 (p) REVERT: Y 162 TYR cc_start: 0.6916 (m-80) cc_final: 0.6581 (m-80) REVERT: Y 260 GLU cc_start: 0.7520 (pp20) cc_final: 0.6671 (pm20) REVERT: Y 262 THR cc_start: 0.9004 (p) cc_final: 0.8677 (p) REVERT: Z 109 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8681 (ttpt) REVERT: Z 171 CYS cc_start: 0.7837 (m) cc_final: 0.6742 (t) REVERT: Z 183 MET cc_start: 0.7981 (mtp) cc_final: 0.7333 (mtp) REVERT: Z 206 ARG cc_start: 0.6925 (tmm-80) cc_final: 0.6400 (tmm-80) REVERT: 1 53 LEU cc_start: 0.8315 (mt) cc_final: 0.8101 (mt) REVERT: 1 73 ILE cc_start: 0.8476 (pt) cc_final: 0.8275 (pt) REVERT: 1 95 THR cc_start: 0.8815 (p) cc_final: 0.8581 (p) REVERT: 1 97 MET cc_start: 0.7652 (tmm) cc_final: 0.7319 (tmm) REVERT: 1 102 MET cc_start: 0.8069 (tpp) cc_final: 0.7483 (tpp) REVERT: 1 113 CYS cc_start: 0.5745 (m) cc_final: 0.4981 (m) REVERT: 1 115 VAL cc_start: 0.8761 (t) cc_final: 0.7608 (t) REVERT: 1 185 MET cc_start: 0.5221 (ptp) cc_final: 0.4761 (ptp) REVERT: 2 76 LEU cc_start: 0.7691 (pp) cc_final: 0.7442 (pp) REVERT: 2 93 SER cc_start: 0.8962 (p) cc_final: 0.8741 (p) REVERT: 2 260 GLU cc_start: 0.7084 (pp20) cc_final: 0.6879 (pp20) outliers start: 10 outliers final: 2 residues processed: 2324 average time/residue: 0.6114 time to fit residues: 2374.2797 Evaluate side-chains 1701 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1699 time to evaluate : 5.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 378 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 566 optimal weight: 0.8980 chunk 463 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 681 optimal weight: 5.9990 chunk 736 optimal weight: 8.9990 chunk 606 optimal weight: 1.9990 chunk 675 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 102 GLN M 140 ASN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 18 GLN ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** O 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 154 HIS O 175 ASN O 205 ASN ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 227 HIS Q 190 HIS ** R 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 GLN B 153 GLN C 7 GLN D 53 ASN D 143 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 192 HIS ** G 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 120 GLN ** b 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN d 144 ASN e 24 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 172 GLN f 140 ASN f 189 HIS g 30 HIS g 119 GLN g 146 GLN H 188 HIS ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 185 ASN K 47 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN S 169 GLN T 63 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 168 GLN T 193 ASN U 64 HIS ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 191 HIS V 230 ASN V 258 HIS ** W 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 124 GLN X 253 GLN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 HIS 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 82 HIS 2 142 ASN 2 157 ASN 2 269 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.123 61042 Z= 0.453 Angle : 0.865 16.407 82480 Z= 0.453 Chirality : 0.051 0.247 9289 Planarity : 0.006 0.092 10629 Dihedral : 5.452 36.534 8371 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.74 % 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: -0.89 (0.09), residues: 7577 helix: -0.22 (0.08), residues: 3241 sheet: -0.35 (0.13), residues: 1418 loop : -0.96 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP d 216 HIS 0.015 0.002 HIS F 127 PHE 0.035 0.003 PHE F 138 TYR 0.034 0.003 TYR S 96 ARG 0.025 0.001 ARG X 123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2092 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2085 time to evaluate : 5.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 LYS cc_start: 0.9037 (mttt) cc_final: 0.8667 (ttmm) REVERT: L 33 ASN cc_start: 0.7613 (t0) cc_final: 0.7035 (t0) REVERT: M 44 VAL cc_start: 0.9012 (t) cc_final: 0.8516 (p) REVERT: M 63 HIS cc_start: 0.4539 (m-70) cc_final: 0.3759 (m170) REVERT: M 64 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7369 (mmmt) REVERT: M 137 CYS cc_start: 0.6355 (t) cc_final: 0.5984 (t) REVERT: M 188 ILE cc_start: 0.9155 (mt) cc_final: 0.8859 (mt) REVERT: N 153 SER cc_start: 0.8287 (p) cc_final: 0.7631 (t) REVERT: N 237 ILE cc_start: 0.5531 (mt) cc_final: 0.5049 (mm) REVERT: O 54 GLN cc_start: 0.7557 (pt0) cc_final: 0.7171 (pt0) REVERT: O 71 MET cc_start: 0.8151 (ppp) cc_final: 0.7855 (ppp) REVERT: O 73 PHE cc_start: 0.8013 (p90) cc_final: 0.7592 (p90) REVERT: O 79 ASP cc_start: 0.8154 (m-30) cc_final: 0.7897 (m-30) REVERT: O 90 GLU cc_start: 0.8659 (tp30) cc_final: 0.7974 (tp30) REVERT: O 99 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7086 (tp30) REVERT: O 115 LYS cc_start: 0.9092 (mttt) cc_final: 0.8672 (mtmm) REVERT: O 153 TYR cc_start: 0.8680 (p90) cc_final: 0.8297 (p90) REVERT: O 156 TRP cc_start: 0.7844 (m100) cc_final: 0.7407 (m-10) REVERT: O 211 MET cc_start: 0.6352 (tmm) cc_final: 0.6087 (tmm) REVERT: P 53 ARG cc_start: 0.7416 (ttt90) cc_final: 0.6999 (ptm160) REVERT: P 87 THR cc_start: 0.8638 (p) cc_final: 0.8101 (p) REVERT: P 118 ASN cc_start: 0.8613 (t0) cc_final: 0.7804 (t0) REVERT: P 156 MET cc_start: 0.6833 (tmm) cc_final: 0.6579 (tmm) REVERT: Q 16 GLN cc_start: 0.9337 (mp-120) cc_final: 0.9014 (mp10) REVERT: Q 112 ILE cc_start: 0.8639 (pt) cc_final: 0.8177 (pt) REVERT: Q 117 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8130 (tm-30) REVERT: Q 173 GLU cc_start: 0.6785 (pp20) cc_final: 0.6020 (tm-30) REVERT: Q 176 MET cc_start: 0.6687 (tmm) cc_final: 0.6434 (tmm) REVERT: Q 198 THR cc_start: 0.8229 (p) cc_final: 0.7690 (p) REVERT: Q 229 VAL cc_start: 0.7527 (t) cc_final: 0.7227 (m) REVERT: R 14 THR cc_start: 0.8937 (m) cc_final: 0.8495 (p) REVERT: R 123 TYR cc_start: 0.8264 (m-10) cc_final: 0.8046 (m-10) REVERT: R 148 GLN cc_start: 0.7489 (tt0) cc_final: 0.7060 (tt0) REVERT: R 157 VAL cc_start: 0.8803 (t) cc_final: 0.8567 (t) REVERT: R 168 LYS cc_start: 0.7475 (tttt) cc_final: 0.6327 (ptpt) REVERT: R 206 LYS cc_start: 0.4125 (tttt) cc_final: 0.3874 (tptt) REVERT: R 212 LEU cc_start: 0.8118 (pp) cc_final: 0.7886 (pp) REVERT: A 9 LEU cc_start: 0.5990 (pt) cc_final: 0.5098 (mp) REVERT: A 25 PHE cc_start: 0.7594 (t80) cc_final: 0.7006 (m-80) REVERT: A 26 GLN cc_start: 0.7298 (mt0) cc_final: 0.6357 (pp30) REVERT: A 40 ILE cc_start: 0.6912 (mt) cc_final: 0.6344 (pt) REVERT: A 128 LEU cc_start: 0.8494 (mt) cc_final: 0.8122 (mt) REVERT: A 185 MET cc_start: 0.7390 (mmp) cc_final: 0.7044 (mmm) REVERT: A 203 ARG cc_start: 0.6940 (ttt90) cc_final: 0.5738 (ppt170) REVERT: B 5 ARG cc_start: 0.6026 (mtt180) cc_final: 0.4089 (mmp-170) REVERT: B 109 LYS cc_start: 0.5878 (ttmt) cc_final: 0.5390 (mmtt) REVERT: B 168 GLU cc_start: 0.7638 (pt0) cc_final: 0.7436 (pt0) REVERT: B 174 ILE cc_start: 0.8233 (mt) cc_final: 0.8016 (pt) REVERT: B 192 PRO cc_start: 0.6128 (Cg_endo) cc_final: 0.5742 (Cg_exo) REVERT: C 108 GLU cc_start: 0.7389 (tt0) cc_final: 0.6456 (pm20) REVERT: C 233 ASN cc_start: 0.7226 (m-40) cc_final: 0.6648 (p0) REVERT: D 20 PHE cc_start: 0.6217 (m-10) cc_final: 0.5870 (m-80) REVERT: E 127 GLN cc_start: 0.6605 (mm-40) cc_final: 0.6173 (tp40) REVERT: E 132 THR cc_start: 0.8397 (m) cc_final: 0.8052 (m) REVERT: E 136 GLN cc_start: 0.7355 (mt0) cc_final: 0.6803 (mt0) REVERT: F 48 GLN cc_start: 0.6103 (mm110) cc_final: 0.5896 (mm110) REVERT: F 124 TRP cc_start: 0.5816 (t60) cc_final: 0.5608 (t60) REVERT: F 133 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6918 (pt0) REVERT: F 171 ARG cc_start: 0.6050 (mtp85) cc_final: 0.5191 (mmp80) REVERT: F 191 VAL cc_start: 0.6377 (m) cc_final: 0.5805 (m) REVERT: F 194 ARG cc_start: 0.7117 (mmp80) cc_final: 0.6849 (mmp80) REVERT: F 203 ARG cc_start: 0.5266 (ptm160) cc_final: 0.5048 (ptm160) REVERT: G 40 LEU cc_start: 0.7384 (mt) cc_final: 0.7022 (mt) REVERT: a 102 VAL cc_start: 0.8856 (t) cc_final: 0.8485 (t) REVERT: a 143 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6713 (mmm160) REVERT: a 196 LEU cc_start: 0.7290 (mt) cc_final: 0.6864 (mt) REVERT: a 207 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6198 (tm-30) REVERT: b 73 HIS cc_start: 0.7057 (p90) cc_final: 0.6799 (p90) REVERT: b 134 SER cc_start: 0.9357 (p) cc_final: 0.8918 (p) REVERT: b 147 ASP cc_start: 0.5726 (m-30) cc_final: 0.5087 (m-30) REVERT: b 156 MET cc_start: 0.7485 (ttm) cc_final: 0.6895 (ttm) REVERT: b 227 HIS cc_start: 0.6676 (t-90) cc_final: 0.6292 (t-90) REVERT: c 26 MET cc_start: 0.7096 (mmt) cc_final: 0.6327 (mmt) REVERT: c 31 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7438 (mm-40) REVERT: c 51 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7844 (tpm170) REVERT: c 88 MET cc_start: 0.8236 (mmt) cc_final: 0.7796 (mmt) REVERT: c 164 ARG cc_start: 0.6270 (ptm160) cc_final: 0.4748 (ptt180) REVERT: c 180 MET cc_start: 0.7012 (mmp) cc_final: 0.6763 (mmp) REVERT: c 185 ASN cc_start: 0.8409 (m-40) cc_final: 0.7829 (t0) REVERT: c 186 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7725 (mm-30) REVERT: d 31 VAL cc_start: 0.7020 (t) cc_final: 0.6740 (t) REVERT: d 59 TYR cc_start: 0.8377 (m-80) cc_final: 0.7691 (m-80) REVERT: d 145 ASP cc_start: 0.8393 (m-30) cc_final: 0.8158 (m-30) REVERT: d 185 MET cc_start: 0.5971 (ptp) cc_final: 0.5534 (ptm) REVERT: e 71 LYS cc_start: 0.8592 (tttt) cc_final: 0.8231 (tttt) REVERT: e 101 TRP cc_start: 0.8836 (t-100) cc_final: 0.8290 (t-100) REVERT: e 121 ILE cc_start: 0.9486 (mt) cc_final: 0.9104 (mt) REVERT: e 138 MET cc_start: 0.8531 (tmm) cc_final: 0.8307 (tmm) REVERT: e 227 PHE cc_start: 0.8895 (t80) cc_final: 0.8660 (t80) REVERT: e 229 ILE cc_start: 0.7594 (mm) cc_final: 0.7151 (mp) REVERT: f 44 VAL cc_start: 0.9166 (t) cc_final: 0.8713 (p) REVERT: f 136 ILE cc_start: 0.9356 (mt) cc_final: 0.9096 (mt) REVERT: f 173 PHE cc_start: 0.7627 (m-10) cc_final: 0.7212 (m-80) REVERT: f 177 ARG cc_start: 0.7615 (ptp-170) cc_final: 0.6839 (tpp80) REVERT: g 72 MET cc_start: 0.7777 (mtt) cc_final: 0.7524 (mtt) REVERT: g 108 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8002 (mm-30) REVERT: g 159 TRP cc_start: 0.8040 (m100) cc_final: 0.7586 (m100) REVERT: H 34 MET cc_start: 0.8220 (ttt) cc_final: 0.7790 (ttp) REVERT: H 69 PHE cc_start: 0.9145 (t80) cc_final: 0.8739 (t80) REVERT: H 71 LEU cc_start: 0.9328 (tp) cc_final: 0.9047 (tp) REVERT: H 90 MET cc_start: 0.9101 (mmm) cc_final: 0.8856 (tpt) REVERT: H 120 PHE cc_start: 0.8565 (t80) cc_final: 0.8356 (t80) REVERT: H 136 PHE cc_start: 0.8416 (p90) cc_final: 0.8128 (p90) REVERT: H 144 GLU cc_start: 0.8699 (mp0) cc_final: 0.8461 (mp0) REVERT: H 149 MET cc_start: 0.7289 (tpp) cc_final: 0.6970 (tpp) REVERT: H 153 LEU cc_start: 0.8356 (mt) cc_final: 0.7916 (mt) REVERT: H 159 ASP cc_start: 0.6741 (p0) cc_final: 0.6215 (p0) REVERT: H 161 GLU cc_start: 0.7207 (mp0) cc_final: 0.6788 (mp0) REVERT: H 162 HIS cc_start: 0.7961 (m-70) cc_final: 0.7676 (m90) REVERT: H 169 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7695 (tm-30) REVERT: I 43 LEU cc_start: 0.8139 (tt) cc_final: 0.7468 (tp) REVERT: I 78 THR cc_start: 0.8867 (p) cc_final: 0.8480 (t) REVERT: I 85 ARG cc_start: 0.8989 (ttp80) cc_final: 0.8344 (ttt-90) REVERT: I 91 TYR cc_start: 0.7847 (m-80) cc_final: 0.7455 (m-80) REVERT: I 196 PHE cc_start: 0.6474 (m-10) cc_final: 0.6251 (m-10) REVERT: J 88 ASP cc_start: 0.7423 (m-30) cc_final: 0.6962 (m-30) REVERT: J 93 THR cc_start: 0.9056 (m) cc_final: 0.8810 (m) REVERT: J 172 MET cc_start: 0.8644 (mpp) cc_final: 0.8314 (mpp) REVERT: J 184 LYS cc_start: 0.4953 (mmtt) cc_final: 0.3941 (ttmt) REVERT: K 67 ILE cc_start: 0.8051 (mt) cc_final: 0.7736 (mt) REVERT: K 95 MET cc_start: 0.8568 (tmm) cc_final: 0.8215 (tmm) REVERT: K 258 HIS cc_start: 0.6626 (m-70) cc_final: 0.5879 (t-90) REVERT: S 67 LEU cc_start: 0.9264 (tp) cc_final: 0.9052 (tp) REVERT: S 145 GLN cc_start: 0.7941 (mt0) cc_final: 0.7577 (mp10) REVERT: S 172 LEU cc_start: 0.8455 (mt) cc_final: 0.8189 (mt) REVERT: S 173 ASN cc_start: 0.8861 (m110) cc_final: 0.8491 (m110) REVERT: S 183 MET cc_start: 0.7768 (mpp) cc_final: 0.7502 (mpp) REVERT: S 198 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6454 (mtm180) REVERT: T 52 ASP cc_start: 0.8018 (m-30) cc_final: 0.7804 (m-30) REVERT: T 65 GLN cc_start: 0.7873 (mm-40) cc_final: 0.7497 (mp10) REVERT: T 102 LEU cc_start: 0.8989 (pp) cc_final: 0.8766 (pp) REVERT: T 140 LEU cc_start: 0.8476 (mt) cc_final: 0.8114 (mt) REVERT: T 168 GLN cc_start: 0.8060 (tt0) cc_final: 0.7549 (tp-100) REVERT: T 171 PHE cc_start: 0.9050 (t80) cc_final: 0.8826 (t80) REVERT: U 120 LEU cc_start: 0.8792 (tp) cc_final: 0.8518 (tp) REVERT: U 129 PHE cc_start: 0.6879 (m-10) cc_final: 0.6548 (m-10) REVERT: V 201 LYS cc_start: 0.5801 (mttt) cc_final: 0.4994 (tptt) REVERT: W 21 THR cc_start: 0.8768 (m) cc_final: 0.8414 (p) REVERT: W 23 ILE cc_start: 0.9353 (pt) cc_final: 0.9007 (pt) REVERT: W 71 ASP cc_start: 0.8322 (t0) cc_final: 0.7930 (t0) REVERT: W 88 MET cc_start: 0.8816 (tpp) cc_final: 0.8286 (tpp) REVERT: W 89 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8517 (mm-30) REVERT: W 101 ASN cc_start: 0.7924 (t0) cc_final: 0.7278 (t0) REVERT: X 127 PHE cc_start: 0.7756 (t80) cc_final: 0.7432 (t80) REVERT: X 185 MET cc_start: 0.6203 (tpp) cc_final: 0.5870 (tpp) REVERT: Y 153 LYS cc_start: 0.8651 (tttt) cc_final: 0.7970 (tppt) REVERT: Y 176 TRP cc_start: 0.7458 (t-100) cc_final: 0.7258 (t60) REVERT: Y 187 ASP cc_start: 0.8600 (t70) cc_final: 0.8375 (t70) REVERT: Y 189 ASN cc_start: 0.8052 (m-40) cc_final: 0.7654 (m-40) REVERT: Y 211 MET cc_start: 0.7984 (ptp) cc_final: 0.7752 (ptp) REVERT: