Starting phenix.real_space_refine on Fri Oct 11 08:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t08_40938/10_2024/8t08_40938.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.105 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 202 5.16 5 C 35064 2.51 5 N 9242 2.21 5 O 10596 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55104 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1823 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1891 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1827 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain breaks: 1 Chain: "D" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain breaks: 3 Chain: "E" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "F" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1803 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain: "G" Number of atoms: 1809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1809 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 9, 'TRANS': 224} Chain breaks: 2 Chain: "H" Number of atoms: 977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 977 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain breaks: 1 Chain: "I" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1738 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Chain: "J" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1359 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain breaks: 3 Chain: "L" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 821 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 3 Chain: "M" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1590 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 196} Chain breaks: 1 Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1550 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "O" Number of atoms: 1845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1845 Classifications: {'peptide': 237} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 218} Chain breaks: 2 Chain: "P" Number of atoms: 1852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1852 Classifications: {'peptide': 227} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 213} Chain breaks: 5 Chain: "Q" Number of atoms: 1576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1576 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain breaks: 1 Restraints were copied for chains: S, Y, h, Z, W, e, a, X, b, T, c, d, U, V, g, f, R Time building chain proxies: 23.39, per 1000 atoms: 0.42 Number of scatterers: 55104 At special positions: 0 Unit cell: (210.94, 208.82, 137.8, 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 202 16.00 O 10596 8.00 N 9242 7.00 C 35064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 92 " distance=2.04 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: 10.46 Conformation dependent library (CDL) restraints added in 5.4 seconds 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13032 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 72 sheets defined 40.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 4.006A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 35 removed outlier: 3.599A pdb=" N PHE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 3.523A pdb=" N THR A 68 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 removed outlier: 4.153A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 131 removed outlier: 3.614A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.641A pdb=" N ASN A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.840A pdb=" N VAL A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'B' and resid 18 through 31 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.504A pdb=" N HIS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.728A pdb=" N ALA B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 178 Processing helix chain 'B' and resid 184 through 200 removed outlier: 3.521A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.524A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.964A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.548A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 Processing helix chain 'C' and resid 185 through 201 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 231 through 243 Processing helix chain 'D' and resid 17 through 29 removed outlier: 3.646A pdb=" N LEU D 24 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.913A pdb=" N THR D 60 " --> pdb=" O THR D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 100 removed outlier: 3.524A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.627A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'E' and resid 21 through 34 removed outlier: 3.632A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 64 Processing helix chain 'E' and resid 81 through 104 removed outlier: 4.124A pdb=" N SER E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 121 Processing helix chain 'E' and resid 122 through 124 No H-bonds generated for 'chain 'E' and resid 122 through 124' Processing helix chain 'E' and resid 175 through 187 Processing helix chain 'E' and resid 192 through 208 removed outlier: 3.569A pdb=" N GLN E 206 " --> pdb=" O LYS E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 247 Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.938A pdb=" N TYR F 6 " --> pdb=" O PHE F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 29 removed outlier: 3.724A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 77 through 100 removed outlier: 3.947A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 97 " --> pdb=" O ASN F 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL F 98 " --> pdb=" O TYR F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.654A pdb=" N LEU F 112 " --> pdb=" O ALA F 108 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 115 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR F 120 " --> pdb=" O ALA F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 4.456A pdb=" N ALA F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 180 removed outlier: 3.639A pdb=" N ILE F 180 " --> pdb=" O LEU F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 199 removed outlier: 3.650A pdb=" N GLN F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 231 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 81 through 104 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.717A pdb=" N HIS G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.536A pdb=" N VAL G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 232 through 243 removed outlier: 3.613A pdb=" N LEU G 236 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.283A pdb=" N SER H 55 " --> pdb=" O HIS H 51 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR H 56 " --> pdb=" O PRO H 52 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 77 Processing helix chain 'H' and resid 78 through 95 Processing helix chain 'H' and resid 104 through 112 removed outlier: 3.694A pdb=" N ILE H 109 " --> pdb=" O ILE H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 123 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.782A pdb=" N LYS H 141 " --> pdb=" O ASP H 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.519A pdb=" N ALA I 108 " --> pdb=" O ARG I 104 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.568A pdb=" N VAL I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 195 Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 removed outlier: 3.546A pdb=" N GLN J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.535A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY J 148 " --> pdb=" O ASP J 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET J 149 " --> pdb=" O GLN J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 175 Processing helix chain 'K' and resid 51 through 72 removed outlier: 3.922A pdb=" N PHE K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 93 Processing helix chain 'K' and resid 134 through 138 removed outlier: 3.712A pdb=" N PHE K 138 " --> pdb=" O TYR K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 148 removed outlier: 3.857A pdb=" N LEU K 143 " --> pdb=" O TYR K 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS K 146 " --> pdb=" O PHE K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 Processing helix chain 'L' and resid 127 through 145 Processing helix chain 'L' and resid 150 through 165 Processing helix chain 'M' and resid 76 through 98 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 161 through 174 Proline residue: M 167 - end of helix removed outlier: 3.578A pdb=" N GLN M 172 " --> pdb=" O PHE M 168 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 214 Processing helix chain 'N' and resid 68 through 90 removed outlier: 3.691A pdb=" N GLN N 88 " --> pdb=" O LEU N 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 108 Processing helix chain 'N' and resid 149 through 152 Processing helix chain 'N' and resid 153 through 161 removed outlier: 3.566A pdb=" N ASP N 158 " --> pdb=" O TYR N 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS N 159 " --> pdb=" O GLY N 155 " (cutoff:3.500A) Processing helix chain 'N' and resid 166 through 185 Processing helix chain 'N' and resid 208 through 213 removed outlier: 3.549A pdb=" N TYR N 212 " --> pdb=" O TYR N 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 47 Processing helix chain 'O' and resid 54 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 62 through 67 removed outlier: 3.638A pdb=" N GLN O 67 " --> pdb=" O LYS O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 159 removed outlier: 3.988A pdb=" N GLY O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 195 through 206 Processing helix chain 'O' and resid 231 through 247 removed outlier: 3.717A pdb=" N LEU O 241 " --> pdb=" O SER O 237 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP O 245 " --> pdb=" O LEU O 241 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 263 removed outlier: 3.662A pdb=" N ARG O 259 " --> pdb=" O GLU O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 268 through 273 removed outlier: 4.247A pdb=" N SER O 272 " --> pdb=" O GLY O 269 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 13 through 26 Processing helix chain 'P' and resid 94 through 102 Processing helix chain 'P' and resid 102 through 111 removed outlier: 3.542A pdb=" N PHE P 106 " --> pdb=" O ILE P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 193 removed outlier: 3.760A pdb=" N LYS P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) Processing helix chain 'P' and resid 217 through 231 Processing helix chain 'P' and resid 246 through 254 removed outlier: 4.224A pdb=" N TYR P 253 " --> pdb=" O GLN P 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 108 removed outlier: 3.556A pdb=" N LEU Q 99 " --> pdb=" O HIS Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 139 Processing helix chain 'Q' and