Y 212 ASP cc_start: 0.8660 (t70) cc_final: 0.8399 (t0) REVERT: Y 239 ASP cc_start: 0.9275 (t0) cc_final: 0.9039 (t0) REVERT: Y 248 MET cc_start: 0.7158 (ttm) cc_final: 0.6775 (ttm) REVERT: Y 260 GLU cc_start: 0.7676 (pp20) cc_final: 0.6898 (pm20) REVERT: Z 57 LEU cc_start: 0.7423 (mt) cc_final: 0.6681 (mt) REVERT: Z 106 ILE cc_start: 0.9061 (mt) cc_final: 0.8801 (mp) REVERT: Z 109 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8772 (mtpt) REVERT: 1 90 ASP cc_start: 0.8497 (m-30) cc_final: 0.8081 (m-30) REVERT: 1 96 ARG cc_start: 0.8394 (ptp-170) cc_final: 0.8179 (ptp-170) REVERT: 1 102 MET cc_start: 0.8338 (tpp) cc_final: 0.7495 (tpp) REVERT: 1 113 CYS cc_start: 0.6606 (m) cc_final: 0.5954 (m) REVERT: 1 185 MET cc_start: 0.6448 (ptp) cc_final: 0.6004 (ptp) REVERT: 1 224 MET cc_start: 0.7665 (ttt) cc_final: 0.7358 (tmm) REVERT: 2 189 ASN cc_start: 0.7949 (p0) cc_final: 0.7401 (p0) REVERT: 2 200 THR cc_start: 0.8903 (t) cc_final: 0.8676 (t) REVERT: 2 256 TRP cc_start: 0.6401 (p-90) cc_final: 0.5963 (p-90) REVERT: 2 260 GLU cc_start: 0.8338 (pp20) cc_final: 0.7903 (pp20) outliers start: 7 outliers final: 1 residues processed: 2090 average time/residue: 0.5820 time to fit residues: 2014.2532 Evaluate side-chains 1581 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1580 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 673 optimal weight: 1.9990 chunk 512 optimal weight: 1.9990 chunk 353 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 325 optimal weight: 0.3980 chunk 457 optimal weight: 0.9990 chunk 683 optimal weight: 2.9990 chunk 723 optimal weight: 2.9990 chunk 357 optimal weight: 4.9990 chunk 648 optimal weight: 7.9990 chunk 195 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN ** M 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 HIS ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 94 HIS O 120 GLN ** P 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 73 HIS P 227 HIS ** Q 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 143 HIS Q 190 HIS ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 191 GLN C 153 GLN ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS a 23 GLN ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 121 GLN ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 189 HIS g 30 HIS g 119 GLN H 7 ASN I 63 ASN I 71 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 162 HIS ** S 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 233 GLN V 258 HIS W 101 ASN W 142 GLN ** Y 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 86 HIS 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 157 ASN 2 269 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.6928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 61042 Z= 0.219 Angle : 0.669 12.409 82480 Z= 0.347 Chirality : 0.045 0.256 9289 Planarity : 0.005 0.062 10629 Dihedral : 5.055 38.087 8371 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer: Outliers : 0.12 % Allowed : 2.92 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -0.41 (0.09), residues: 7577 helix: 0.29 (0.09), residues: 3220 sheet: -0.17 (0.13), residues: 1381 loop : -0.81 (0.11), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP d 216 HIS 0.009 0.001 HIS Q 69 PHE 0.035 0.002 PHE F 138 TYR 0.033 0.002 TYR E 177 ARG 0.010 0.001 ARG N 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2055 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2047 time to evaluate : 6.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 26 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7426 (mt-10) REVERT: L 30 LYS cc_start: 0.9000 (mttt) cc_final: 0.8515 (ttmm) REVERT: L 33 ASN cc_start: 0.7289 (t0) cc_final: 0.6874 (t0) REVERT: L 123 GLN cc_start: 0.9256 (tp40) cc_final: 0.8587 (tp40) REVERT: L 124 VAL cc_start: 0.8982 (t) cc_final: 0.8741 (p) REVERT: M 63 HIS cc_start: 0.4413 (m-70) cc_final: 0.3789 (m170) REVERT: M 64 LYS cc_start: 0.7806 (mmmt) cc_final: 0.7228 (mmmt) REVERT: M 89 ARG cc_start: 0.8134 (mtp85) cc_final: 0.7880 (mtp85) REVERT: M 136 ILE cc_start: 0.8409 (mm) cc_final: 0.8133 (mm) REVERT: N 110 LEU cc_start: 0.8904 (pp) cc_final: 0.8517 (tp) REVERT: N 124 PHE cc_start: 0.7022 (p90) cc_final: 0.6742 (p90) REVERT: N 153 SER cc_start: 0.8204 (p) cc_final: 0.7470 (t) REVERT: N 216 LEU cc_start: 0.7484 (tp) cc_final: 0.7132 (tp) REVERT: O 73 PHE cc_start: 0.7967 (p90) cc_final: 0.7501 (p90) REVERT: O 90 GLU cc_start: 0.8292 (tp30) cc_final: 0.7960 (tp30) REVERT: O 148 ASP cc_start: 0.7578 (t0) cc_final: 0.7206 (m-30) REVERT: O 153 TYR cc_start: 0.8690 (p90) cc_final: 0.8368 (p90) REVERT: O 156 TRP cc_start: 0.7740 (m100) cc_final: 0.7250 (m-10) REVERT: P 16 SER cc_start: 0.9061 (m) cc_final: 0.8701 (p) REVERT: P 118 ASN cc_start: 0.8315 (t0) cc_final: 0.7914 (t0) REVERT: P 161 THR cc_start: 0.8733 (p) cc_final: 0.8518 (p) REVERT: P 189 MET cc_start: 0.3012 (ttm) cc_final: 0.2089 (mtp) REVERT: Q 16 GLN cc_start: 0.9117 (mp-120) cc_final: 0.8880 (mp10) REVERT: Q 112 ILE cc_start: 0.8635 (pt) cc_final: 0.8181 (pt) REVERT: Q 117 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8132 (tm-30) REVERT: Q 121 GLN cc_start: 0.6805 (tt0) cc_final: 0.6508 (tt0) REVERT: Q 173 GLU cc_start: 0.6593 (pp20) cc_final: 0.5843 (tm-30) REVERT: Q 190 HIS cc_start: 0.7778 (m90) cc_final: 0.7562 (m-70) REVERT: Q 229 VAL cc_start: 0.7019 (t) cc_final: 0.6588 (m) REVERT: R 141 TYR cc_start: 0.6939 (t80) cc_final: 0.6645 (t80) REVERT: R 148 GLN cc_start: 0.6737 (tt0) cc_final: 0.6033 (tt0) REVERT: R 168 LYS cc_start: 0.7478 (tttt) cc_final: 0.6256 (ptpt) REVERT: A 25 PHE cc_start: 0.7651 (t80) cc_final: 0.6949 (m-80) REVERT: A 26 GLN cc_start: 0.7272 (mt0) cc_final: 0.6335 (pp30) REVERT: A 40 ILE cc_start: 0.7283 (mt) cc_final: 0.6897 (pt) REVERT: A 128 LEU cc_start: 0.8463 (mt) cc_final: 0.8110 (mt) REVERT: A 185 MET cc_start: 0.7442 (mmp) cc_final: 0.7241 (mmm) REVERT: B 5 ARG cc_start: 0.6002 (mtt180) cc_final: 0.4024 (mmp-170) REVERT: B 104 VAL cc_start: 0.7896 (t) cc_final: 0.7669 (t) REVERT: B 109 LYS cc_start: 0.6062 (ttmt) cc_final: 0.5614 (mmtt) REVERT: B 138 GLN cc_start: 0.8321 (mm-40) cc_final: 0.8100 (mm110) REVERT: B 168 GLU cc_start: 0.7475 (pt0) cc_final: 0.7270 (pt0) REVERT: B 192 PRO cc_start: 0.6043 (Cg_endo) cc_final: 0.5663 (Cg_exo) REVERT: B 215 MET cc_start: 0.6458 (mpp) cc_final: 0.5209 (tpt) REVERT: B 227 TYR cc_start: 0.5309 (t80) cc_final: 0.5016 (t80) REVERT: C 57 LEU cc_start: 0.4008 (mp) cc_final: 0.3631 (mp) REVERT: C 233 ASN cc_start: 0.7350 (m-40) cc_final: 0.6736 (p0) REVERT: D 20 PHE cc_start: 0.6141 (m-10) cc_final: 0.5903 (m-80) REVERT: D 31 PHE cc_start: 0.6845 (m-80) cc_final: 0.6607 (m-10) REVERT: D 138 PHE cc_start: 0.6037 (t80) cc_final: 0.5544 (p90) REVERT: D 153 VAL cc_start: 0.9099 (t) cc_final: 0.8758 (t) REVERT: D 163 THR cc_start: 0.7846 (m) cc_final: 0.7480 (p) REVERT: E 49 LEU cc_start: 0.5311 (mm) cc_final: 0.4958 (tp) REVERT: E 127 GLN cc_start: 0.6550 (mm-40) cc_final: 0.6095 (tp40) REVERT: E 132 THR cc_start: 0.8222 (m) cc_final: 0.7803 (p) REVERT: E 136 GLN cc_start: 0.7060 (mt0) cc_final: 0.6687 (mt0) REVERT: E 227 TYR cc_start: 0.6916 (t80) cc_final: 0.6464 (t80) REVERT: E 228 ASP cc_start: 0.7955 (m-30) cc_final: 0.7643 (m-30) REVERT: F 48 GLN cc_start: 0.5953 (mm110) cc_final: 0.5732 (mm110) REVERT: F 124 TRP cc_start: 0.5417 (t60) cc_final: 0.5088 (t60) REVERT: F 171 ARG cc_start: 0.5927 (mtp85) cc_final: 0.5171 (mmp80) REVERT: F 203 ARG cc_start: 0.5195 (ptm160) cc_final: 0.4850 (ptp-170) REVERT: G 40 LEU cc_start: 0.7217 (mt) cc_final: 0.6916 (mt) REVERT: G 199 GLN cc_start: 0.7479 (pt0) cc_final: 0.7278 (pt0) REVERT: G 230 ILE cc_start: 0.7600 (mm) cc_final: 0.7264 (mt) REVERT: a 102 VAL cc_start: 0.8972 (t) cc_final: 0.8726 (t) REVERT: a 143 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6729 (mmm160) REVERT: a 196 LEU cc_start: 0.7319 (mt) cc_final: 0.6940 (mt) REVERT: b 73 HIS cc_start: 0.7029 (p90) cc_final: 0.6708 (p90) REVERT: b 134 SER cc_start: 0.9201 (p) cc_final: 0.8914 (p) REVERT: b 156 MET cc_start: 0.7617 (ttm) cc_final: 0.6960 (ttm) REVERT: b 227 HIS cc_start: 0.6617 (t-90) cc_final: 0.6358 (t-90) REVERT: c 24 TYR cc_start: 0.7211 (m-10) cc_final: 0.6947 (m-80) REVERT: c 26 MET cc_start: 0.6622 (mmt) cc_final: 0.6267 (mmt) REVERT: c 88 MET cc_start: 0.8442 (mmt) cc_final: 0.7904 (mmt) REVERT: c 137 TYR cc_start: 0.7107 (t80) cc_final: 0.6683 (t80) REVERT: c 164 ARG cc_start: 0.6061 (ptm160) cc_final: 0.4620 (ptt180) REVERT: c 186 GLU cc_start: 0.8444 (mt-10) cc_final: 0.7652 (mm-30) REVERT: c 190 HIS cc_start: 0.7816 (m-70) cc_final: 0.7073 (m-70) REVERT: c 217 LYS cc_start: 0.7048 (ptpp) cc_final: 0.6832 (ptpp) REVERT: d 28 MET cc_start: 0.8052 (mmt) cc_final: 0.7788 (mmt) REVERT: d 31 VAL cc_start: 0.7230 (t) cc_final: 0.6920 (t) REVERT: d 59 TYR cc_start: 0.8273 (m-80) cc_final: 0.7733 (m-10) REVERT: d 102 ASN cc_start: 0.8463 (m110) cc_final: 0.7986 (m110) REVERT: d 115 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7906 (mmt-90) REVERT: d 145 ASP cc_start: 0.8355 (m-30) cc_final: 0.8119 (m-30) REVERT: e 27 TYR cc_start: 0.8638 (m-10) cc_final: 0.8337 (m-10) REVERT: e 101 TRP cc_start: 0.8887 (t-100) cc_final: 0.8096 (t-100) REVERT: e 121 ILE cc_start: 0.9372 (mt) cc_final: 0.9012 (mt) REVERT: e 138 MET cc_start: 0.8443 (tmm) cc_final: 0.8047 (tmm) REVERT: e 227 PHE cc_start: 0.8755 (t80) cc_final: 0.8523 (t80) REVERT: e 229 ILE cc_start: 0.7522 (mm) cc_final: 0.7104 (mp) REVERT: f 136 ILE cc_start: 0.9275 (mt) cc_final: 0.9072 (mt) REVERT: g 92 LEU cc_start: 0.8954 (tp) cc_final: 0.8749 (tt) REVERT: g 140 ASP cc_start: 0.7230 (p0) cc_final: 0.6858 (p0) REVERT: g 159 TRP cc_start: 0.7911 (m100) cc_final: 0.7076 (m-10) REVERT: g 222 LYS cc_start: 0.5904 (pptt) cc_final: 0.5505 (pptt) REVERT: g 224 VAL cc_start: 0.8459 (p) cc_final: 0.7824 (p) REVERT: H 71 LEU cc_start: 0.9223 (tp) cc_final: 0.8943 (tp) REVERT: H 136 PHE cc_start: 0.8494 (p90) cc_final: 0.8202 (p90) REVERT: H 149 MET cc_start: 0.7659 (tpp) cc_final: 0.7227 (tpp) REVERT: H 153 LEU cc_start: 0.8438 (mt) cc_final: 0.8044 (mt) REVERT: H 162 HIS cc_start: 0.7850 (m-70) cc_final: 0.7619 (m90) REVERT: H 169 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7889 (tm-30) REVERT: I 5 ILE cc_start: 0.8783 (tt) cc_final: 0.8172 (tt) REVERT: I 8 GLN cc_start: 0.8088 (tt0) cc_final: 0.7821 (tt0) REVERT: I 55 GLN cc_start: 0.8464 (tt0) cc_final: 0.8235 (tt0) REVERT: I 85 ARG cc_start: 0.8971 (ttp80) cc_final: 0.8154 (tmt170) REVERT: J 119 MET cc_start: 0.9258 (tpp) cc_final: 0.8742 (tpp) REVERT: J 172 MET cc_start: 0.8407 (mpp) cc_final: 0.8172 (mpp) REVERT: J 184 LYS cc_start: 0.4943 (mmtt) cc_final: 0.3805 (mttt) REVERT: K 57 LEU cc_start: 0.8870 (mt) cc_final: 0.8387 (mt) REVERT: K 67 ILE cc_start: 0.8212 (mt) cc_final: 0.7952 (mt) REVERT: K 81 PHE cc_start: 0.7191 (m-10) cc_final: 0.6970 (m-10) REVERT: K 95 MET cc_start: 0.8451 (tmm) cc_final: 0.8152 (tmm) REVERT: K 142 TYR cc_start: 0.8820 (t80) cc_final: 0.8339 (t80) REVERT: K 258 HIS cc_start: 0.6995 (m-70) cc_final: 0.6069 (t-90) REVERT: S 15 LYS cc_start: 0.8277 (mttm) cc_final: 0.7963 (mmmm) REVERT: S 30 ILE cc_start: 0.9310 (mt) cc_final: 0.8274 (mt) REVERT: S 96 TYR cc_start: 0.7953 (t80) cc_final: 0.7095 (t80) REVERT: S 145 GLN cc_start: 0.8075 (mt0) cc_final: 0.7328 (mp10) REVERT: S 198 ARG cc_start: 0.7323 (mtm110) cc_final: 0.6395 (mtm180) REVERT: T 28 MET cc_start: 0.7239 (mmp) cc_final: 0.6987 (mmm) REVERT: T 168 GLN cc_start: 0.7771 (tt0) cc_final: 0.7363 (tp-100) REVERT: U 129 PHE cc_start: 0.6605 (m-10) cc_final: 0.6265 (m-10) REVERT: U 133 TYR cc_start: 0.7036 (t80) cc_final: 0.6705 (t80) REVERT: U 160 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7709 (tpp80) REVERT: U 186 MET cc_start: 0.5820 (mmm) cc_final: 0.4938 (mtp) REVERT: V 60 LYS cc_start: 0.8314 (mttm) cc_final: 0.8098 (mmmt) REVERT: V 86 ARG cc_start: 0.7818 (mmt90) cc_final: 0.7538 (mmt90) REVERT: V 90 VAL cc_start: 0.7349 (t) cc_final: 0.7107 (t) REVERT: V 201 LYS cc_start: 0.5893 (mttt) cc_final: 0.5184 (tptt) REVERT: V 232 PHE cc_start: 0.7214 (p90) cc_final: 0.6795 (p90) REVERT: V 233 GLN cc_start: 0.7851 (mp10) cc_final: 0.7627 (mp10) REVERT: W 21 THR cc_start: 0.8726 (m) cc_final: 0.8249 (p) REVERT: W 37 ASP cc_start: 0.7399 (p0) cc_final: 0.6803 (p0) REVERT: W 71 ASP cc_start: 0.8217 (t0) cc_final: 0.8003 (t0) REVERT: W 91 GLU cc_start: 0.8518 (mp0) cc_final: 0.8307 (mp0) REVERT: W 101 ASN cc_start: 0.7843 (t0) cc_final: 0.7157 (t0) REVERT: W 124 ASP cc_start: 0.6696 (p0) cc_final: 0.6377 (p0) REVERT: W 135 MET cc_start: 0.7288 (ttm) cc_final: 0.6986 (ttm) REVERT: X 93 MET cc_start: 0.7429 (mmp) cc_final: 0.7117 (mmm) REVERT: X 120 ARG cc_start: 0.7414 (ptm160) cc_final: 0.7033 (ptm-80) REVERT: X 121 MET cc_start: 0.8268 (mtp) cc_final: 0.7749 (tpp) REVERT: X 127 PHE cc_start: 0.7802 (t80) cc_final: 0.7542 (t80) REVERT: X 185 MET cc_start: 0.5849 (tpp) cc_final: 0.5510 (tpp) REVERT: Y 153 LYS cc_start: 0.8589 (tttt) cc_final: 0.8020 (tppt) REVERT: Y 212 ASP cc_start: 0.8620 (t70) cc_final: 0.8398 (t0) REVERT: Y 239 ASP cc_start: 0.9196 (t0) cc_final: 0.8982 (t0) REVERT: Y 248 MET cc_start: 0.7053 (ttm) cc_final: 0.6644 (ttm) REVERT: Y 260 GLU cc_start: 0.7534 (pp20) cc_final: 0.6701 (pm20) REVERT: Z 104 ARG cc_start: 0.7900 (ttt-90) cc_final: 0.7642 (ttt-90) REVERT: Z 106 ILE cc_start: 0.9057 (mt) cc_final: 0.8796 (mp) REVERT: Z 108 TYR cc_start: 0.8824 (t80) cc_final: 0.8572 (t80) REVERT: Z 109 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8592 (mtpt) REVERT: Z 112 GLU cc_start: 0.6902 (mp0) cc_final: 0.6535 (pt0) REVERT: 1 90 ASP cc_start: 0.7962 (m-30) cc_final: 0.7403 (m-30) REVERT: 1 96 ARG cc_start: 0.8187 (ptp-170) cc_final: 0.7605 (mtp180) REVERT: 1 97 MET cc_start: 0.7320 (tmm) cc_final: 0.7025 (tmm) REVERT: 1 102 MET cc_start: 0.8404 (tpp) cc_final: 0.7782 (tpp) REVERT: 1 113 CYS cc_start: 0.6972 (m) cc_final: 0.6299 (m) REVERT: 1 115 VAL cc_start: 0.8759 (t) cc_final: 0.8507 (t) REVERT: 1 224 MET cc_start: 0.7434 (ttt) cc_final: 0.7143 (tmm) REVERT: 2 81 GLN cc_start: 0.7795 (tm-30) cc_final: 0.7480 (tm-30) REVERT: 2 118 SER cc_start: 0.8902 (t) cc_final: 0.8543 (m) outliers start: 8 outliers final: 1 residues processed: 2052 average time/residue: 0.5761 time to fit residues: 1975.3151 Evaluate side-chains 1603 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1602 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 602 optimal weight: 10.0000 chunk 410 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 539 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 chunk 617 optimal weight: 0.9990 chunk 500 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 369 optimal weight: 2.9990 chunk 649 optimal weight: 8.9990 chunk 182 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN P 221 GLN Q 60 GLN ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS D 143 GLN D 161 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS a 23 GLN ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 73 HIS ** d 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 140 ASN ** f 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 HIS g 53 HIS H 7 ASN H 18 ASN I 71 ASN I 87 ASN I 99 HIS ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 GLN T 87 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 159 GLN ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 HIS W 101 ASN W 142 GLN X 105 HIS ** Y 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN 1 48 GLN ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.7362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 61042 Z= 0.234 Angle : 0.667 11.861 82480 Z= 0.346 Chirality : 0.045 0.332 9289 Planarity : 0.005 0.068 10629 Dihedral : 4.972 34.369 8371 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.61 % Rotamer: Outliers : 0.06 % Allowed : 2.13 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 7577 helix: 0.46 (0.09), residues: 3230 sheet: -0.08 (0.13), residues: 1384 loop : -0.73 (0.11), residues: 2963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP d 216 HIS 0.007 0.001 HIS c 190 PHE 0.035 0.002 PHE F 138 TYR 0.040 0.002 TYR a 110 ARG 0.011 0.001 ARG Y 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1952 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1948 time to evaluate : 5.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 23 TYR cc_start: 0.8014 (m-80) cc_final: 0.7065 (m-80) REVERT: L 30 LYS cc_start: 0.9130 (mttt) cc_final: 0.8806 (ttmm) REVERT: L 33 ASN cc_start: 0.7514 (t0) cc_final: 0.7219 (t0) REVERT: L 71 LYS cc_start: 0.8067 (mttm) cc_final: 0.7669 (mmtt) REVERT: L 92 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8314 (tm-30) REVERT: L 108 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7812 (tm-30) REVERT: L 109 ILE cc_start: 0.8974 (tt) cc_final: 0.8379 (tt) REVERT: L 123 GLN cc_start: 0.9272 (tp40) cc_final: 0.8637 (tp40) REVERT: L 125 TYR cc_start: 0.9109 (m-10) cc_final: 0.8759 (m-10) REVERT: M 63 HIS cc_start: 0.4475 (m-70) cc_final: 0.3818 (m170) REVERT: M 64 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7464 (mmmt) REVERT: M 136 ILE cc_start: 0.8384 (mm) cc_final: 0.8099 (mm) REVERT: M 145 TYR cc_start: 0.6999 (m-80) cc_final: 0.6677 (m-80) REVERT: M 155 TYR cc_start: 0.8643 (p90) cc_final: 0.8415 (p90) REVERT: M 163 MET cc_start: 0.7316 (ptp) cc_final: 0.7065 (ptm) REVERT: M 169 ASN cc_start: 0.8132 (p0) cc_final: 0.7889 (p0) REVERT: M 188 ILE cc_start: 0.9243 (mt) cc_final: 0.8925 (mt) REVERT: M 209 GLU cc_start: 0.7867 (mp0) cc_final: 0.7626 (mp0) REVERT: N 110 LEU cc_start: 0.8925 (pp) cc_final: 0.8473 (tp) REVERT: N 153 SER cc_start: 0.8140 (p) cc_final: 0.7343 (t) REVERT: N 200 THR cc_start: 0.8222 (p) cc_final: 0.7962 (p) REVERT: N 216 LEU cc_start: 0.7726 (tp) cc_final: 0.7302 (tp) REVERT: O 54 GLN cc_start: 0.7319 (pt0) cc_final: 0.7112 (pt0) REVERT: O 71 MET cc_start: 0.8067 (ppp) cc_final: 0.7859 (ppp) REVERT: O 73 PHE cc_start: 0.7896 (p90) cc_final: 0.7448 (p90) REVERT: O 79 ASP cc_start: 0.8331 (m-30) cc_final: 0.7808 (m-30) REVERT: O 90 GLU cc_start: 0.8430 (tp30) cc_final: 0.8168 (tp30) REVERT: O 156 TRP cc_start: 0.7891 (m100) cc_final: 0.7409 (m-10) REVERT: O 185 ASP cc_start: 0.7593 (m-30) cc_final: 0.7047 (p0) REVERT: P 16 SER cc_start: 0.9003 (m) cc_final: 0.8559 (p) REVERT: P 96 THR cc_start: 0.8792 (m) cc_final: 0.8524 (m) REVERT: P 122 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7359 (tm-30) REVERT: P 189 MET cc_start: 0.3137 (ttm) cc_final: 0.2259 (mtp) REVERT: Q 112 ILE cc_start: 0.8590 (pt) cc_final: 0.8142 (pt) REVERT: Q 117 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8315 (tm-30) REVERT: Q 154 PHE cc_start: 0.8055 (m-80) cc_final: 0.7741 (m-10) REVERT: Q 159 MET cc_start: 0.5084 (tpt) cc_final: 0.4809 (ttt) REVERT: Q 173 GLU cc_start: 0.6638 (pp20) cc_final: 0.5972 (tm-30) REVERT: Q 176 MET cc_start: 0.6933 (tmm) cc_final: 0.6343 (tmm) REVERT: Q 237 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6119 (tm-30) REVERT: R 141 TYR cc_start: 0.7031 (t80) cc_final: 0.6474 (t80) REVERT: R 148 GLN cc_start: 0.6954 (tt0) cc_final: 0.6156 (tt0) REVERT: R 168 LYS cc_start: 0.7670 (tttt) cc_final: 0.6266 (ptpt) REVERT: A 25 PHE cc_start: 0.7678 (t80) cc_final: 0.6965 (m-80) REVERT: A 26 GLN cc_start: 0.7379 (mt0) cc_final: 0.6386 (pp30) REVERT: A 40 ILE cc_start: 0.7514 (mt) cc_final: 0.7175 (pt) REVERT: A 128 LEU cc_start: 0.8451 (mt) cc_final: 0.8162 (mm) REVERT: B 5 ARG cc_start: 0.6118 (mtt180) cc_final: 0.4327 (mmp-170) REVERT: B 104 VAL cc_start: 0.8019 (t) cc_final: 0.7794 (t) REVERT: B 109 LYS cc_start: 0.6044 (ttmt) cc_final: 0.5613 (mmtt) REVERT: B 138 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8102 (mm110) REVERT: B 168 GLU cc_start: 0.7584 (pt0) cc_final: 0.7348 (pt0) REVERT: B 192 PRO cc_start: 0.5955 (Cg_endo) cc_final: 0.5708 (Cg_exo) REVERT: B 215 MET cc_start: 0.6518 (mpp) cc_final: 0.5175 (tpp) REVERT: B 227 TYR cc_start: 0.5326 (t80) cc_final: 0.5050 (t80) REVERT: C 21 LEU cc_start: 0.7115 (mt) cc_final: 0.6345 (pp) REVERT: C 233 ASN cc_start: 0.7485 (m-40) cc_final: 0.6828 (p0) REVERT: D 31 PHE cc_start: 0.6822 (m-80) cc_final: 0.6590 (m-10) REVERT: D 138 PHE cc_start: 0.6279 (t80) cc_final: 0.5572 (p90) REVERT: D 153 VAL cc_start: 0.9095 (t) cc_final: 0.8801 (t) REVERT: E 49 LEU cc_start: 0.5240 (mm) cc_final: 0.5025 (tp) REVERT: E 127 GLN cc_start: 0.6935 (mm-40) cc_final: 0.6355 (tp40) REVERT: E 132 THR cc_start: 0.8250 (m) cc_final: 0.7944 (p) REVERT: E 136 GLN cc_start: 0.7158 (mt0) cc_final: 0.6732 (mt0) REVERT: E 227 TYR cc_start: 0.6889 (t80) cc_final: 0.6505 (t80) REVERT: E 228 ASP cc_start: 0.7930 (m-30) cc_final: 0.7532 (m-30) REVERT: F 48 GLN cc_start: 0.6157 (mm110) cc_final: 0.5918 (mm110) REVERT: F 124 TRP cc_start: 0.5554 (t60) cc_final: 0.5125 (t60) REVERT: F 151 ASN cc_start: 0.7494 (p0) cc_final: 0.7183 (p0) REVERT: F 171 ARG cc_start: 0.6152 (mtp85) cc_final: 0.5383 (mmp80) REVERT: F 188 ARG cc_start: 0.2900 (ptm-80) cc_final: 0.2573 (ptm-80) REVERT: G 40 LEU cc_start: 0.7423 (mt) cc_final: 0.7090 (pp) REVERT: G 147 ASN cc_start: 0.5339 (m-40) cc_final: 0.5107 (m-40) REVERT: G 210 ARG cc_start: 0.4481 (mtm180) cc_final: 0.3687 (mtp85) REVERT: G 230 ILE cc_start: 0.7480 (mm) cc_final: 0.7196 (mt) REVERT: a 23 GLN cc_start: 0.8417 (mt0) cc_final: 0.8077 (mm-40) REVERT: a 143 ARG cc_start: 0.7220 (mmm160) cc_final: 0.6644 (mmm160) REVERT: a 148 ASP cc_start: 0.8947 (t0) cc_final: 0.8689 (t0) REVERT: a 196 LEU cc_start: 0.7373 (mt) cc_final: 0.6917 (mt) REVERT: b 134 SER cc_start: 0.9195 (p) cc_final: 0.8932 (p) REVERT: b 156 MET cc_start: 0.7517 (ttm) cc_final: 0.6723 (ttm) REVERT: c 24 TYR cc_start: 0.7458 (m-10) cc_final: 0.7200 (m-80) REVERT: c 88 MET cc_start: 0.8541 (mmt) cc_final: 0.8047 (mmt) REVERT: c 137 TYR cc_start: 0.7285 (t80) cc_final: 0.6882 (t80) REVERT: c 186 GLU cc_start: 0.8458 (mt-10) cc_final: 0.7774 (mm-30) REVERT: c 217 LYS cc_start: 0.6954 (ptpp) cc_final: 0.6686 (ptpp) REVERT: c 233 LEU cc_start: 0.8242 (mt) cc_final: 0.7729 (tp) REVERT: d 31 VAL cc_start: 0.7228 (t) cc_final: 0.7021 (t) REVERT: d 59 TYR cc_start: 0.8295 (m-80) cc_final: 0.7750 (m-10) REVERT: d 102 ASN cc_start: 0.8455 (m110) cc_final: 0.8052 (m110) REVERT: d 145 ASP cc_start: 0.8356 (m-30) cc_final: 0.8085 (m-30) REVERT: e 27 TYR cc_start: 0.8631 (m-10) cc_final: 0.8290 (m-10) REVERT: e 71 LYS cc_start: 0.8257 (tttt) cc_final: 0.7959 (ttmt) REVERT: e 117 ARG cc_start: 0.7320 (tpt-90) cc_final: 0.6910 (mmm160) REVERT: e 118 ILE cc_start: 0.9040 (mt) cc_final: 0.8677 (tp) REVERT: e 227 PHE cc_start: 0.8749 (t80) cc_final: 0.8506 (t80) REVERT: f 83 TYR cc_start: 0.7013 (t80) cc_final: 0.6808 (t80) REVERT: f 118 MET cc_start: 0.7689 (ttm) cc_final: 0.7451 (ttp) REVERT: f 136 ILE cc_start: 0.9351 (mt) cc_final: 0.9123 (mt) REVERT: g 5 TYR cc_start: 0.5867 (m-80) cc_final: 0.5487 (m-80) REVERT: g 25 MET cc_start: 0.8086 (mmm) cc_final: 0.7847 (mmm) REVERT: g 53 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: g 90 LEU cc_start: 0.8673 (mt) cc_final: 0.8264 (mt) REVERT: g 92 LEU cc_start: 0.9012 (tp) cc_final: 0.8739 (tt) REVERT: g 140 ASP cc_start: 0.7304 (p0) cc_final: 0.6977 (p0) REVERT: g 159 TRP cc_start: 0.7921 (m100) cc_final: 0.7347 (m-10) REVERT: g 222 LYS cc_start: 0.5742 (pptt) cc_final: 0.5366 (pptt) REVERT: g 224 VAL cc_start: 0.8453 (p) cc_final: 0.7849 (p) REVERT: H 66 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7990 (mmm-85) REVERT: H 136 PHE cc_start: 0.8615 (p90) cc_final: 0.8210 (p90) REVERT: H 149 MET cc_start: 0.7430 (tpp) cc_final: 0.7038 (tpp) REVERT: H 153 LEU cc_start: 0.8489 (mt) cc_final: 0.8096 (mt) REVERT: H 162 HIS cc_start: 0.8029 (m-70) cc_final: 0.7757 (m90) REVERT: H 169 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7762 (tm-30) REVERT: I 85 ARG cc_start: 0.8930 (ttp80) cc_final: 0.8401 (ttt-90) REVERT: I 119 ASP cc_start: 0.7821 (p0) cc_final: 0.7592 (p0) REVERT: J 66 ARG cc_start: 0.8088 (mtm180) cc_final: 0.7852 (mmm-85) REVERT: J 119 MET cc_start: 0.9441 (tpp) cc_final: 0.8835 (tpp) REVERT: J 172 MET cc_start: 0.8418 (mpp) cc_final: 0.8213 (mpp) REVERT: J 184 LYS cc_start: 0.4701 (mmtt) cc_final: 0.3605 (mttt) REVERT: J 219 ASP cc_start: 0.6825 (m-30) cc_final: 0.6472 (m-30) REVERT: K 57 LEU cc_start: 0.8810 (mt) cc_final: 0.8536 (mt) REVERT: K 95 MET cc_start: 0.8540 (tmm) cc_final: 0.8321 (tmm) REVERT: K 218 MET cc_start: 0.8555 (mmp) cc_final: 0.8196 (tpp) REVERT: K 258 HIS cc_start: 0.6666 (m-70) cc_final: 0.5982 (t-90) REVERT: S 96 TYR cc_start: 0.8105 (t80) cc_final: 0.7065 (t80) REVERT: S 145 GLN cc_start: 0.8263 (mt0) cc_final: 0.7695 (mp10) REVERT: S 169 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8889 (mm110) REVERT: S 178 ASP cc_start: 0.9080 (t0) cc_final: 0.8701 (t70) REVERT: S 183 MET cc_start: 0.7917 (mpp) cc_final: 0.7634 (mpp) REVERT: S 198 ARG cc_start: 0.7435 (mtm110) cc_final: 0.6697 (mtm180) REVERT: T 168 GLN cc_start: 0.7826 (tt0) cc_final: 0.7480 (tp-100) REVERT: U 99 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7494 (mtt180) REVERT: U 133 TYR cc_start: 0.7004 (t80) cc_final: 0.6675 (t80) REVERT: U 186 MET cc_start: 0.5839 (mmm) cc_final: 0.4487 (mtp) REVERT: U 217 THR cc_start: 0.8300 (m) cc_final: 0.8064 (m) REVERT: V 60 LYS cc_start: 0.8391 (mttm) cc_final: 0.8182 (mmmt) REVERT: V 86 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7641 (mmt90) REVERT: V 201 LYS cc_start: 0.6166 (mttt) cc_final: 0.5090 (tptt) REVERT: V 218 MET cc_start: 0.8613 (mmm) cc_final: 0.8081 (mmm) REVERT: V 219 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7956 (ptm160) REVERT: W 21 THR cc_start: 0.8815 (m) cc_final: 0.8376 (p) REVERT: W 37 ASP cc_start: 0.7522 (p0) cc_final: 0.7107 (p0) REVERT: W 71 ASP cc_start: 0.8202 (t0) cc_final: 0.7847 (t0) REVERT: W 91 GLU cc_start: 0.8513 (mp0) cc_final: 0.8263 (mp0) REVERT: W 101 ASN cc_start: 0.8279 (t0) cc_final: 0.7608 (t0) REVERT: W 124 ASP cc_start: 0.7156 (p0) cc_final: 0.6844 (p0) REVERT: W 135 MET cc_start: 0.7375 (ttm) cc_final: 0.6740 (ttm) REVERT: W 153 TYR cc_start: 0.7547 (m-10) cc_final: 0.7337 (m-10) REVERT: X 121 MET cc_start: 0.8460 (mtp) cc_final: 0.7937 (tpp) REVERT: X 127 PHE cc_start: 0.7932 (t80) cc_final: 0.7652 (t80) REVERT: X 224 MET cc_start: 0.7736 (mmp) cc_final: 0.7289 (mmm) REVERT: Y 102 LYS cc_start: 0.8322 (mmtp) cc_final: 0.8056 (mmtp) REVERT: Y 138 TYR cc_start: 0.8789 (t80) cc_final: 0.8516 (t80) REVERT: Y 153 LYS cc_start: 0.8514 (tttt) cc_final: 0.8037 (tppt) REVERT: Y 212 ASP cc_start: 0.8858 (t70) cc_final: 0.8512 (t0) REVERT: Y 239 ASP cc_start: 0.9236 (t0) cc_final: 0.9019 (t0) REVERT: Y 248 MET cc_start: 0.7341 (ttm) cc_final: 0.6805 (ttm) REVERT: Y 260 GLU cc_start: 0.7593 (pp20) cc_final: 0.6598 (pm20) REVERT: Z 101 ASN cc_start: 0.7729 (t0) cc_final: 0.7408 (t0) REVERT: Z 106 ILE cc_start: 0.9240 (mt) cc_final: 0.8941 (mp) REVERT: Z 108 TYR cc_start: 0.8879 (t80) cc_final: 0.8660 (t80) REVERT: Z 109 LYS cc_start: 0.8787 (ttpt) cc_final: 0.8537 (ttpt) REVERT: Z 132 TYR cc_start: 0.8744 (m-80) cc_final: 0.8289 (m-80) REVERT: 1 97 MET cc_start: 0.7389 (tmm) cc_final: 0.7000 (tmm) REVERT: 1 102 MET cc_start: 0.8327 (tpp) cc_final: 0.7404 (tpp) REVERT: 1 113 CYS cc_start: 0.7054 (m) cc_final: 0.6335 (m) REVERT: 1 115 VAL cc_start: 0.8686 (t) cc_final: 0.8303 (t) REVERT: 1 149 LEU cc_start: 0.9396 (tp) cc_final: 0.9193 (tp) REVERT: 1 224 MET cc_start: 0.7421 (ttt) cc_final: 0.7115 (tmm) REVERT: 2 81 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7627 (tm-30) REVERT: 2 116 THR cc_start: 0.8515 (p) cc_final: 0.8225 (p) REVERT: 2 118 SER cc_start: 0.8884 (t) cc_final: 0.8621 (m) REVERT: 2 159 MET cc_start: 0.8212 (ppp) cc_final: 0.7914 (ppp) outliers start: 4 outliers final: 0 residues processed: 1950 average time/residue: 0.5778 time to fit residues: 1883.4111 Evaluate side-chains 1567 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1566 time to evaluate : 5.