resid 179 through 192 removed outlier: 3.572A pdb=" N MET Q 183 " --> pdb=" O PHE Q 179 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN Q 185 " --> pdb=" O ALA Q 181 " (cutoff:3.500A) Proline residue: Q 186 - end of helix removed outlier: 3.833A pdb=" N VAL Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 198 Processing helix chain 'Q' and resid 202 through 221 Processing helix chain 'R' and resid 12 through 16 Processing helix chain 'R' and resid 25 through 35 removed outlier: 3.599A pdb=" N PHE R 32 " --> pdb=" O VAL R 28 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS R 33 " --> pdb=" O GLU R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 69 removed outlier: 3.522A pdb=" N THR R 68 " --> pdb=" O ASP R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 109 removed outlier: 4.152A pdb=" N ALA R 102 " --> pdb=" O LYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 131 removed outlier: 3.614A pdb=" N TYR R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 186 removed outlier: 3.640A pdb=" N ASN R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 215 removed outlier: 3.840A pdb=" N VAL R 202 " --> pdb=" O SER R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 250 Processing helix chain 'S' and resid 18 through 31 Processing helix chain 'S' and resid 57 through 61 Processing helix chain 'S' and resid 78 through 96 removed outlier: 3.504A pdb=" N HIS S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 97 through 102 Processing helix chain 'S' and resid 106 through 121 removed outlier: 3.729A pdb=" N ALA S 121 " --> pdb=" O ILE S 117 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 178 Processing helix chain 'S' and resid 184 through 200 removed outlier: 3.520A pdb=" N GLU S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER S 199 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 218 through 222 Processing helix chain 'S' and resid 239 through 249 removed outlier: 3.523A pdb=" N ALA S 249 " --> pdb=" O ASP S 245 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 30 Processing helix chain 'T' and resid 80 through 103 removed outlier: 3.963A pdb=" N ILE T 86 " --> pdb=" O ALA T 82 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 123 removed outlier: 3.547A pdb=" N THR T 123 " --> pdb=" O LYS T 119 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 180 Processing helix chain 'T' and resid 185 through 201 Processing helix chain 'T' and resid 207 through 209 No H-bonds generated for 'chain 'T' and resid 207 through 209' Processing helix chain 'T' and resid 231 through 243 Processing helix chain 'U' and resid 17 through 29 removed outlier: 3.646A pdb=" N LEU U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA U 26 " --> pdb=" O TYR U 22 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 60 removed outlier: 3.912A pdb=" N THR U 60 " --> pdb=" O THR U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 100 removed outlier: 3.524A pdb=" N ILE U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 105 through 120 Processing helix chain 'U' and resid 168 through 179 Processing helix chain 'U' and resid 187 through 201 removed outlier: 3.627A pdb=" N GLU U 201 " --> pdb=" O ARG U 197 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 237 Processing helix chain 'V' and resid 21 through 34 removed outlier: 3.632A pdb=" N LEU V 33 " --> pdb=" O GLU V 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY V 34 " --> pdb=" O ALA V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 64 Processing helix chain 'V' and resid 81 through 104 removed outlier: 4.125A pdb=" N SER V 87 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET V 88 " --> pdb=" O ASP V 84 " (cutoff:3.500A) Processing helix chain 'V' and resid 108 through 121 Processing helix chain 'V' and resid 122 through 124 No H-bonds generated for 'chain 'V' and resid 122 through 124' Processing helix chain 'V' and resid 175 through 187 Processing helix chain 'V' and resid 192 through 208 removed outlier: 3.568A pdb=" N GLN V 206 " --> pdb=" O LYS V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 232 through 247 Processing helix chain 'W' and resid 2 through 7 removed outlier: 3.938A pdb=" N TYR W 6 " --> pdb=" O PHE W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 29 removed outlier: 3.723A pdb=" N ALA W 25 " --> pdb=" O GLN W 21 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE W 29 " --> pdb=" O ALA W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 30 through 32 No H-bonds generated for 'chain 'W' and resid 30 through 32' Processing helix chain 'W' and resid 77 through 100 removed outlier: 3.946A pdb=" N SER W 96 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU W 97 " --> pdb=" O ASN W 93 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL W 98 " --> pdb=" O TYR W 94 " (cutoff:3.500A) Processing helix chain 'W' and resid 104 through 120 removed outlier: 3.653A pdb=" N LEU W 112 " --> pdb=" O ALA W 108 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP W 114 " --> pdb=" O HIS W 110 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS W 115 " --> pdb=" O LEU W 111 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN W 119 " --> pdb=" O LYS W 115 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR W 120 " --> pdb=" O ALA W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 4.456A pdb=" N ALA W 168 " --> pdb=" O ARG W 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 