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 243 optimal weight: 0.0010 chunk 651 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 chunk 425 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 724 optimal weight: 0.1980 chunk 601 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 239 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 24 GLN L 34 GLN L 68 HIS ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 ASN ** Q 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 190 HIS R 121 HIS ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 GLN E 164 HIS ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 HIS d 111 HIS ** e 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 127 GLN ** f 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 HIS ** g 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN H 162 HIS I 87 ASN I 168 GLN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 65 GLN T 63 ASN T 87 ASN ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN U 64 HIS ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 126 HIS V 230 ASN V 258 HIS W 101 ASN Z 101 ASN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.7682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 61042 Z= 0.215 Angle : 0.649 12.675 82480 Z= 0.337 Chirality : 0.045 0.211 9289 Planarity : 0.005 0.073 10629 Dihedral : 4.907 35.066 8371 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.09), residues: 7577 helix: 0.57 (0.09), residues: 3251 sheet: -0.06 (0.13), residues: 1382 loop : -0.72 (0.11), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP d 216 HIS 0.013 0.001 HIS c 190 PHE 0.034 0.002 PHE N 145 TYR 0.029 0.002 TYR B 223 ARG 0.009 0.001 ARG S 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1961 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1959 time to evaluate : 5.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 ASN cc_start: 0.7338 (t0) cc_final: 0.7013 (t0) REVERT: L 108 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7869 (tm-30) REVERT: L 109 ILE cc_start: 0.9020 (tt) cc_final: 0.8332 (tt) REVERT: L 123 GLN cc_start: 0.9217 (tp40) cc_final: 0.8648 (tp40) REVERT: M 63 HIS cc_start: 0.4424 (m-70) cc_final: 0.3870 (m170) REVERT: M 64 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7319 (mmmt) REVERT: M 120 GLU cc_start: 0.6386 (tm-30) cc_final: 0.6044 (tm-30) REVERT: M 127 VAL cc_start: 0.9388 (t) cc_final: 0.9159 (p) REVERT: M 145 TYR cc_start: 0.7271 (m-80) cc_final: 0.6976 (m-80) REVERT: M 155 TYR cc_start: 0.8786 (p90) cc_final: 0.8523 (p90) REVERT: M 169 ASN cc_start: 0.8263 (p0) cc_final: 0.7858 (p0) REVERT: M 188 ILE cc_start: 0.9191 (mt) cc_final: 0.8983 (mt) REVERT: M 209 GLU cc_start: 0.7860 (mp0) cc_final: 0.7548 (mp0) REVERT: N 110 LEU cc_start: 0.8910 (pp) cc_final: 0.8486 (tp) REVERT: N 127 LYS cc_start: 0.8346 (mttt) cc_final: 0.7743 (mmtp) REVERT: N 153 SER cc_start: 0.7971 (p) cc_final: 0.7396 (t) REVERT: N 216 LEU cc_start: 0.7610 (tp) cc_final: 0.7299 (tp) REVERT: O 54 GLN cc_start: 0.7341 (pt0) cc_final: 0.7119 (pt0) REVERT: O 73 PHE cc_start: 0.7911 (p90) cc_final: 0.7394 (p90) REVERT: O 79 ASP cc_start: 0.8324 (m-30) cc_final: 0.7850 (m-30) REVERT: O 90 GLU cc_start: 0.8398 (tp30) cc_final: 0.8087 (tp30) REVERT: O 156 TRP cc_start: 0.7735 (m100) cc_final: 0.7412 (m-10) REVERT: P 16 SER cc_start: 0.8984 (m) cc_final: 0.8551 (p) REVERT: P 122 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7392 (tm-30) REVERT: P 189 MET cc_start: 0.3181 (ttm) cc_final: 0.2292 (mtp) REVERT: Q 16 GLN cc_start: 0.9373 (mp10) cc_final: 0.9118 (mp10) REVERT: Q 112 ILE cc_start: 0.8674 (pt) cc_final: 0.8211 (pt) REVERT: Q 117 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8276 (tm-30) REVERT: Q 154 PHE cc_start: 0.8054 (m-80) cc_final: 0.7775 (m-10) REVERT: Q 173 GLU cc_start: 0.6654 (pp20) cc_final: 0.5995 (tm-30) REVERT: Q 176 MET cc_start: 0.7120 (tmm) cc_final: 0.6562 (tmm) REVERT: Q 229 VAL cc_start: 0.7256 (t) cc_final: 0.7006 (m) REVERT: Q 237 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6323 (tm-30) REVERT: R 25 GLU cc_start: 0.8204 (tp30) cc_final: 0.7480 (tp30) REVERT: R 123 TYR cc_start: 0.8131 (m-10) cc_final: 0.7837 (m-10) REVERT: R 148 GLN cc_start: 0.6946 (tt0) cc_final: 0.6233 (tt0) REVERT: R 168 LYS cc_start: 0.7670 (tttt) cc_final: 0.6239 (ptpt) REVERT: R 222 ASN cc_start: 0.8455 (t0) cc_final: 0.8022 (t0) REVERT: A 25 PHE cc_start: 0.7758 (t80) cc_final: 0.7051 (m-80) REVERT: A 26 GLN cc_start: 0.7433 (mt0) cc_final: 0.6588 (pp30) REVERT: A 40 ILE cc_start: 0.7236 (mt) cc_final: 0.6990 (pt) REVERT: A 128 LEU cc_start: 0.8477 (mt) cc_final: 0.8255 (mm) REVERT: B 5 ARG cc_start: 0.6153 (mtt180) cc_final: 0.4213 (mmp-170) REVERT: B 18 ARG cc_start: 0.7235 (tmm-80) cc_final: 0.6800 (tmm160) REVERT: B 104 VAL cc_start: 0.7706 (t) cc_final: 0.7475 (t) REVERT: B 109 LYS cc_start: 0.6060 (ttmt) cc_final: 0.5602 (mmtt) REVERT: B 138 GLN cc_start: 0.8362 (mm-40) cc_final: 0.7659 (mm110) REVERT: B 168 GLU cc_start: 0.7338 (pt0) cc_final: 0.7088 (pt0) REVERT: B 215 MET cc_start: 0.6548 (mpp) cc_final: 0.5375 (tpt) REVERT: B 227 TYR cc_start: 0.5279 (t80) cc_final: 0.5002 (t80) REVERT: C 160 MET cc_start: 0.9030 (ptt) cc_final: 0.8733 (ppp) REVERT: C 164 HIS cc_start: 0.6713 (m-70) cc_final: 0.6382 (m90) REVERT: C 219 ILE cc_start: 0.6592 (tt) cc_final: 0.6334 (tt) REVERT: D 138 PHE cc_start: 0.6349 (t80) cc_final: 0.5663 (p90) REVERT: D 153 VAL cc_start: 0.8885 (t) cc_final: 0.8624 (t) REVERT: E 49 LEU cc_start: 0.5398 (mm) cc_final: 0.5176 (tp) REVERT: E 127 GLN cc_start: 0.6926 (mm-40) cc_final: 0.6407 (tp40) REVERT: E 132 THR cc_start: 0.7981 (m) cc_final: 0.7620 (p) REVERT: E 135 LEU cc_start: 0.8445 (mm) cc_final: 0.8076 (mm) REVERT: E 136 GLN cc_start: 0.6742 (mt0) cc_final: 0.6416 (mt0) REVERT: E 227 TYR cc_start: 0.6883 (t80) cc_final: 0.6501 (t80) REVERT: E 228 ASP cc_start: 0.7980 (m-30) cc_final: 0.7524 (m-30) REVERT: F 121 VAL cc_start: 0.7198 (t) cc_final: 0.6968 (t) REVERT: F 124 TRP cc_start: 0.5553 (t60) cc_final: 0.5269 (t60) REVERT: F 125 ILE cc_start: 0.8674 (mt) cc_final: 0.8457 (pt) REVERT: F 143 GLN cc_start: 0.8193 (tt0) cc_final: 0.7758 (tp40) REVERT: F 151 ASN cc_start: 0.7503 (p0) cc_final: 0.7174 (p0) REVERT: F 171 ARG cc_start: 0.6228 (mtp85) cc_final: 0.5583 (mmp80) REVERT: F 188 ARG cc_start: 0.3162 (ptm-80) cc_final: 0.2797 (ptm-80) REVERT: F 212 PHE cc_start: 0.6875 (m-80) cc_final: 0.6484 (m-80) REVERT: G 147 ASN cc_start: 0.5375 (m-40) cc_final: 0.5161 (m-40) REVERT: G 210 ARG cc_start: 0.4404 (mtm180) cc_final: 0.3583 (mtp85) REVERT: G 230 ILE cc_start: 0.7600 (mm) cc_final: 0.7317 (mt) REVERT: a 23 GLN cc_start: 0.8385 (mt0) cc_final: 0.8100 (mm-40) REVERT: a 99 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7765 (mm-30) REVERT: a 102 VAL cc_start: 0.8965 (t) cc_final: 0.8724 (t) REVERT: a 143 ARG cc_start: 0.7164 (mmm160) cc_final: 0.6631 (mmm160) REVERT: a 148 ASP cc_start: 0.8947 (t0) cc_final: 0.8708 (t0) REVERT: a 196 LEU cc_start: 0.7350 (mt) cc_final: 0.6934 (mt) REVERT: a 207 GLU cc_start: 0.6628 (tm-30) cc_final: 0.6159 (tm-30) REVERT: a 208 LEU cc_start: 0.6996 (mm) cc_final: 0.6770 (mm) REVERT: b 93 ARG cc_start: 0.8495 (mtm-85) cc_final: 0.8240 (mtp180) REVERT: b 134 SER cc_start: 0.9120 (p) cc_final: 0.8889 (p) REVERT: b 156 MET cc_start: 0.7573 (ttm) cc_final: 0.6833 (ttm) REVERT: b 206 MET cc_start: 0.6183 (mtm) cc_final: 0.5465 (mtm) REVERT: c 24 TYR cc_start: 0.7668 (m-10) cc_final: 0.7462 (m-80) REVERT: c 87 PHE cc_start: 0.7026 (t80) cc_final: 0.6702 (t80) REVERT: c 88 MET cc_start: 0.8578 (mmt) cc_final: 0.8033 (mmt) REVERT: c 137 TYR cc_start: 0.7285 (t80) cc_final: 0.6912 (t80) REVERT: c 190 HIS cc_start: 0.7519 (m-70) cc_final: 0.6923 (p90) REVERT: c 233 LEU cc_start: 0.8230 (mt) cc_final: 0.7722 (tp) REVERT: d 22 PHE cc_start: 0.5861 (m-10) cc_final: 0.5295 (m-10) REVERT: d 59 TYR cc_start: 0.8271 (m-10) cc_final: 0.7895 (m-10) REVERT: d 102 ASN cc_start: 0.8520 (m110) cc_final: 0.8034 (m110) REVERT: d 145 ASP cc_start: 0.8265 (m-30) cc_final: 0.7969 (m-30) REVERT: d 164 CYS cc_start: 0.6714 (p) cc_final: 0.5879 (p) REVERT: d 244 LEU cc_start: 0.4074 (mt) cc_final: 0.3594 (tt) REVERT: e 27 TYR cc_start: 0.8658 (m-10) cc_final: 0.8222 (m-10) REVERT: e 113 MET cc_start: 0.8171 (mmm) cc_final: 0.7847 (tpt) REVERT: e 138 MET cc_start: 0.8032 (tmm) cc_final: 0.7735 (tmm) REVERT: f 100 VAL cc_start: 0.8967 (m) cc_final: 0.8767 (t) REVERT: f 118 MET cc_start: 0.7673 (ttm) cc_final: 0.7427 (ttp) REVERT: f 136 ILE cc_start: 0.9350 (mt) cc_final: 0.9126 (mt) REVERT: f 196 LYS cc_start: 0.8355 (mmtt) cc_final: 0.7739 (tptp) REVERT: g 1 MET cc_start: 0.7361 (mmm) cc_final: 0.6709 (mmm) REVERT: g 5 TYR cc_start: 0.6023 (m-80) cc_final: 0.5787 (m-80) REVERT: g 72 MET cc_start: 0.7318 (mtt) cc_final: 0.6729 (mtp) REVERT: g 90 LEU cc_start: 0.8632 (mt) cc_final: 0.8273 (mt) REVERT: g 123 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7934 (mm-40) REVERT: g 140 ASP cc_start: 0.7181 (p0) cc_final: 0.6775 (p0) REVERT: g 159 TRP cc_start: 0.7804 (m100) cc_final: 0.7274 (m-10) REVERT: g 192 LEU cc_start: 0.7827 (mt) cc_final: 0.7557 (tp) REVERT: g 222 LYS cc_start: 0.5727 (pptt) cc_final: 0.5341 (pptt) REVERT: g 224 VAL cc_start: 0.8423 (p) cc_final: 0.7828 (p) REVERT: H 66 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8032 (mmm-85) REVERT: H 136 PHE cc_start: 0.8670 (p90) cc_final: 0.8137 (p90) REVERT: H 142 CYS cc_start: 0.7101 (p) cc_final: 0.6825 (t) REVERT: H 149 MET cc_start: 0.7372 (tpp) cc_final: 0.6900 (tpp) REVERT: H 153 LEU cc_start: 0.8523 (mt) cc_final: 0.8138 (mt) REVERT: H 162 HIS cc_start: 0.7872 (m90) cc_final: 0.7312 (m90) REVERT: H 169 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7652 (tm-30) REVERT: H 189 ILE cc_start: 0.6617 (mt) cc_final: 0.6356 (mt) REVERT: H 198 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6964 (mmm-85) REVERT: H 204 MET cc_start: 0.6076 (mmt) cc_final: 0.5509 (mmt) REVERT: I 5 ILE cc_start: 0.8538 (tt) cc_final: 0.8262 (tp) REVERT: I 19 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7119 (mtp85) REVERT: I 43 LEU cc_start: 0.8236 (tt) cc_final: 0.7917 (mt) REVERT: I 85 ARG cc_start: 0.8897 (ttp80) cc_final: 0.8380 (ttt-90) REVERT: I 102 LEU cc_start: 0.9024 (pt) cc_final: 0.8768 (pt) REVERT: J 66 ARG cc_start: 0.8097 (mtm180) cc_final: 0.7835 (mmm-85) REVERT: J 119 MET cc_start: 0.9468 (tpp) cc_final: 0.8763 (tpp) REVERT: J 184 LYS cc_start: 0.4719 (mmtt) cc_final: 0.3587 (mttt) REVERT: J 219 ASP cc_start: 0.6911 (m-30) cc_final: 0.6611 (m-30) REVERT: K 57 LEU cc_start: 0.8678 (mt) cc_final: 0.8418 (tp) REVERT: K 218 MET cc_start: 0.8461 (mmp) cc_final: 0.8163 (tpp) REVERT: K 258 HIS cc_start: 0.6722 (m-70) cc_final: 0.5987 (t-90) REVERT: S 26 ARG cc_start: 0.6716 (tpp80) cc_final: 0.6504 (tpp80) REVERT: S 38 ASP cc_start: 0.8113 (t0) cc_final: 0.7779 (t70) REVERT: S 96 TYR cc_start: 0.8008 (t80) cc_final: 0.7094 (t80) REVERT: S 145 GLN cc_start: 0.8328 (mt0) cc_final: 0.7786 (mp10) REVERT: S 169 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8738 (mm110) REVERT: S 178 ASP cc_start: 0.9076 (t0) cc_final: 0.8657 (t70) REVERT: S 198 ARG cc_start: 0.7527 (mtm110) cc_final: 0.7095 (mtm110) REVERT: S 205 ASP cc_start: 0.5992 (t0) cc_final: 0.4773 (m-30) REVERT: T 118 MET cc_start: 0.7305 (ttm) cc_final: 0.7079 (ttm) REVERT: T 168 GLN cc_start: 0.7946 (tt0) cc_final: 0.7717 (tp40) REVERT: U 97 GLU cc_start: 0.7082 (tp30) cc_final: 0.6837 (tp30) REVERT: U 133 TYR cc_start: 0.6879 (t80) cc_final: 0.6606 (t80) REVERT: U 241 ASP cc_start: 0.7202 (p0) cc_final: 0.6906 (p0) REVERT: V 201 LYS cc_start: 0.6116 (mttt) cc_final: 0.5146 (tptt) REVERT: V 218 MET cc_start: 0.8664 (mmm) cc_final: 0.8359 (mmp) REVERT: V 219 ARG cc_start: 0.8115 (ptm160) cc_final: 0.7903 (ptm160) REVERT: V 232 PHE cc_start: 0.7256 (p90) cc_final: 0.6961 (p90) REVERT: V 233 GLN cc_start: 0.7518 (mp10) cc_final: 0.6884 (mp10) REVERT: W 21 THR cc_start: 0.8972 (m) cc_final: 0.8264 (p) REVERT: W 23 ILE cc_start: 0.9511 (pt) cc_final: 0.9194 (pt) REVERT: W 37 ASP cc_start: 0.7499 (p0) cc_final: 0.7199 (p0) REVERT: W 66 SER cc_start: 0.9062 (t) cc_final: 0.8844 (m) REVERT: W 71 ASP cc_start: 0.8189 (t0) cc_final: 0.7973 (t0) REVERT: W 91 GLU cc_start: 0.8543 (mp0) cc_final: 0.8256 (mp0) REVERT: W 101 ASN cc_start: 0.8246 (t0) cc_final: 0.7700 (t0) REVERT: W 135 MET cc_start: 0.7341 (ttm) cc_final: 0.7000 (ttm) REVERT: X 185 MET cc_start: 0.6362 (tpp) cc_final: 0.5659 (tpp) REVERT: X 224 MET cc_start: 0.7618 (mmp) cc_final: 0.7255 (mmm) REVERT: Y 102 LYS cc_start: 0.8322 (mmtp) cc_final: 0.8022 (mmtp) REVERT: Y 142 ASN cc_start: 0.8578 (p0) cc_final: 0.8336 (p0) REVERT: Y 153 LYS cc_start: 0.8589 (tttt) cc_final: 0.7972 (tppt) REVERT: Y 239 ASP cc_start: 0.9229 (t0) cc_final: 0.8972 (t0) REVERT: Y 259 VAL cc_start: 0.7133 (t) cc_final: 0.5372 (t) REVERT: Y 260 GLU cc_start: 0.7720 (pp20) cc_final: 0.7025 (mp0) REVERT: Z 106 ILE cc_start: 0.9187 (mt) cc_final: 0.8920 (mp) REVERT: Z 108 TYR cc_start: 0.8986 (t80) cc_final: 0.8667 (t80) REVERT: Z 132 TYR cc_start: 0.8640 (m-80) cc_final: 0.8354 (m-80) REVERT: 1 97 MET cc_start: 0.7134 (tmm) cc_final: 0.6770 (tmm) REVERT: 1 202 ILE cc_start: 0.9100 (mm) cc_final: 0.8818 (mm) REVERT: 1 224 MET cc_start: 0.7409 (ttt) cc_final: 0.7109 (tmm) REVERT: 2 81 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7624 (tm-30) REVERT: 2 116 THR cc_start: 0.8566 (p) cc_final: 0.8263 (p) REVERT: 2 118 SER cc_start: 0.8949 (t) cc_final: 0.8666 (m) REVERT: 2 251 MET cc_start: 0.6401 (tpt) cc_final: 0.5998 (tmm) REVERT: 2 253 GLU cc_start: 0.6531 (tp30) cc_final: 0.6009 (tp30) outliers start: 2 outliers final: 0 residues processed: 1961 average time/residue: 0.5703 time to fit residues: 1878.3392 Evaluate side-chains 1565 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1565 time to evaluate : 5.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 698 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 412 optimal weight: 4.9990 chunk 529 optimal weight: 7.9990 chunk 410 optimal weight: 5.9990 chunk 610 optimal weight: 9.9990 chunk 404 optimal weight: 4.9990 chunk 721 optimal weight: 7.9990 chunk 451 optimal weight: 4.9990 chunk 440 optimal weight: 1.9990 chunk 333 optimal weight: 0.0070 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 GLN ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 146 GLN ** N 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN C 233 ASN D 143 GLN D 161 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 HIS c 60 GLN d 111 HIS ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 GLN f 207 ASN g 30 HIS g 53 HIS g 119 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 71 ASN I 87 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 ASN T 193 ASN ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN W 101 ASN Z 101 ASN 1 124 GLN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 61042 Z= 0.266 Angle : 0.690 10.651 82480 Z= 0.361 Chirality : 0.046 0.201 9289 Planarity : 0.005 0.093 10629 Dihedral : 5.030 37.418 8371 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.72 % Favored : 96.27 % Rotamer: Outliers : 0.05 % Allowed : 1.83 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.09), residues: 7577 helix: 0.54 (0.09), residues: 3269 sheet: -0.19 (0.13), residues: 1424 loop : -0.75 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP d 216 HIS 0.014 0.001 HIS E 202 PHE 0.026 0.002 PHE B 234 TYR 0.038 0.002 TYR f 83 ARG 0.013 0.001 ARG X 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1906 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1903 time to evaluate : 5.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 ASN cc_start: 0.7422 (t0) cc_final: 0.7088 (t0) REVERT: L 80 MET cc_start: 0.6896 (mmp) cc_final: 0.5453 (mmp) REVERT: L 108 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7893 (tm-30) REVERT: L 109 ILE cc_start: 0.9041 (tt) cc_final: 0.8361 (tt) REVERT: L 123 GLN cc_start: 0.9204 (tp40) cc_final: 0.8681 (tp40) REVERT: L 152 TYR cc_start: 0.8537 (m-10) cc_final: 0.8291 (m-10) REVERT: M 63 HIS cc_start: 0.4533 (m-70) cc_final: 0.4171 (m170) REVERT: M 64 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7415 (mmmt) REVERT: M 79 MET cc_start: 0.8371 (mpp) cc_final: 0.8096 (mpp) REVERT: M 110 LEU cc_start: 0.8694 (tp) cc_final: 0.8328 (tp) REVERT: M 120 GLU cc_start: 0.6185 (tm-30) cc_final: 0.5841 (tm-30) REVERT: M 127 VAL cc_start: 0.9369 (t) cc_final: 0.9123 (p) REVERT: M 145 TYR cc_start: 0.7437 (m-80) cc_final: 0.7110 (m-80) REVERT: M 188 ILE cc_start: 0.9204 (mt) cc_final: 0.8892 (mt) REVERT: N 93 ILE cc_start: 0.8937 (mm) cc_final: 0.8610 (tp) REVERT: N 110 LEU cc_start: 0.8999 (pp) cc_final: 0.8551 (tp) REVERT: N 127 LYS cc_start: 0.8241 (mttt) cc_final: 0.7714 (mmtp) REVERT: N 153 SER cc_start: 0.8101 (p) cc_final: 0.7424 (t) REVERT: N 216 LEU cc_start: 0.7649 (tp) cc_final: 0.7255 (tt) REVERT: O 73 PHE cc_start: 0.8055 (p90) cc_final: 0.7574 (p90) REVERT: O 79 ASP cc_start: 0.7955 (m-30) cc_final: 0.7667 (m-30) REVERT: O 90 GLU cc_start: 0.8334 (tp30) cc_final: 0.8123 (tp30) REVERT: O 156 TRP cc_start: 0.7907 (m100) cc_final: 0.7603 (m-10) REVERT: O 185 ASP cc_start: 0.7704 (m-30) cc_final: 0.7026 (p0) REVERT: O 211 MET cc_start: 0.6402 (tmm) cc_final: 0.6180 (tmm) REVERT: P 122 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7644 (tm-30) REVERT: P 189 MET cc_start: 0.3517 (ttm) cc_final: 0.2948 (mtp) REVERT: P 206 MET cc_start: 0.6478 (mpp) cc_final: 0.6274 (mpp) REVERT: Q 16 GLN cc_start: 0.9321 (mp10) cc_final: 0.9118 (mp10) REVERT: Q 112 ILE cc_start: 0.8775 (pt) cc_final: 0.8268 (pt) REVERT: Q 117 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8274 (tm-30) REVERT: Q 164 ARG cc_start: 0.7389 (tpm170) cc_final: 0.7087 (tpp80) REVERT: Q 173 GLU cc_start: 0.6733 (pp20) cc_final: 0.6261 (tm-30) REVERT: Q 176 MET cc_start: 0.7291 (tmm) cc_final: 0.6854 (tmm) REVERT: Q 229 VAL cc_start: 0.7250 (t) cc_final: 0.7038 (m) REVERT: Q 237 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6151 (tm-30) REVERT: R 14 THR cc_start: 0.8725 (m) cc_final: 0.8514 (p) REVERT: R 25 GLU cc_start: 0.8170 (tp30) cc_final: 0.7369 (tp30) REVERT: R 123 TYR cc_start: 0.8169 (m-10) cc_final: 0.7959 (m-10) REVERT: R 141 TYR cc_start: 0.7200 (t80) cc_final: 0.6911 (t80) REVERT: R 148 GLN cc_start: 0.7036 (tt0) cc_final: 0.6332 (tt0) REVERT: R 171 GLN cc_start: 0.8707 (pm20) cc_final: 0.8458 (pm20) REVERT: R 206 LYS cc_start: 0.4085 (tttt) cc_final: 0.3604 (tptt) REVERT: R 222 ASN cc_start: 0.8507 (t0) cc_final: 0.8105 (t0) REVERT: A 25 PHE cc_start: 0.7830 (t80) cc_final: 0.7041 (m-80) REVERT: A 26 GLN cc_start: 0.7423 (mt0) cc_final: 0.6673 (pp30) REVERT: A 40 ILE cc_start: 0.7270 (mt) cc_final: 0.6982 (pt) REVERT: A 128 LEU cc_start: 0.8520 (mt) cc_final: 0.8151 (mm) REVERT: B 5 ARG cc_start: 0.6186 (mtt180) cc_final: 0.4359 (mmp-170) REVERT: B 18 ARG cc_start: 0.7353 (tmm-80) cc_final: 0.6923 (tmm160) REVERT: B 109 LYS cc_start: 0.6182 (ttmt) cc_final: 0.5718 (mmtt) REVERT: B 138 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7717 (mm110) REVERT: B 168 GLU cc_start: 0.7461 (pt0) cc_final: 0.7056 (pt0) REVERT: B 204 LEU cc_start: 0.4453 (tt) cc_final: 0.4189 (tt) REVERT: B 215 MET cc_start: 0.6747 (mpp) cc_final: 0.5243 (tpp) REVERT: B 227 TYR cc_start: 0.5325 (t80) cc_final: 0.5112 (t80) REVERT: C 154 GLU cc_start: 0.8979 (tt0) cc_final: 0.8482 (mm-30) REVERT: C 160 MET cc_start: 0.9008 (ptt) cc_final: 0.8796 (ptm) REVERT: C 164 HIS cc_start: 0.6762 (m-70) cc_final: 0.6428 (m90) REVERT: C 227 TYR cc_start: 0.6888 (t80) cc_final: 0.6628 (t80) REVERT: D 31 PHE cc_start: 0.6922 (m-10) cc_final: 0.6624 (m-10) REVERT: D 138 PHE cc_start: 0.6591 (t80) cc_final: 0.5718 (p90) REVERT: D 149 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6696 (ttp-170) REVERT: D 153 VAL cc_start: 0.8876 (t) cc_final: 0.8582 (t) REVERT: E 127 GLN cc_start: 0.7043 (mm-40) cc_final: 0.6651 (mp10) REVERT: E 132 THR cc_start: 0.8211 (m) cc_final: 0.7953 (m) REVERT: E 136 GLN cc_start: 0.6795 (mt0) cc_final: 0.6534 (mt0) REVERT: E 227 TYR cc_start: 0.6889 (t80) cc_final: 0.6467 (t80) REVERT: E 228 ASP cc_start: 0.7842 (m-30) cc_final: 0.7353 (m-30) REVERT: F 110 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7308 (tp30) REVERT: F 124 TRP cc_start: 0.5487 (t60) cc_final: 0.5180 (t60) REVERT: F 151 ASN cc_start: 0.7534 (p0) cc_final: 0.7175 (p0) REVERT: F 171 ARG cc_start: 0.6452 (mtp85) cc_final: 0.5822 (mmp80) REVERT: F 194 ARG cc_start: 0.7321 (mmp80) cc_final: 0.6517 (mpt180) REVERT: G 40 LEU cc_start: 0.7351 (mt) cc_final: 0.7093 (mt) REVERT: G 147 ASN cc_start: 0.5154 (m-40) cc_final: 0.4953 (m-40) REVERT: G 210 ARG cc_start: 0.4357 (mtm180) cc_final: 0.3547 (mtp85) REVERT: G 230 ILE cc_start: 0.7647 (mm) cc_final: 0.7382 (mt) REVERT: a 8 THR cc_start: 0.8500 (m) cc_final: 0.8251 (p) REVERT: a 99 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7730 (mm-30) REVERT: a 102 VAL cc_start: 0.9010 (t) cc_final: 0.8640 (t) REVERT: a 143 ARG cc_start: 0.7242 (mmm160) cc_final: 0.6760 (mmm160) REVERT: a 196 LEU cc_start: 0.7160 (mt) cc_final: 0.6759 (mt) REVERT: b 84 ASP cc_start: 0.8274 (m-30) cc_final: 0.8049 (m-30) REVERT: b 147 ASP cc_start: 0.6633 (m-30) cc_final: 0.6103 (m-30) REVERT: c 87 PHE cc_start: 0.7503 (t80) cc_final: 0.7230 (t80) REVERT: c 88 MET cc_start: 0.8417 (mmt) cc_final: 0.8010 (mmt) REVERT: c 164 ARG cc_start: 0.6217 (ptm160) cc_final: 0.4927 (ptt180) REVERT: c 190 HIS cc_start: 0.7972 (m-70) cc_final: 0.7315 (m-70) REVERT: d 59 TYR cc_start: 0.8337 (m-10) cc_final: 0.7780 (m-10) REVERT: d 71 ASP cc_start: 0.7945 (t0) cc_final: 0.7578 (t0) REVERT: d 102 ASN cc_start: 0.8526 (m110) cc_final: 0.7912 (m110) REVERT: d 145 ASP cc_start: 0.8396 (m-30) cc_final: 0.8105 (m-30) REVERT: d 185 MET cc_start: 0.7277 (ptm) cc_final: 0.6002 (pmm) REVERT: e 27 TYR cc_start: 0.8715 (m-10) cc_final: 0.8341 (m-10) REVERT: e 33 ASN cc_start: 0.8050 (m-40) cc_final: 0.7268 (t0) REVERT: e 71 LYS cc_start: 0.8382 (tttt) cc_final: 0.8057 (ttmt) REVERT: e 117 ARG cc_start: 0.7226 (tpt-90) cc_final: 0.6910 (tpt-90) REVERT: e 138 MET cc_start: 0.8264 (tmm) cc_final: 0.7952 (tmm) REVERT: f 44 VAL cc_start: 0.9196 (t) cc_final: 0.8786 (p) REVERT: f 119 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8269 (tm-30) REVERT: g 1 MET cc_start: 0.7410 (mmm) cc_final: 0.6846 (mmm) REVERT: g 53 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: g 90 LEU cc_start: 0.8767 (mt) cc_final: 0.8451 (mt) REVERT: g 92 LEU cc_start: 0.9145 (tp) cc_final: 0.8895 (tt) REVERT: g 140 ASP cc_start: 0.7206 (p0) cc_final: 0.6975 (p0) REVERT: g 148 TYR cc_start: 0.8239 (m-80) cc_final: 0.7985 (m-80) REVERT: g 159 TRP cc_start: 0.7818 (m100) cc_final: 0.7151 (m-10) REVERT: g 192 LEU cc_start: 0.7825 (mt) cc_final: 0.7617 (tp) REVERT: g 222 LYS cc_start: 0.5337 (pptt) cc_final: 0.5023 (pptt) REVERT: H 66 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8119 (mmm-85) REVERT: H 96 TYR cc_start: 0.9266 (t80) cc_final: 0.9060 (t80) REVERT: H 149 MET cc_start: 0.7635 (tpp) cc_final: 0.6992 (tpp) REVERT: H 153 LEU cc_start: 0.8720 (mt) cc_final: 0.8329 (mt) REVERT: H 155 GLU cc_start: 0.7386 (mm-30) cc_final: 0.6798 (mm-30) REVERT: I 5 ILE cc_start: 0.8570 (tt) cc_final: 0.8141 (tp) REVERT: I 85 ARG cc_start: 0.8902 (ttp80) cc_final: 0.8549 (tmm-80) REVERT: J 119 MET cc_start: 0.9466 (tpp) cc_final: 0.9041 (tpp) REVERT: J 184 LYS cc_start: 0.4718 (mmtt) cc_final: 0.3479 (mttt) REVERT: K 57 LEU cc_start: 0.8766 (mt) cc_final: 0.8442 (tp) REVERT: K 67 ILE cc_start: 0.8316 (mt) cc_final: 0.8085 (mt) REVERT: K 121 LEU cc_start: 0.8924 (mt) cc_final: 0.8660 (mt) REVERT: K 155 MET cc_start: 0.7452 (mmm) cc_final: 0.7201 (mmt) REVERT: K 220 VAL cc_start: 0.8525 (t) cc_final: 0.8221 (t) REVERT: K 223 TYR cc_start: 0.8390 (m-10) cc_final: 0.7899 (m-80) REVERT: K 258 HIS cc_start: 0.6882 (m-70) cc_final: 0.6147 (t-90) REVERT: S 96 TYR cc_start: 0.8112 (t80) cc_final: 0.7372 (t80) REVERT: S 136 PHE cc_start: 0.8197 (p90) cc_final: 0.7649 (p90) REVERT: S 145 GLN cc_start: 0.8649 (mt0) cc_final: 0.8248 (mp10) REVERT: S 169 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8842 (mm110) REVERT: S 178 ASP cc_start: 0.8997 (t0) cc_final: 0.8636 (t70) REVERT: S 198 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7104 (mtm110) REVERT: S 204 MET cc_start: 0.7254 (mpp) cc_final: 0.6592 (mpp) REVERT: S 205 ASP cc_start: 0.6138 (t0) cc_final: 0.4866 (m-30) REVERT: T 73 TYR cc_start: 0.4735 (m-80) cc_final: 0.4500 (m-10) REVERT: T 118 MET cc_start: 0.7723 (ttm) cc_final: 0.7420 (ttm) REVERT: T 178 PHE cc_start: 0.7118 (m-80) cc_final: 0.6915 (m-80) REVERT: U 133 TYR cc_start: 0.6958 (t80) cc_final: 0.6467 (t80) REVERT: U 186 MET cc_start: 0.5776 (mmm) cc_final: 0.4692 (mtp) REVERT: U 201 ARG cc_start: 0.7998 (ttt180) cc_final: 0.7441 (tpp80) REVERT: U 217 THR cc_start: 0.8462 (m) cc_final: 0.8216 (m) REVERT: V 149 ASN cc_start: 0.7503 (t0) cc_final: 0.7284 (t0) REVERT: V 201 LYS cc_start: 0.6229 (mttt) cc_final: 0.5152 (tptt) REVERT: W 21 THR cc_start: 0.9106 (m) cc_final: 0.8489 (p) REVERT: W 23 ILE cc_start: 0.9503 (pt) cc_final: 0.9143 (pt) REVERT: W 37 ASP cc_start: 0.7695 (p0) cc_final: 0.7310 (p0) REVERT: W 66 SER cc_start: 0.9108 (t) cc_final: 0.8874 (m) REVERT: W 91 GLU cc_start: 0.8646 (mp0) cc_final: 0.8381 (mp0) REVERT: W 101 ASN cc_start: 0.8345 (t160) cc_final: 0.7781 (t0) REVERT: X 185 MET cc_start: 0.6455 (tpp) cc_final: 0.6135 (tpp) REVERT: X 224 MET cc_start: 0.7820 (mmp) cc_final: 0.7504 (mmm) REVERT: Y 114 LEU cc_start: 0.7914 (tt) cc_final: 0.7452 (tt) REVERT: Y 142 ASN cc_start: 0.8565 (p0) cc_final: 0.8141 (p0) REVERT: Y 153 LYS cc_start: 0.8551 (tttt) cc_final: 0.7967 (tppt) REVERT: Y 239 ASP cc_start: 0.9278 (t0) cc_final: 0.9016 (t0) REVERT: Y 260 GLU cc_start: 0.7534 (pp20) cc_final: 0.6823 (pm20) REVERT: Z 49 ARG cc_start: 0.7380 (ptt90) cc_final: 0.6740 (ppt170) REVERT: Z 101 ASN cc_start: 0.8101 (t160) cc_final: 0.7896 (t0) REVERT: Z 108 TYR cc_start: 0.8986 (t80) cc_final: 0.8759 (t80) REVERT: Z 132 TYR cc_start: 0.8690 (m-80) cc_final: 0.8368 (m-80) REVERT: 1 90 ASP cc_start: 0.8033 (m-30) cc_final: 0.7565 (m-30) REVERT: 1 97 MET cc_start: 0.7201 (tmm) cc_final: 