175 through 180 removed outlier: 3.638A pdb=" N ILE W 180 " --> pdb=" O LEU W 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 199 removed outlier: 3.651A pdb=" N GLN W 199 " --> pdb=" O GLU W 195 " (cutoff:3.500A) Processing helix chain 'W' and resid 228 through 231 Processing helix chain 'X' and resid 21 through 33 Processing helix chain 'X' and resid 81 through 104 Processing helix chain 'X' and resid 108 through 123 removed outlier: 3.718A pdb=" N HIS X 123 " --> pdb=" O TYR X 119 " (cutoff:3.500A) Processing helix chain 'X' and resid 169 through 183 Processing helix chain 'X' and resid 188 through 204 removed outlier: 3.536A pdb=" N VAL X 193 " --> pdb=" O ALA X 189 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS X 194 " --> pdb=" O ARG X 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 221 through 225 Processing helix chain 'X' and resid 232 through 243 removed outlier: 3.613A pdb=" N LEU X 236 " --> pdb=" O LYS X 232 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 47 Processing helix chain 'Y' and resid 51 through 59 removed outlier: 4.282A pdb=" N SER Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN Y 59 " --> pdb=" O SER Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 59 through 77 Processing helix chain 'Y' and resid 78 through 95 Processing helix chain 'Y' and resid 104 through 112 removed outlier: 3.695A pdb=" N ILE Y 109 " --> pdb=" O ILE Y 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 118 through 123 Processing helix chain 'Y' and resid 137 through 147 removed outlier: 3.781A pdb=" N LYS Y 141 " --> pdb=" O ASP Y 137 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 18 Processing helix chain 'Z' and resid 77 through 100 Processing helix chain 'Z' and resid 104 through 119 removed outlier: 3.519A pdb=" N ALA Z 108 " --> pdb=" O ARG Z 104 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 159 through 171 removed outlier: 3.568A pdb=" N VAL Z 166 " --> pdb=" O ALA Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 176 through 195 Processing helix chain 'a' and resid 56 through 79 Processing helix chain 'a' and resid 83 through 97 removed outlier: 3.547A pdb=" N GLN a 89 " --> pdb=" O GLU a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 154 removed outlier: 3.535A pdb=" N LEU a 146 " --> pdb=" O ALA a 142 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY a 148 " --> pdb=" O ASP a 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N MET a 149 " --> pdb=" O GLN a 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 159 through 175 Processing helix chain 'b' and resid 51 through 72 removed outlier: 3.923A pdb=" N PHE b 56 " --> pdb=" O ASP b 52 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 93 Processing helix chain 'b' and resid 134 through 138 removed outlier: 3.712A pdb=" N PHE b 138 " --> pdb=" O TYR b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 148 removed outlier: 3.858A pdb=" N LEU b 143 " --> pdb=" O TYR b 139 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N HIS b 146 " --> pdb=" O PHE b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 153 through 172 Processing helix chain 'c' and resid 127 through 145 Processing helix chain 'c' and resid 150 through 165 Processing helix chain 'd' and resid 76 through 98 Processing helix chain 'd' and resid 104 through 118 Processing helix chain 'd' and resid 161 through 174 Proline residue: d 167 - end of helix removed outlier: 3.578A pdb=" N GLN d 172 " --> pdb=" O PHE d 168 " (cutoff:3.500A) Processing helix chain 'd' and resid 198 through 214 Processing helix chain 'e' and resid 68 through 90 removed outlier: 3.692A pdb=" N GLN e 88 " --> pdb=" O LEU e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 93 through 108 Processing helix chain 'e' and resid 149 through 152 Processing helix chain 'e' and resid 153 through 161 removed outlier: 3.565A pdb=" N ASP e 158 " --> pdb=" O TYR e 154 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS e 159 " --> pdb=" O GLY e 155 " (cutoff:3.500A) Processing helix chain 'e' and resid 166 through 185 Processing helix chain 'e' and resid 208 through 213 removed outlier: 3.550A pdb=" N TYR e 212 " --> pdb=" O TYR e 208 " (cutoff:3.500A) Processing helix chain 'f' and resid 43 through 47 Processing helix chain 'f' and resid 54 through 61 Proline residue: f 59 - end of helix Processing helix chain 'f' and resid 62 through 67 removed outlier: 3.639A pdb=" N GLN f 67 " --> pdb=" O LYS f 63 " (cutoff:3.500A) Processing helix chain 'f' and resid 143 through 159 removed outlier: 3.987A pdb=" N GLY f 147 " --> pdb=" O SER f 143 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 206 Processing helix chain 'f' and resid 231 through 247 removed outlier: 3.716A pdb=" N LEU f 241 " --> pdb=" O SER f 237 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN f 244 " --> pdb=" O ASP f 240 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP f 245 " --> pdb=" O LEU f 241 " (cutoff:3.500A) Processing helix chain 'f' and resid 249 through 263 removed outlier: 3.661A pdb=" N ARG f 259 " --> pdb=" O GLU f 255 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 273 removed outlier: 4.248A pdb=" N SER f 272 " --> pdb=" O GLY f 269 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 12 No H-bonds generated for 'chain 'g' and resid 10 through 12' Processing helix chain 'g' and resid 13 through 26 Processing helix chain 'g' and resid 94 through 102 Processing