0.6804 (tmm) REVERT: 1 202 ILE cc_start: 0.9064 (mm) cc_final: 0.8749 (mm) REVERT: 1 224 MET cc_start: 0.7291 (ttt) cc_final: 0.6978 (tmm) REVERT: 2 81 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7873 (tm-30) REVERT: 2 116 THR cc_start: 0.9111 (p) cc_final: 0.8139 (m) REVERT: 2 118 SER cc_start: 0.9022 (t) cc_final: 0.8729 (m) REVERT: 2 159 MET cc_start: 0.8465 (ppp) cc_final: 0.7603 (ppp) REVERT: 2 205 SER cc_start: 0.9016 (p) cc_final: 0.8702 (p) REVERT: 2 251 MET cc_start: 0.6552 (tpt) cc_final: 0.6073 (tmm) REVERT: 2 253 GLU cc_start: 0.6634 (tp30) cc_final: 0.6208 (tp30) REVERT: 2 260 GLU cc_start: 0.8668 (pp20) cc_final: 0.8389 (pp20) outliers start: 3 outliers final: 0 residues processed: 1905 average time/residue: 0.5613 time to fit residues: 1800.2431 Evaluate side-chains 1533 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1532 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 446 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 431 optimal weight: 0.8980 chunk 217 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 139 optimal weight: 0.6980 chunk 458 optimal weight: 5.9990 chunk 491 optimal weight: 0.9990 chunk 356 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 567 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 172 GLN L 224 ASN M 95 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 54 GLN P 155 HIS ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 218 HIS E 164 HIS E 233 ASN ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 122 ASN b 97 GLN ** b 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 HIS ** g 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 119 GLN H 7 ASN H 65 GLN I 87 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN K 192 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN T 63 ASN T 87 ASN T 132 HIS ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 91 ASN V 92 ASN W 101 ASN ** Z 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 101 ASN 1 124 GLN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.8276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 61042 Z= 0.191 Angle : 0.649 14.421 82480 Z= 0.335 Chirality : 0.044 0.216 9289 Planarity : 0.005 0.078 10629 Dihedral : 4.866 35.996 8371 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.08 % Allowed : 0.96 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.09), residues: 7577 helix: 0.67 (0.09), residues: 3270 sheet: -0.10 (0.13), residues: 1430 loop : -0.66 (0.12), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP d 216 HIS 0.015 0.001 HIS E 202 PHE 0.029 0.002 PHE G 43 TYR 0.027 0.002 TYR C 223 ARG 0.016 0.001 ARG X 123 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1910 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1905 time to evaluate : 5.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 ASN cc_start: 0.7220 (t0) cc_final: 0.6879 (t0) REVERT: L 80 MET cc_start: 0.7011 (mmp) cc_final: 0.6548 (mmp) REVERT: L 108 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7746 (tm-30) REVERT: L 109 ILE cc_start: 0.9062 (tt) cc_final: 0.8374 (tt) REVERT: L 123 GLN cc_start: 0.9240 (tp40) cc_final: 0.8788 (tp40) REVERT: L 152 TYR cc_start: 0.8372 (m-10) cc_final: 0.8168 (m-10) REVERT: M 79 MET cc_start: 0.8280 (mpp) cc_final: 0.7998 (mpp) REVERT: M 89 ARG cc_start: 0.8184 (mtp85) cc_final: 0.7980 (mtp85) REVERT: M 110 LEU cc_start: 0.8661 (tp) cc_final: 0.8252 (tp) REVERT: M 119 GLN cc_start: 0.8479 (tp40) cc_final: 0.8213 (tp40) REVERT: M 120 GLU cc_start: 0.6440 (tm-30) cc_final: 0.5941 (tm-30) REVERT: M 136 ILE cc_start: 0.8272 (mm) cc_final: 0.7937 (mm) REVERT: M 145 TYR cc_start: 0.7438 (m-80) cc_final: 0.7084 (m-10) REVERT: M 155 TYR cc_start: 0.8962 (p90) cc_final: 0.8703 (p90) REVERT: N 93 ILE cc_start: 0.8958 (mm) cc_final: 0.8647 (tp) REVERT: N 110 LEU cc_start: 0.8916 (pp) cc_final: 0.8406 (tp) REVERT: N 127 LYS cc_start: 0.8160 (mttt) cc_final: 0.7832 (mmtp) REVERT: N 149 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7525 (tm-30) REVERT: N 153 SER cc_start: 0.7958 (p) cc_final: 0.7438 (t) REVERT: N 198 ASN cc_start: 0.7025 (p0) cc_final: 0.6258 (p0) REVERT: N 216 LEU cc_start: 0.7594 (tp) cc_final: 0.7195 (tt) REVERT: O 54 GLN cc_start: 0.7521 (pt0) cc_final: 0.7189 (pt0) REVERT: O 57 ARG cc_start: 0.7715 (mmp80) cc_final: 0.7157 (mpt180) REVERT: O 73 PHE cc_start: 0.7929 (p90) cc_final: 0.7340 (p90) REVERT: O 90 GLU cc_start: 0.8307 (tp30) cc_final: 0.8063 (tp30) REVERT: O 117 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8022 (mtm180) REVERT: O 185 ASP cc_start: 0.7648 (m-30) cc_final: 0.7020 (p0) REVERT: P 122 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7594 (tm-30) REVERT: P 189 MET cc_start: 0.3503 (ttm) cc_final: 0.2995 (mtp) REVERT: P 206 MET cc_start: 0.6500 (mpp) cc_final: 0.6149 (mpp) REVERT: Q 112 ILE cc_start: 0.8751 (pt) cc_final: 0.8367 (pt) REVERT: Q 117 GLN cc_start: 0.8808 (tm-30) cc_final: 0.8232 (tm-30) REVERT: Q 146 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8215 (tm-30) REVERT: Q 164 ARG cc_start: 0.7388 (tpm170) cc_final: 0.7131 (tpp80) REVERT: Q 173 GLU cc_start: 0.6686 (pp20) cc_final: 0.6052 (tm-30) REVERT: Q 176 MET cc_start: 0.6980 (tmm) cc_final: 0.6612 (tmm) REVERT: R 25 GLU cc_start: 0.8053 (tp30) cc_final: 0.7255 (tp30) REVERT: R 141 TYR cc_start: 0.6971 (t80) cc_final: 0.6702 (t80) REVERT: R 145 ASP cc_start: 0.6088 (p0) cc_final: 0.5742 (p0) REVERT: R 148 GLN cc_start: 0.6916 (tt0) cc_final: 0.6055 (tt0) REVERT: R 206 LYS cc_start: 0.4057 (tttt) cc_final: 0.3532 (tptt) REVERT: A 25 PHE cc_start: 0.7810 (t80) cc_final: 0.7055 (m-80) REVERT: A 26 GLN cc_start: 0.7400 (mt0) cc_final: 0.6598 (pp30) REVERT: A 40 ILE cc_start: 0.7250 (mt) cc_final: 0.7026 (pt) REVERT: A 128 LEU cc_start: 0.8506 (mt) cc_final: 0.8058 (mm) REVERT: A 212 PHE cc_start: 0.6072 (m-80) cc_final: 0.5807 (m-80) REVERT: B 5 ARG cc_start: 0.6265 (mtt180) cc_final: 0.4377 (mmp-170) REVERT: B 109 LYS cc_start: 0.6078 (ttmt) cc_final: 0.5674 (mmtt) REVERT: B 138 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7642 (mm110) REVERT: B 168 GLU cc_start: 0.7611 (pt0) cc_final: 0.7321 (pt0) REVERT: B 215 MET cc_start: 0.6762 (mpp) cc_final: 0.5371 (tpp) REVERT: C 154 GLU cc_start: 0.8999 (tt0) cc_final: 0.8416 (mm-30) REVERT: C 164 HIS cc_start: 0.6704 (m-70) cc_final: 0.6407 (m90) REVERT: C 166 LYS cc_start: 0.7011 (mtmt) cc_final: 0.6742 (ptmm) REVERT: C 227 TYR cc_start: 0.6831 (t80) cc_final: 0.6543 (t80) REVERT: D 31 PHE cc_start: 0.6800 (m-10) cc_final: 0.6536 (m-10) REVERT: D 138 PHE cc_start: 0.6635 (t80) cc_final: 0.5438 (p90) REVERT: D 153 VAL cc_start: 0.8877 (t) cc_final: 0.8585 (t) REVERT: D 187 TYR cc_start: 0.6439 (t80) cc_final: 0.6142 (t80) REVERT: E 127 GLN cc_start: 0.6912 (mm-40) cc_final: 0.6646 (mp10) REVERT: E 132 THR cc_start: 0.7952 (m) cc_final: 0.7682 (m) REVERT: E 136 GLN cc_start: 0.6695 (mt0) cc_final: 0.6463 (mt0) REVERT: E 228 ASP cc_start: 0.7905 (m-30) cc_final: 0.7454 (m-30) REVERT: F 110 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7315 (tp30) REVERT: F 124 TRP cc_start: 0.5479 (t60) cc_final: 0.5174 (t60) REVERT: F 125 ILE cc_start: 0.8708 (mt) cc_final: 0.8464 (pt) REVERT: F 143 GLN cc_start: 0.8150 (tt0) cc_final: 0.7881 (tp40) REVERT: F 171 ARG cc_start: 0.6575 (mtp85) cc_final: 0.5883 (mmp80) REVERT: F 194 ARG cc_start: 0.7322 (mmp80) cc_final: 0.7117 (mmp80) REVERT: G 147 ASN cc_start: 0.5116 (m-40) cc_final: 0.4889 (m-40) REVERT: G 210 ARG cc_start: 0.4317 (mtm180) cc_final: 0.3537 (mtp85) REVERT: a 8 THR cc_start: 0.8452 (m) cc_final: 0.8187 (p) REVERT: a 99 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7770 (mm-30) REVERT: a 143 ARG cc_start: 0.7199 (mmm160) cc_final: 0.6859 (mmm160) REVERT: a 196 LEU cc_start: 0.7112 (mt) cc_final: 0.6673 (mt) REVERT: b 147 ASP cc_start: 0.6388 (m-30) cc_final: 0.5869 (m-30) REVERT: c 88 MET cc_start: 0.8341 (mmt) cc_final: 0.7942 (mmt) REVERT: c 137 TYR cc_start: 0.7517 (t80) cc_final: 0.6958 (t80) REVERT: c 164 ARG cc_start: 0.6415 (ptm160) cc_final: 0.4818 (ptt180) REVERT: c 190 HIS cc_start: 0.7846 (m-70) cc_final: 0.7189 (m-70) REVERT: c 234 GLU cc_start: 0.8468 (pp20) cc_final: 0.8253 (pp20) REVERT: d 59 TYR cc_start: 0.8313 (m-10) cc_final: 0.7981 (m-10) REVERT: d 71 ASP cc_start: 0.7844 (t0) cc_final: 0.7516 (t0) REVERT: d 102 ASN cc_start: 0.8469 (m110) cc_final: 0.7809 (m110) REVERT: d 145 ASP cc_start: 0.8583 (m-30) cc_final: 0.8320 (m-30) REVERT: d 157 VAL cc_start: 0.8787 (t) cc_final: 0.8323 (p) REVERT: d 164 CYS cc_start: 0.6779 (p) cc_final: 0.6460 (p) REVERT: e 27 TYR cc_start: 0.8546 (m-10) cc_final: 0.8157 (m-10) REVERT: e 113 MET cc_start: 0.8229 (mmm) cc_final: 0.7850 (tpt) REVERT: e 138 MET cc_start: 0.8233 (tmm) cc_final: 0.7898 (tmm) REVERT: f 100 VAL cc_start: 0.9080 (t) cc_final: 0.8834 (t) REVERT: f 119 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8152 (tm-30) REVERT: f 218 PHE cc_start: 0.8521 (t80) cc_final: 0.8306 (t80) REVERT: g 5 TYR cc_start: 0.6351 (m-80) cc_final: 0.5938 (m-80) REVERT: g 90 LEU cc_start: 0.8633 (mt) cc_final: 0.8353 (mt) REVERT: g 92 LEU cc_start: 0.9118 (tp) cc_final: 0.8875 (tt) REVERT: g 118 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7841 (mttt) REVERT: g 159 TRP cc_start: 0.7685 (m100) cc_final: 0.7258 (m-10) REVERT: g 222 LYS cc_start: 0.5480 (pptt) cc_final: 0.5161 (pptt) REVERT: H 27 ARG cc_start: 0.8748 (ptm-80) cc_final: 0.8512 (ptm-80) REVERT: H 66 ARG cc_start: 0.8317 (tpp80) cc_final: 0.8101 (mmm-85) REVERT: H 96 TYR cc_start: 0.9155 (t80) cc_final: 0.8937 (t80) REVERT: H 109 ILE cc_start: 0.9489 (mp) cc_final: 0.9288 (mp) REVERT: H 136 PHE cc_start: 0.8811 (p90) cc_final: 0.8300 (p90) REVERT: H 149 MET cc_start: 0.7493 (tpp) cc_final: 0.7042 (tpp) REVERT: H 204 MET cc_start: 0.6542 (mmt) cc_final: 0.6042 (mmt) REVERT: I 5 ILE cc_start: 0.8559 (tt) cc_final: 0.8201 (tp) REVERT: I 60 ILE cc_start: 0.9450 (mm) cc_final: 0.9204 (mm) REVERT: I 85 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8369 (tmt170) REVERT: I 119 ASP cc_start: 0.7515 (p0) cc_final: 0.7305 (p0) REVERT: I 168 GLN cc_start: 0.8482 (mt0) cc_final: 0.8264 (mt0) REVERT: J 66 ARG cc_start: 0.8122 (mtm180) cc_final: 0.7843 (mmm-85) REVERT: J 119 MET cc_start: 0.9480 (tpp) cc_final: 0.9057 (tpp) REVERT: J 177 LEU cc_start: 0.8245 (mm) cc_final: 0.8036 (mm) REVERT: J 184 LYS cc_start: 0.4852 (mmtt) cc_final: 0.3611 (mttt) REVERT: J 219 ASP cc_start: 0.7071 (m-30) cc_final: 0.6726 (m-30) REVERT: K 57 LEU cc_start: 0.8427 (mt) cc_final: 0.8092 (mt) REVERT: K 121 LEU cc_start: 0.8872 (mt) cc_final: 0.8590 (mt) REVERT: K 220 VAL cc_start: 0.8492 (t) cc_final: 0.8075 (t) REVERT: K 258 HIS cc_start: 0.6723 (m-70) cc_final: 0.5666 (t-90) REVERT: S 26 ARG cc_start: 0.7357 (tpp80) cc_final: 0.6776 (tpp80) REVERT: S 27 ARG cc_start: 0.8898 (tmt170) cc_final: 0.8435 (tmt170) REVERT: S 38 ASP cc_start: 0.8141 (t0) cc_final: 0.7612 (t0) REVERT: S 96 TYR cc_start: 0.8064 (t80) cc_final: 0.7090 (t80) REVERT: S 145 GLN cc_start: 0.8639 (mt0) cc_final: 0.8169 (mp10) REVERT: S 169 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8835 (mm110) REVERT: S 178 ASP cc_start: 0.8998 (t0) cc_final: 0.8573 (t70) REVERT: S 183 MET cc_start: 0.7866 (mpp) cc_final: 0.6982 (mpp) REVERT: S 198 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7116 (mtm110) REVERT: S 204 MET cc_start: 0.7216 (mpp) cc_final: 0.6803 (mpp) REVERT: S 205 ASP cc_start: 0.6013 (t0) cc_final: 0.4829 (m-30) REVERT: U 133 TYR cc_start: 0.6872 (t80) cc_final: 0.6417 (t80) REVERT: U 186 MET cc_start: 0.5984 (mmm) cc_final: 0.4644 (mtp) REVERT: U 241 ASP cc_start: 0.7239 (p0) cc_final: 0.6922 (p0) REVERT: V 175 VAL cc_start: 0.8331 (t) cc_final: 0.8085 (t) REVERT: V 201 LYS cc_start: 0.6193 (mttt) cc_final: 0.5116 (tptt) REVERT: V 218 MET cc_start: 0.8724 (mmp) cc_final: 0.8433 (mmm) REVERT: W 21 THR cc_start: 0.9058 (m) cc_final: 0.8513 (p) REVERT: W 23 ILE cc_start: 0.9524 (pt) cc_final: 0.9167 (pt) REVERT: W 37 ASP cc_start: 0.7916 (p0) cc_final: 0.7623 (p0) REVERT: W 66 SER cc_start: 0.9047 (t) cc_final: 0.8839 (m) REVERT: W 91 GLU cc_start: 0.8572 (mp0) cc_final: 0.8323 (mp0) REVERT: W 101 ASN cc_start: 0.8223 (t160) cc_final: 0.7734 (t0) REVERT: W 176 THR cc_start: 0.8927 (m) cc_final: 0.8662 (p) REVERT: W 186 ASP cc_start: 0.8798 (t70) cc_final: 0.8551 (t0) REVERT: X 113 CYS cc_start: 0.6269 (m) cc_final: 0.3730 (m) REVERT: X 120 ARG cc_start: 0.7665 (ptm-80) cc_final: 0.7254 (ptp-170) REVERT: X 185 MET cc_start: 0.6141 (tpp) cc_final: 0.5781 (tpp) REVERT: X 224 MET cc_start: 0.7894 (mmp) cc_final: 0.7203 (mmm) REVERT: Y 138 TYR cc_start: 0.8727 (t80) cc_final: 0.8410 (t80) REVERT: Y 142 ASN cc_start: 0.8651 (p0) cc_final: 0.8207 (p0) REVERT: Y 153 LYS cc_start: 0.8627 (tttt) cc_final: 0.7780 (tppt) REVERT: Y 192 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7900 (ttp-170) REVERT: Y 204 ASN cc_start: 0.8463 (p0) cc_final: 0.8074 (p0) REVERT: Y 239 ASP cc_start: 0.9231 (t0) cc_final: 0.9010 (t0) REVERT: Y 260 GLU cc_start: 0.7496 (pp20) cc_final: 0.7033 (pp20) REVERT: Z 101 ASN cc_start: 0.8034 (t160) cc_final: 0.7743 (t0) REVERT: Z 108 TYR cc_start: 0.8896 (t80) cc_final: 0.8638 (t80) REVERT: Z 166 MET cc_start: 0.7090 (mtt) cc_final: 0.6714 (mtt) REVERT: 1 96 ARG cc_start: 0.7810 (mtp180) cc_final: 0.7572 (mtp180) REVERT: 1 202 ILE cc_start: 0.8929 (mm) cc_final: 0.8628 (mm) REVERT: 2 81 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7954 (tm-30) REVERT: 2 105 LYS cc_start: 0.8685 (mttm) cc_final: 0.8062 (mttm) REVERT: 2 118 SER cc_start: 0.8939 (t) cc_final: 0.8678 (m) REVERT: 2 165 MET cc_start: 0.7854 (mtt) cc_final: 0.7506 (mtt) REVERT: 2 205 SER cc_start: 0.8860 (p) cc_final: 0.8469 (p) REVERT: 2 251 MET cc_start: 0.6463 (tpt) cc_final: 0.6011 (tmm) REVERT: 2 253 GLU cc_start: 0.6486 (tp30) cc_final: 0.6091 (tp30) REVERT: 2 256 TRP cc_start: 0.6958 (p-90) cc_final: 0.6418 (p-90) outliers start: 5 outliers final: 1 residues processed: 1906 average time/residue: 0.5623 time to fit residues: 1805.1885 Evaluate side-chains 1533 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1532 time to evaluate : 5.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 656 optimal weight: 5.9990 chunk 691 optimal weight: 0.9980 chunk 631 optimal weight: 5.9990 chunk 672 optimal weight: 0.6980 chunk 404 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 528 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 607 optimal weight: 7.9990 chunk 636 optimal weight: 3.9990 chunk 670 optimal weight: 0.7980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN P 73 HIS P 186 HIS ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 222 ASN ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 45 GLN D 143 GLN D 218 HIS E 164 HIS ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 97 GLN ** b 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 HIS d 111 HIS e 90 GLN ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 30 HIS g 53 HIS H 7 ASN I 71 ASN I 87 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN W 86 HIS W 101 ASN X 253 GLN Z 101 ASN Z 205 HIS 1 124 GLN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.8565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 61042 Z= 0.244 Angle : 0.688 14.582 82480 Z= 0.356 Chirality : 0.046 0.426 9289 Planarity : 0.005 0.075 10629 Dihedral : 4.954 36.824 8371 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.23 % Rotamer: Outliers : 0.08 % Allowed : 0.74 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.10), residues: 7577 helix: 0.66 (0.09), residues: 3264 sheet: -0.15 (0.13), residues: 1437 loop : -0.70 (0.12), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP d 216 HIS 0.016 0.001 HIS E 202 PHE 0.031 0.002 PHE P 101 TYR 0.051 0.002 TYR f 83 ARG 0.013 0.001 ARG Y 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1831 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1826 time to evaluate : 5.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 ASN cc_start: 0.7201 (t0) cc_final: 0.6863 (t0) REVERT: L 108 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7774 (tm-30) REVERT: L 109 ILE cc_start: 0.9103 (tt) cc_final: 0.8361 (tt) REVERT: L 123 GLN cc_start: 0.9200 (tp40) cc_final: 0.8791 (tp40) REVERT: M 66 GLU cc_start: 0.8613 (mp0) cc_final: 0.8230 (mp0) REVERT: M 79 MET cc_start: 0.8313 (mpp) cc_final: 0.7979 (mpp) REVERT: M 110 LEU cc_start: 0.8708 (tp) cc_final: 0.8261 (tp) REVERT: M 119 GLN cc_start: 0.8632 (tp40) cc_final: 0.8364 (tp40) REVERT: M 120 GLU cc_start: 0.6184 (tm-30) cc_final: 0.5825 (tm-30) REVERT: M 136 ILE cc_start: 0.8509 (mm) cc_final: 0.8234 (mm) REVERT: M 188 ILE cc_start: 0.9205 (mt) cc_final: 0.8967 (mt) REVERT: N 110 LEU cc_start: 0.8967 (pp) cc_final: 0.8487 (tp) REVERT: N 127 LYS cc_start: 0.8157 (mttt) cc_final: 0.7847 (mmtp) REVERT: N 149 GLN cc_start: 0.7829 (tm-30) cc_final: 0.7572 (tm-30) REVERT: N 153 SER cc_start: 0.8085 (p) cc_final: 0.7527 (t) REVERT: N 216 LEU cc_start: 0.7649 (tp) cc_final: 0.7260 (tt) REVERT: O 54 GLN cc_start: 0.7491 (pt0) cc_final: 0.7158 (pt0) REVERT: O 57 ARG cc_start: 0.8237 (mmp80) cc_final: 0.7408 (mmm160) REVERT: O 73 PHE cc_start: 0.8026 (p90) cc_final: 0.7381 (p90) REVERT: O 79 ASP cc_start: 0.8165 (m-30) cc_final: 0.7947 (m-30) REVERT: O 90 GLU cc_start: 0.8335 (tp30) cc_final: 0.8097 (tp30) REVERT: O 132 LEU cc_start: 0.9305 (mp) cc_final: 0.9094 (mt) REVERT: O 185 ASP cc_start: 0.7720 (m-30) cc_final: 0.7048 (p0) REVERT: P 122 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7673 (tm-30) REVERT: P 189 MET cc_start: 0.3712 (ttm) cc_final: 0.3158 (mtp) REVERT: Q 112 ILE cc_start: 0.8821 (pt) cc_final: 0.8355 (pt) REVERT: Q 117 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8257 (tm-30) REVERT: Q 159 MET cc_start: 0.5790 (tpt) cc_final: 0.5549 (ttt) REVERT: Q 173 GLU cc_start: 0.6767 (pp20) cc_final: 0.6043 (tm-30) REVERT: Q 176 MET cc_start: 0.6932 (tmm) cc_final: 0.6603 (tmm) REVERT: R 25 GLU cc_start: 0.8137 (tp30) cc_final: 0.7364 (tp30) REVERT: R 141 TYR cc_start: 0.7207 (t80) cc_final: 0.6903 (t80) REVERT: R 145 ASP cc_start: 0.6132 (p0) cc_final: 0.5854 (p0) REVERT: R 148 GLN cc_start: 0.6964 (tt0) cc_final: 0.6147 (tt0) REVERT: R 157 VAL cc_start: 0.8611 (t) cc_final: 0.8272 (t) REVERT: R 206 LYS cc_start: 0.4146 (tttt) cc_final: 0.3583 (tptt) REVERT: A 25 PHE cc_start: 0.8073 (t80) cc_final: 0.7182 (m-80) REVERT: A 26 GLN cc_start: 0.7331 (mt0) cc_final: 0.6600 (pp30) REVERT: A 40 ILE cc_start: 0.7203 (mt) cc_final: 0.6922 (pt) REVERT: A 128 LEU cc_start: 0.8518 (mt) cc_final: 0.8044 (mm) REVERT: B 5 ARG cc_start: 0.6281 (mtt180) cc_final: 0.4174 (mmp-170) REVERT: B 109 LYS cc_start: 0.6155 (ttmt) cc_final: 0.5689 (mmtt) REVERT: B 130 LEU cc_start: 0.8096 (tp) cc_final: 0.7894 (tp) REVERT: B 138 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7787 (mm110) REVERT: B 168 GLU cc_start: 0.7542 (pt0) cc_final: 0.7185 (pt0) REVERT: B 215 MET cc_start: 0.6739 (mpp) cc_final: 0.5361 (tpp) REVERT: C 154 GLU cc_start: 0.8914 (tt0) cc_final: 0.8321 (mm-30) REVERT: C 215 MET cc_start: 0.7584 (ppp) cc_final: 0.7348 (ppp) REVERT: C 227 TYR cc_start: 0.6845 (t80) cc_final: 0.6583 (t80) REVERT: D 138 PHE cc_start: 0.6533 (t80) cc_final: 0.5446 (p90) REVERT: D 153 VAL cc_start: 0.8892 (t) cc_final: 0.8637 (t) REVERT: D 187 TYR cc_start: 0.6362 (t80) cc_final: 0.6113 (t80) REVERT: E 127 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6703 (mp10) REVERT: E 132 THR cc_start: 0.8212 (m) cc_final: 0.7880 (m) REVERT: E 228 ASP cc_start: 0.7949 (m-30) cc_final: 0.7459 (m-30) REVERT: F 110 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7328 (tp30) REVERT: F 121 VAL cc_start: 0.7349 (t) cc_final: 0.7129 (t) REVERT: F 124 TRP cc_start: 0.5534 (t60) cc_final: 0.5240 (t60) REVERT: F 171 ARG cc_start: 0.6624 (mtp85) cc_final: 0.5929 (mmp80) REVERT: F 194 ARG cc_start: 0.7301 (mmp80) cc_final: 0.6643 (mpt180) REVERT: G 40 LEU cc_start: 0.7443 (mt) cc_final: 0.7219 (mt) REVERT: G 210 ARG cc_start: 0.4551 (mtm180) cc_final: 0.3811 (mtp85) REVERT: a 8 THR cc_start: 0.8463 (m) cc_final: 0.8223 (p) REVERT: a 143 ARG cc_start: 0.7218 (mmm160) cc_final: 0.6728 (mmm160) REVERT: a 196 LEU cc_start: 0.7152 (mt) cc_final: 0.6729 (mt) REVERT: b 147 ASP cc_start: 0.6838 (m-30) cc_final: 0.6333 (m-30) REVERT: c 87 PHE cc_start: 0.6942 (t80) cc_final: 0.6342 (t80) REVERT: c 88 MET cc_start: 0.8259 (mmt) cc_final: 0.7893 (mmt) REVERT: c 164 ARG cc_start: 0.6444 (ptm160) cc_final: 0.4878 (ptt180) REVERT: c 190 HIS cc_start: 0.7948 (m-70) cc_final: 0.7247 (m-70) REVERT: c 234 GLU cc_start: 0.8656 (pp20) cc_final: 0.8412 (pp20) REVERT: d 59 TYR cc_start: 0.8371 (m-10) cc_final: 0.7991 (m-10) REVERT: d 71 ASP cc_start: 0.7913 (t0) cc_final: 0.7705 (t0) REVERT: d 102 ASN cc_start: 0.8487 (m110) cc_final: 0.7906 (m110) REVERT: d 145 ASP cc_start: 0.8509 (m-30) cc_final: 0.8194 (m-30) REVERT: d 157 VAL cc_start: 0.8850 (t) cc_final: 0.8495 (p) REVERT: d 185 MET cc_start: 0.6461 (ptt) cc_final: 0.5385 (pmm) REVERT: e 27 TYR cc_start: 0.8647 (m-10) cc_final: 0.8259 (m-10) REVERT: e 33 ASN cc_start: 0.7900 (m-40) cc_final: 0.7269 (t0) REVERT: e 67 THR cc_start: 0.6342 (p) cc_final: 0.6127 (p) REVERT: e 113 MET cc_start: 0.8335 (mmm) cc_final: 0.7915 (tpt) REVERT: e 114 LEU cc_start: 0.8399 (tp) cc_final: 0.8144 (tp) REVERT: f 44 VAL cc_start: 0.9250 (t) cc_final: 0.8698 (m) REVERT: f 112 GLN cc_start: 0.6729 (tm-30) cc_final: 0.6513 (tm-30) REVERT: f 119 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8398 (tm-30) REVERT: f 120 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7214 (mm-30) REVERT: f 145 TYR cc_start: 0.7331 (m-80) cc_final: 0.6984 (m-80) REVERT: f 218 PHE cc_start: 0.8659 (t80) cc_final: 0.8397 (t80) REVERT: g 1 MET cc_start: 0.7308 (mmm) cc_final: 0.7086 (mmm) REVERT: g 5 TYR cc_start: 0.6342 (m-80) cc_final: 0.6039 (m-80) REVERT: g 53 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7307 (t-90) REVERT: g 90 LEU cc_start: 0.8651 (mt) cc_final: 0.8435 (mt) REVERT: g 92 LEU cc_start: 0.9139 (tp) cc_final: 0.8903 (tt) REVERT: g 159 TRP cc_start: 0.7804 (m100) cc_final: 0.7203 (m-10) REVERT: g 218 ARG cc_start: 0.6438 (ptt90) cc_final: 0.6156 (ptt90) REVERT: g 222 LYS cc_start: 0.5384 (pptt) cc_final: 0.5061 (pptt) REVERT: H 96 TYR cc_start: 0.9232 (t80) cc_final: 0.9027 (t80) REVERT: H 136 PHE cc_start: 0.8762 (p90) cc_final: 0.8295 (p90) REVERT: H 142 CYS cc_start: 0.6740 (t) cc_final: 0.6472 (t) REVERT: H 146 MET cc_start: 0.8048 (mtm) cc_final: 0.7759 (mtm) REVERT: H 149 MET cc_start: 0.7391 (tpp) cc_final: 0.7148 (tpp) REVERT: I 5 ILE cc_start: 0.8607 (tt) cc_final: 0.8228 (tp) REVERT: I 70 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8165 (ttp-170) REVERT: I 85 ARG cc_start: 0.8927 (ttp80) cc_final: 0.8623 (tmm-80) REVERT: J 66 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7904 (mmm-85) REVERT: J 119 MET cc_start: 0.9420 (tpp) cc_final: 0.8945 (tpp) REVERT: J 177 LEU cc_start: 0.8284 (mm) cc_final: 0.8037 (mm) REVERT: J 219 ASP cc_start: 0.6918 (m-30) cc_final: 0.6472 (m-30) REVERT: K 121 LEU cc_start: 0.8958 (mt) cc_final: 0.8672 (mt) REVERT: K 220 VAL cc_start: 0.8504 (t) cc_final: 0.8244 (t) REVERT: K 258 HIS cc_start: 0.6842 (m-70) cc_final: 0.5692 (t-90) REVERT: S 96 TYR cc_start: 0.8212 (t80) cc_final: 0.7292 (t80) REVERT: S 145 GLN cc_start: 0.8738 (mt0) cc_final: 0.8218 (mp10) REVERT: S 169 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8847 (mm110) REVERT: S 178 ASP cc_start: 0.8985 (t0) cc_final: 0.8555 (t70) REVERT: S 183 MET cc_start: 0.7833 (mpp) cc_final: 0.6943 (mpp) REVERT: S 198 ARG cc_start: 0.7657 (mtm110) cc_final: 0.7160 (mtm110) REVERT: S 204 MET cc_start: 0.7309 (mpp) cc_final: 0.6869 (mpp) REVERT: S 205 ASP cc_start: 0.6135 (t0) cc_final: 0.4989 (m-30) REVERT: T 168 GLN cc_start: 0.8231 (tp40) cc_final: 0.8011 (tp-100) REVERT: U 82 CYS cc_start: 0.7765 (m) cc_final: 0.7321 (m) REVERT: U 133 TYR cc_start: 0.6879 (t80) cc_final: 0.6420 (t80) REVERT: U 186 MET cc_start: 0.5850 (mmm) cc_final: 0.4756 (mtp) REVERT: U 217 THR cc_start: 0.8395 (m) cc_final: 0.8141 (m) REVERT: V 201 LYS cc_start: 0.6251 (mttt) cc_final: 0.5154 (tptt) REVERT: V 218 MET cc_start: 0.8822 (mmp) cc_final: 0.8574 (mmm) REVERT: W 23 ILE cc_start: 0.9551 (pt) cc_final: 0.9187 (pt) REVERT: W 37 ASP cc_start: 0.8022 (p0) cc_final: 0.7695 (p0) REVERT: W 65 LEU cc_start: 0.8751 (mt) cc_final: 0.8395 (mt) REVERT: W 101 ASN cc_start: 0.8331 (t160) cc_final: 0.7883 (t0) REVERT: W 185 ARG cc_start: 0.8987 (mmt180) cc_final: 0.8390 (mmt180) REVERT: X 224 MET cc_start: 0.7774 (mmp) cc_final: 0.7287 (mmm) REVERT: Y 79 LYS cc_start: 0.8398 (ttmt) cc_final: 0.8061 (tptm) REVERT: Y 138 TYR cc_start: 0.8843 (t80) cc_final: 0.8472 (t80) REVERT: Y 142 ASN cc_start: 0.8740 (p0) cc_final: 0.8268 (p0) REVERT: Y 153 LYS cc_start: 0.8565 (tttt) cc_final: 0.7895 (tppt) REVERT: Y 204 ASN cc_start: 0.8485 (p0) cc_final: 0.8089 (p0) REVERT: Y 239 ASP cc_start: 0.9287 (t0) cc_final: 0.9013 (t0) REVERT: Y 248 MET cc_start: 0.7300 (ttm) cc_final: 0.6348 (mtp) REVERT: Y 260 GLU cc_start: 0.7341 (pp20) cc_final: 0.5717 (pp20) REVERT: Z 101 ASN cc_start: 0.8064 (t160) cc_final: 0.7859 (t0) REVERT: Z 108 TYR cc_start: 0.8976 (t80) cc_final: 0.8682 (t80) REVERT: Z 166 MET cc_start: 0.7160 (mtt) cc_final: 0.6817 (mtt) REVERT: 1 96 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7552 (mtp180) REVERT: 1 202 ILE cc_start: 0.8900 (mm) cc_final: 0.8598 (mm) REVERT: 2 81 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7879 (tm-30) REVERT: 2 105 LYS cc_start: 0.8788 (mttm) cc_final: 0.8240 (mttm) REVERT: 2 159 MET cc_start: 0.8524 (ppp) cc_final: 0.7643 (ppp) REVERT: 2 165 MET cc_start: 0.7768 (mtt) cc_final: 0.7412 (mtt) REVERT: 2 205 SER cc_start: 0.8918 (p) cc_final: 0.8516 (p) REVERT: 2 253 GLU cc_start: 0.6532 (tp30) cc_final: 0.6227 (tp30) outliers start: 5 outliers final: 0 residues processed: 1828 average time/residue: 0.5598 time to fit residues: 1727.7911 Evaluate side-chains 1502 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1501 time to evaluate : 5.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 441 optimal weight: 1.9990 chunk 711 optimal weight: 10.0000 chunk 434 optimal weight: 7.9990 chunk 337 optimal weight: 4.9990 chunk 494 optimal weight: 7.9990 chunk 746 optimal weight: 5.9990 chunk 686 optimal weight: 4.9990 chunk 594 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 458 optimal weight: 7.9990 chunk 364 optimal weight: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 HIS ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 224 ASN ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN P 221 GLN Q 121 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 HIS ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 218 HIS E 164 HIS ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 43 HIS d 23 GLN d 111 HIS ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 112 GLN ** g 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN I 63 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 106 GLN ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 153 ASN K 192 GLN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN W 101 ASN Z 101 ASN 1 124 GLN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.8934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 61042 Z= 0.275 Angle : 0.721 15.736 82480 Z= 0.374 Chirality : 0.046 0.203 9289 Planarity : 0.005 0.075 10629 Dihedral : 5.102 38.113 8371 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 0.05 % Allowed : 0.50 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.09), residues: 7577 helix: 0.57 (0.09), residues: 3285 sheet: -0.22 (0.13), residues: 1423 loop : -0.80 (0.12), residues: 2869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP d 216 HIS 0.022 0.001 HIS W 117 PHE 0.028 0.002 PHE Q 97 TYR 0.031 0.002 TYR E 177 ARG 0.019 0.001 ARG H 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15154 Ramachandran restraints generated. 7577 Oldfield, 0 Emsley, 7577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1813 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1810 time to evaluate : 5.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 ASN cc_start: 0.7199 (t0) cc_final: 0.6864 (t0) REVERT: L 80 MET cc_start: 0.7060 (mmp) cc_final: 0.6746 (mmp) REVERT: L 108 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7576 (tm-30) REVERT: L 109 ILE cc_start: 0.9100 (tt) cc_final: 0.8353 (tt) REVERT: L 121 ILE cc_start: 0.9377 (mm) cc_final: 0.9169 (tt) REVERT: L 123 GLN cc_start: 0.9234 (tp40) cc_final: 0.8791 (tp40) REVERT: M 29 VAL cc_start: 0.9302 (t) cc_final: 0.9101 (t) REVERT: M 66 GLU cc_start: 0.8648 (mp0) cc_final: 0.8391 (mp0) REVERT: M 79 MET cc_start: 0.8420 (mpp) cc_final: 0.8190 (mpp) REVERT: M 83 TYR cc_start: 0.7471 (t80) cc_final: 0.7263 (t80) REVERT: M 120 GLU cc_start: 0.6277 (tm-30) cc_final: 0.5948 (tm-30) REVERT: M 136 ILE cc_start: 0.8583 (mm) cc_final: 0.8348 (mm) REVERT: N 110 LEU cc_start: 0.8924 (pp) cc_final: 0.8479 (tp) REVERT: N 153 SER cc_start: 0.8146 (p) cc_final: 0.7618 (t) REVERT: N 216 LEU cc_start: 0.7642 (tp) cc_final: 0.7314 (tt) REVERT: O 54 GLN cc_start: 0.7451 (pt0) cc_final: 0.7141 (pt0) REVERT: O 57 ARG cc_start: 0.8109 (mmp80) cc_final: 0.7437 (mmm160) REVERT: O 73 PHE cc_start: 0.8028 (p90) cc_final: 0.7654 (p90) REVERT: O 90 GLU cc_start: 0.8326 (tp30) cc_final: 0.8058 (tp30) REVERT: O 185 ASP cc_start: 0.7776 (m-30) cc_final: 0.6795 (p0) REVERT: O 228 TYR cc_start: 0.6728 (m-80) cc_final: 0.6500 (m-80) REVERT: P 13 ASN cc_start: 0.7957 (m-40) cc_final: 0.7751 (m110) REVERT: P 69 GLU cc_start: 0.6742 (tt0) cc_final: 0.6505 (tp30) REVERT: P 122 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7646 (tm-30) REVERT: P 189 MET cc_start: 0.4052 (ttm) cc_final: 0.3389 (mtp) REVERT: Q 112 ILE cc_start: 0.8786 (pt) cc_final: 0.8332 (pt) REVERT: Q 117 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8235 (tm-30) REVERT: Q 159 MET cc_start: 0.5516 (tpt) cc_final: 0.5281 (ttt) REVERT: Q 173 GLU cc_start: 0.6952 (pp20) cc_final: 0.6271 (tm-30) REVERT: Q 176 MET cc_start: 0.7002 (tmm) cc_final: 0.6745 (tmm) REVERT: R 25 GLU cc_start: 0.8132 (tp30) cc_final: 0.7298 (tp30) REVERT: R 141 TYR cc_start: 0.7200 (t80) cc_final: 0.6926 (t80) REVERT: R 145 ASP cc_start: 0.6149 (p0) cc_final: 0.5891 (p0) REVERT: R 148 GLN cc_start: 0.7101 (tt0) cc_final: 0.6460 (tt0) REVERT: R 157 VAL cc_start: 0.8864 (t) cc_final: 0.8574 (t) REVERT: R 206 LYS cc_start: 0.3677 (tttt) cc_final: 0.3107 (tptt) REVERT: A 25 PHE cc_start: 0.8235 (t80) cc_final: 0.7386 (m-80) REVERT: A 26 GLN cc_start: 0.7391 (mt0) cc_final: 0.6622 (pp30) REVERT: A 32 LEU cc_start: 0.7139 (tp) cc_final: 0.6531 (mm) REVERT: A 40 ILE cc_start: 0.7113 (mt) cc_final: 0.6827 (pt) REVERT: A 128 LEU cc_start: 0.8566 (mt) cc_final: 0.8138 (mm) REVERT: A 145 LYS cc_start: 0.8000 (mmmt) cc_final: 0.7494 (tmtt) REVERT: B 5 ARG cc_start: 0.6244 (mtt180) cc_final: 0.4354 (mmp80) REVERT: B 109 LYS cc_start: 0.6100 (ttmt) cc_final: 0.5619 (mmmt) REVERT: B 138 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7730 (mm110) REVERT: B 168 GLU cc_start: 0.7627 (pt0) cc_final: 0.7214 (pt0) REVERT: B 215 MET cc_start: 0.6817 (mpp) cc_final: 0.5507 (tpp) REVERT: C 135 LEU cc_start: 0.8130 (tt) cc_final: 0.7865 (tt) REVERT: C 154 GLU cc_start: 0.8976 (tt0) cc_final: 0.8339 (mm-30) REVERT: C 227 TYR cc_start: 0.6875 (t80) cc_final: 0.6600 (t80) REVERT: D 132 ILE cc_start: 0.6694 (mm) cc_final: 0.6355 (mp) REVERT: D 138 PHE cc_start: 0.6392 (t80) cc_final: 0.5399 (p90) REVERT: E 127 GLN cc_start: 0.6888 (mm-40) cc_final: 0.6399 (mp10) REVERT: E 132 THR cc_start: 0.8199 (m) cc_final: 0.7934 (m) REVERT: E 136 GLN cc_start: 0.6977 (mt0) cc_final: 0.6734 (mt0) REVERT: E 142 ILE cc_start: 0.7190 (mt) cc_final: 0.6922 (mt) REVERT: E 228 ASP cc_start: 0.8004 (m-30) cc_final: 0.7440 (m-30) REVERT: F 124 TRP cc_start: 0.5692 (t60) cc_final: 0.5348 (t60) REVERT: F 171 ARG cc_start: 0.6753 (mtp85) cc_final: 0.6046 (mmp80) REVERT: F 194 ARG cc_start: 0.7081 (mmp80) cc_final: 0.6543 (mpt180) REVERT: G 40 LEU cc_start: 0.7352 (mt) cc_final: 0.7108 (pp) REVERT: G 210 ARG cc_start: 0.4686 (mtm180) cc_final: 0.3935 (mtp85) REVERT: a 8 THR cc_start: 0.8495 (m) cc_final: 0.8252 (p) REVERT: a 99 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7778 (mm-30) REVERT: a 143 ARG cc_start: 0.7394 (mmm160) cc_final: 0.6932 (mmm160) REVERT: a 148 ASP cc_start: 0.8897 (t0) cc_final: 0.8649 (t0) REVERT: a 196 LEU cc_start: 0.7108 (mt) cc_final: 0.6638 (mt) REVERT: b 147 ASP cc_start: 0.7342 (m-30) cc_final: 0.6963 (m-30) REVERT: b 156 MET cc_start: 0.7367 (ttp) cc_final: 0.6964 (tmm) REVERT: b 206 MET cc_start: 0.6452 (mmp) cc_final: 0.6144 (mmm) REVERT: c 88 MET cc_start: 0.8263 (mmt) cc_final: 0.7982 (mmt) REVERT: c 164 ARG cc_start: 0.6410 (ptm160) cc_final: 0.5178 (ptt180) REVERT: c 171 TYR cc_start: 0.6007 (t80) cc_final: 0.5763 (t80) REVERT: c 174 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.6986 (mmt-90) REVERT: c 190 HIS cc_start: 0.7968 (m-70) cc_final: 0.7213 (m-70) REVERT: c 234 GLU cc_start: 0.8543 (pp20) cc_final: 0.8342 (pp20) REVERT: d 59 TYR cc_start: 0.8458 (m-10) cc_final: 0.7987 (m-10) REVERT: d 94 GLU cc_start: 0.8228 (tp30) cc_final: 0.7673 (tp30) REVERT: d 102 ASN cc_start: 0.8508 (m110) cc_final: 0.7981 (m-40) REVERT: d 145 ASP cc_start: 0.8478 (m-30) cc_final: 0.8129 (m-30) REVERT: d 157 VAL cc_start: 0.8876 (t) cc_final: 0.8455 (p) REVERT: d 161 TYR cc_start: 0.5804 (m-80) cc_final: 0.5493 (m-80) REVERT: d 164 CYS cc_start: 0.6577 (p) cc_final: 0.6317 (p) REVERT: d 185 MET cc_start: 0.6504 (ptt) cc_final: 0.5287 (pmm) REVERT: e 27 TYR cc_start: 0.8691 (m-10) cc_final: 0.8327 (m-10) REVERT: e 33 ASN cc_start: 0.7882 (m-40) cc_final: 0.7291 (t0) REVERT: e 101 TRP cc_start: 0.8623 (t-100) cc_final: 0.8274 (t-100) REVERT: e 113 MET cc_start: 0.8334 (mmm) cc_final: 0.7885 (tpt) REVERT: e 114 LEU cc_start: 0.8416 (tp) cc_final: 0.8179 (tp) REVERT: f 44 VAL cc_start: 0.9276 (t) cc_final: 0.8759 (m) REVERT: f 119 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8408 (tm-30) REVERT: f 120 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7132 (mm-30) REVERT: f 218 PHE cc_start: 0.8708 (t80) cc_final: 0.8446 (t80) REVERT: g 1 MET cc_start: 0.7494 (mmm) cc_final: 0.7079 (mmm) REVERT: g 5 TYR cc_start: 0.6186 (m-80) cc_final: 0.5901 (m-80) REVERT: g 118 LYS cc_start: 0.8269 (mtpp) cc_final: 0.8059 (mttt) REVERT: g 159 TRP cc_start: 0.7853 (m100) cc_final: 0.7275 (m-10) REVERT: g 218 ARG cc_start: 0.6471 (ptt90) cc_final: 0.6145 (ptt90) REVERT: g 222 LYS cc_start: 0.5544 (pptt) cc_final: 0.5128 (pptt) REVERT: H 96 TYR cc_start: 0.9269 (t80) cc_final: 0.9055 (t80) REVERT: H 136 PHE cc_start: 0.8732 (p90) cc_final: 0.8294 (p90) REVERT: H 142 CYS cc_start: 0.6663 (t) cc_final: 0.6093 (t) REVERT: H 147 TYR cc_start: 0.7995 (m-80) cc_final: 0.7757 (m-80) REVERT: H 149 MET cc_start: 0.7124 (tpp) cc_final: 0.6908 (tpp) REVERT: H 153 LEU cc_start: 0.8893 (mt) cc_final: 0.8690 (mt) REVERT: I 5 ILE cc_start: 0.8596 (tt) cc_final: 0.8173 (tp) REVERT: I 19 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7230 (mtp180) REVERT: I 60 ILE cc_start: 0.9569 (mm) cc_final: 0.9059 (mm) REVERT: I 70 ARG cc_start: 0.8448 (ttm170) cc_final: 0.8185 (ttp-170) REVERT: I 177 THR cc_start: 0.8501 (m) cc_final: 0.8198 (m) REVERT: J 119 MET cc_start: 0.9378 (tpp) cc_final: 0.8925 (tpp) REVERT: K 121 LEU cc_start: 0.9069 (mt) cc_final: 0.8759 (mt) REVERT: K 220 VAL cc_start: 0.8616 (t) cc_final: 0.8261 (t) REVERT: K 229 TYR cc_start: 0.7208 (t80) cc_final: 0.6685 (t80) REVERT: K 258 HIS cc_start: 0.6925 (m-70) cc_final: 0.6386 (t70) REVERT: S 26 ARG cc_start: 0.7611 (tpp80) cc_final: 0.7266 (tpp80) REVERT: S 27 ARG cc_start: 0.8826 (tmt170) cc_final: 0.8605 (tmt170) REVERT: S 38 ASP cc_start: 0.8155 (t70) cc_final: 0.7667 (t0) REVERT: S 96 TYR cc_start: 0.8140 (t80) cc_final: 0.7347 (t80) REVERT: S 145 GLN cc_start: 0.8783 (mt0) cc_final: 0.8521 (mt0) REVERT: S 169 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8735 (mm110) REVERT: S 178 ASP cc_start: 0.9075 (t0) cc_final: 0.8809 (t70) REVERT: S 183 MET cc_start: 0.7761 (mpp) cc_final: 0.7192 (mpp) REVERT: S 198 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7250 (mtm110) REVERT: S 204 MET cc_start: 0.7302 (mpp) cc_final: 0.7052 (mpp) REVERT: T 2 GLU cc_start: 0.6944 (mp0) cc_final: 0.6718 (mp0) REVERT: U 55 THR cc_start: 0.7951 (p) cc_final: 0.7728 (p) REVERT: U 82 CYS cc_start: 0.7904 (m) cc_final: 0.7107 (m) REVERT: U 133 TYR cc_start: 0.6992 (t80) cc_final: 0.6476 (t80) REVERT: U 186 MET cc_start: 0.5577 (mmm) cc_final: 0.4677 (mtp) REVERT: U 217 THR cc_start: 0.8491 (m) cc_final: 0.8057 (m) REVERT: V 201 LYS cc_start: 0.6110 (mttt) cc_final: 0.5063 (tptt) REVERT: V 218 MET cc_start: 0.8762 (mmp) cc_final: 0.8550 (mmm) REVERT: W 37 ASP cc_start: 0.7962 (p0) cc_final: 0.7518 (p0) REVERT: W 65 LEU cc_start: 0.8720 (mt) cc_final: 0.8381 (mt) REVERT: W 101 ASN cc_start: 0.8393 (t160) cc_final: 0.7912 (t0) REVERT: W 176 THR cc_start: 0.9246 (t) cc_final: 0.9028 (m) REVERT: X 224 MET cc_start: 0.7838 (mmp) cc_final: 0.7033 (mmm) REVERT: Y 138 TYR cc_start: 0.8874 (t80) cc_final: 0.8527 (t80) REVERT: Y 142 ASN cc_start: 0.8886 (p0) cc_final: 0.8292 (p0) REVERT: Y 153 LYS cc_start: 0.8587 (tttt) cc_final: 0.8007 (tppt) REVERT: Y 187 ASP cc_start: 0.8181 (t0) cc_final: 0.7864 (t0) REVERT: Y 248 MET cc_start: 0.7283 (ttm) cc_final: 0.6441 (mtp) REVERT: Y 249 TYR cc_start: 0.5756 (m-10) cc_final: 0.5484 (m-10) REVERT: Y 260 GLU cc_start: 0.7382 (pp20) cc_final: 0.5656 (pp20) REVERT: Z 166 MET cc_start: 0.7028 (mtt) cc_final: 0.6766 (mtt) REVERT: Z 171 CYS cc_start: 0.8233 (m) cc_final: 0.8017 (m) REVERT: 1 90 ASP cc_start: 0.8143 (m-30) cc_final: 0.7703 (m-30) REVERT: 1 96 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7582 (mtp180) REVERT: 1 194 LEU cc_start: 0.8822 (tp) cc_final: 0.8521 (tp) REVERT: 2 81 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8063 (tm-30) REVERT: 2 116 THR cc_start: 0.9095 (p) cc_final: 0.8752 (m) REVERT: 2 124 CYS cc_start: 0.8121 (m) cc_final: 0.7562 (t) REVERT: 2 159 MET cc_start: 0.8203 (ppp) cc_final: 0.7368 (ttp) REVERT: 2 205 SER cc_start: 0.8882 (p) cc_final: 0.8522 (p) outliers start: 3 outliers final: 0 residues processed: 1811 average time/residue: 0.5517 time to fit residues: 1689.4489 Evaluate side-chains 1496 residues out of total 6445 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1496 time to evaluate : 5.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 749 random chunks: chunk 471 optimal weight: 5.9990 chunk 632 optimal weight: 0.2980 chunk 182 optimal weight: 0.0870 chunk 547 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 165 optimal weight: 6.9990 chunk 595 optimal weight: 0.1980 chunk 249 optimal weight: 5.9990 chunk 611 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN ** Q 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 143 GLN D 218 HIS E 164 HIS ** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 111 HIS e 33 ASN e 68 HIS ** e 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 53 HIS g 88 ASN H 7 ASN I 63 ASN I 71 ASN ** J 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 ASN ** J 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 193 ASN ** U 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN W 101 ASN Y 237 HIS Z 101 ASN 1 148 GLN 1 153 HIS ** 1 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.147392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.129029 restraints weight = 137214.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131749 restraints weight = 78103.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.133612 restraints weight = 50874.163| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.9084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 61042 Z= 0.228 Angle : 0.705 18.403 82480 Z= 0.363 Chirality : 0.046 0.304 9289 Planarity : 0.005 0.075 10629 Dihedral : 5.042 37.425 8371 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.79 % Favored : 96.20 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.10), residues: 7577 helix: 0.65 (0.09), residues: 3280 sheet: -0.29 (0.13), residues: 1438 loop : -0.75 (0.12), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP Y 256 HIS 0.017 0.001 HIS c 20 PHE 0.038 0.002 PHE F 212 TYR 0.056 0.002 TYR f 83 ARG 0.011 0.001 ARG Y 136 =============================================================================== Job complete usr+sys time: 25294.41 seconds wall clock time: 432 minutes 16.61 seconds (25936.61 seconds total)