helix chain 'g' and resid 102 through 111 removed outlier: 3.543A pdb=" N PHE g 106 " --> pdb=" O ILE g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 183 through 193 removed outlier: 3.761A pdb=" N LYS g 187 " --> pdb=" O GLN g 183 " (cutoff:3.500A) Processing helix chain 'g' and resid 217 through 231 Processing helix chain 'g' and resid 246 through 254 removed outlier: 4.224A pdb=" N TYR g 253 " --> pdb=" O GLN g 250 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 108 removed outlier: 3.555A pdb=" N LEU h 99 " --> pdb=" O HIS h 95 " (cutoff:3.500A) Processing helix chain 'h' and resid 121 through 139 Processing helix chain 'h' and resid 179 through 192 removed outlier: 3.572A pdb=" N MET h 183 " --> pdb=" O PHE h 179 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN h 185 " --> pdb=" O ALA h 181 " (cutoff:3.500A) Proline residue: h 186 - end of helix removed outlier: 3.833A pdb=" N VAL h 191 " --> pdb=" O LEU h 187 " (cutoff:3.500A) Processing helix chain 'h' and resid 194 through 198 Processing helix chain 'h' and resid 202 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 171 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 73 removed outlier: 3.692A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.691A pdb=" N GLY B 42 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 211 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.629A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 133 " --> pdb=" O SER B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 225 removed outlier: 5.199A pdb=" N ASP I 212 " --> pdb=" O GLU I 208 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU I 208 " --> pdb=" O ASP I 212 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN I 218 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL I 202 " --> pdb=" O ASN I 218 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR I 31 " --> pdb=" O ASP I 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.682A pdb=" N GLY C 43 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.635A pdb=" N LEU C 69 " --> pdb=" O ILE C 73 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU C 148 " --> pdb=" O TRP C 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 161 through 164 removed outlier: 4.016A pdb=" N GLU D 211 " --> pdb=" O CYS D 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 77 Processing sheet with id=AB1, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.641A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 67 through 71 removed outlier: 5.901A pdb=" N ILE E 67 " --> pdb=" O MET E 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET E 78 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU E 69 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS E 76 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP E 148 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 Processing sheet with id=AB4, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.668A pdb=" N ASN F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 164 Processing sheet with id=AB6, first strand: chain 'G' and resid 68 through 71 removed outlier: 6.522A pdb=" N ILE G 74 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP G 158 " --> pdb=" O MET G 150 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 49 through 51 removed outlier: 5.972A pdb=" N GLN I 51 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL I 55 " --> pdb=" O GLN I 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.478A pdb=" N ILE I 70 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR I 126 " --> pdb=" O ALA I 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 241 through 247 removed outlier: 4.117A pdb=" N LYS I 243 " --> pdb=" O TYR J 199 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL J 195 " --> pdb=" O VAL I 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA J 185 " --> pdb=" O LEU J 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 43 through 45 Processing sheet with id=AC2, first strand: chain 'K' and resid 130 through 133 removed outlier: 4.069A pdb=" N ILE K 4 " --> pdb=" O HIS K 133 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL K 181 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP K 185 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 25 through 26 removed outlier: 3.657A pdb=" N ILE L 87 " --> pdb=" O VAL L 255 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 252 " --> pdb=" O HIS L 263 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 35 through 39 removed outlier: 3.646A pdb=" N LEU K 38 " --> pdb=" O THR K 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR K 42 " --> pdb=" O LEU K 38 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 174 through 180 Processing sheet with id=AC6, first strand: chain 'M' and resid 155 through 159 removed outlier: 5.660A pdb=" N THR M 30 " --> pdb=" O ASP M 45 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 48 through 50 removed outlier: 6.669A pdb=" N THR M 50 " --> pdb=" O ILE M 54 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE M 54 " --> pdb=" O THR M 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 63 through 66 removed outlier: 5.728A pdb=" N ILE M 69 " --> pdb=" O CYS M 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN M 74 " --> pdb=" O HIS M 127 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR M 128 " --> pdb=" O PHE M 144 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER M 143 " --> pdb=" O GLU M 151 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY N 66 " --> pdb=" O LEU N 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY N 66 " --> pdb=" O LEU N 18 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 143 through 147 removed outlier: 3.656A pdb=" N GLY N 30 " --> pdb=" O PHE N 27 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 39 through 41 removed outlier: 3.575A pdb=" N ASN N 47 " --> pdb=" O THR N 39 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR N 41 " --> pdb=" O ILE N 45 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N ILE N 45 " --> pdb=" O THR N 41 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 35 through 37 removed outlier: 3.612A pdb=" N THR O 77 " --> pdb=" O LYS O 35 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS O 75 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER O 70 " --> pdb=" O SER O 126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER O 126 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY O 72 " --> pdb=" O ILE O 124 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER O 134 " --> pdb=" O PRO O 123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE O 165 " --> pdb=" O LYS O 215 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LEU O 217 " --> pdb=" O ILE O 165 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL O 167 " --> pdb=" O LEU O 217 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA O 219 " --> pdb=" O VAL O 167 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY O 169 " --> pdb=" O ALA O 219 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 193 through 194 Processing sheet with id=AD6, first strand: chain 'P' and resid 30 through 34 removed outlier: 5.349A pdb=" N TYR P 32 " --> pdb=" O TYR P 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR P 74 " --> pdb=" O TYR P 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU P 34 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N CYS P 3 " --> pdb=" O PHE P 81 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE P 83 " --> pdb=" O CYS P 3 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL P 5 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN P 85 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU P 4 " --> pdb=" O CYS P 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TRP P 118 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU P 6 " --> pdb=" O TRP P 118 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N SER P 120 " --> pdb=" O LEU P 6 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE P 115 " --> pdb=" O SER P 204 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU Q 67 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR Q 63 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU Q 67 " --> pdb=" O TYR Q 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR Q 63 " --> pdb=" O LEU Q 67 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 174 through 176 removed outlier: 5.706A pdb=" N PHE Q 228 " --> pdb=" O ASN Q 244 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN Q 244 " --> pdb=" O PHE Q 228 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 168 through 171 Processing sheet with id=AE2, first strand: chain 'R' and resid 72 through 73 removed outlier: 3.692A pdb=" N ILE R 154 " --> pdb=" O TYR R 166 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'S' and resid 161 through 164 removed outlier: 3.691A pdb=" N GLY S 42 " --> pdb=" O ALA S 39 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU S 211 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 65 through 68 removed outlier: 6.630A pdb=" N ILE S 71 " --> pdb=" O LEU S 67 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER S 133 " --> pdb=" O SER S 76 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 224 through 225 removed outlier: 5.200A pdb=" N ASP Z 212 " --> pdb=" O GLU Z 208 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU Z 208 " --> pdb=" O ASP Z 212 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN Z 218 " --> pdb=" O VAL Z 202 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL Z 202 " --> pdb=" O ASN Z 218 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR Z 31 " --> pdb=" O ASP Z 46 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 162 through 165 removed outlier: 3.683A pdb=" N GLY T 43 " --> pdb=" O ALA T 40 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 66 through 70 removed outlier: 3.634A pdb=" N LEU T 69 " --> pdb=" O ILE T 73 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE T 73 " --> pdb=" O LEU T 69 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU T 148 " --> pdb=" O TRP T 160 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 161 through 164 removed outlier: 4.016A pdb=" N GLU U 211 " --> pdb=" O CYS U 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'U' and resid 71 through 77 Processing sheet with id=AF1, first strand: chain 'V' and resid 169 through 172 removed outlier: 3.641A pdb=" N GLN V 218 " --> pdb=" O VAL V 50 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'V' and resid 67 through 71 removed outlier: 5.900A pdb=" N ILE V 67 " --> pdb=" O MET V 78 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET V 78 " --> pdb=" O ILE V 67 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLU V 69 " --> pdb=" O CYS V 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS V 76 " --> pdb=" O GLU V 69 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP V 148 " --> pdb=" O GLY V 152 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 158 through 161 Processing sheet with id=AF4, first strand: chain 'W' and resid 63 through 65 removed outlier: 3.668A pdb=" N ASN W 152 " --> pdb=" O GLN W 148 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 162 through 164 Processing sheet with id=AF6, first strand: chain 'X' and resid 68 through 71 removed outlier: 6.522A pdb=" N ILE X 74 " --> pdb=" O VAL X 70 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP X 158 " --> pdb=" O MET X 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 49 through 51 removed outlier: 5.973A pdb=" N GLN Z 51 " --> pdb=" O VAL Z 55 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL Z 55 " --> pdb=" O GLN Z 51 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Z' and resid 63 through 67 removed outlier: 6.479A pdb=" N ILE Z 70 " --> pdb=" O ILE Z 66 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR Z 126 " --> pdb=" O ALA Z 75 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 241 through 247 removed outlier: 4.109A pdb=" N LYS Z 243 " --> pdb=" O TYR a 199 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL a 195 " --> pdb=" O VAL Z 247 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA a 185 " --> pdb=" O LEU a 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 43 through 45 Processing sheet with id=AG2, first strand: chain 'b' and resid 130 through 133 removed outlier: 4.069A pdb=" N ILE b 4 " --> pdb=" O HIS b 133 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL b 181 " --> pdb=" O VAL b 192 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP b 185 " --> pdb=" O GLY b 188 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'b' and resid 25 through 26 removed outlier: 3.657A pdb=" N ILE c 87 " --> pdb=" O VAL c 255 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU c 252 " --> pdb=" O HIS c 263 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 35 through 39 removed outlier: 3.647A pdb=" N LEU b 38 " --> pdb=" O THR b 42 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR b 42 " --> pdb=" O LEU b 38 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'c' and resid 174 through 180 Processing sheet with id=AG6, first strand: chain 'd' and resid 155 through 159 removed outlier: 5.660A pdb=" N THR d 30 " --> pdb=" O ASP d 45 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'd' and resid 48 through 50 removed outlier: 6.669A pdb=" N THR d 50 " --> pdb=" O ILE d 54 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE d 54 " --> pdb=" O THR d 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 63 through 66 removed outlier: 5.726A pdb=" N ILE d 69 " --> pdb=" O CYS d 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN d 74 " --> pdb=" O HIS d 127 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR d 128 " --> pdb=" O PHE d 144 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER d 143 " --> pdb=" O GLU d 151 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY e 66 " --> pdb=" O LEU e 18 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE e 60 " --> pdb=" O VAL e 56 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 17 through 18 removed outlier: 4.222A pdb=" N GLY e 66 " --> pdb=" O LEU e 18 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 143 through 147 removed outlier: 3.656A pdb=" N GLY e 30 " --> pdb=" O PHE e 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'e' and resid 39 through 41 removed outlier: 3.575A pdb=" N ASN e 47 " --> pdb=" O THR e 39 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR e 41 " --> pdb=" O ILE e 45 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ILE e 45 " --> pdb=" O THR e 41 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'f' and resid 35 through 37 removed outlier: 3.612A pdb=" N THR f 77 " --> pdb=" O LYS f 35 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS f 75 " --> pdb=" O GLU f 37 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER f 70 " --> pdb=" O SER f 126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N SER f 126 " --> pdb=" O SER f 70 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY f 72 " --> pdb=" O ILE f 124 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER f 134 " --> pdb=" O PRO f 123 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE f 165 " --> pdb=" O LYS f 215 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LEU f 217 " --> pdb=" O ILE f 165 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL f 167 " --> pdb=" O LEU f 217 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ALA f 219 " --> pdb=" O VAL f 167 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY f 169 " --> pdb=" O ALA f 219 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'f' and resid 193 through 194 Processing sheet with id=AH6, first strand: chain 'g' and resid 30 through 34 removed outlier: 5.350A pdb=" N TYR g 32 " --> pdb=" O TYR g 74 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR g 74 " --> pdb=" O TYR g 32 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU g 34 " --> pdb=" O VAL g 72 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS g 3 " --> pdb=" O PHE g 81 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ILE g 83 " --> pdb=" O CYS g 3 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL g 5 " --> pdb=" O ILE g 83 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLN g 85 " --> pdb=" O VAL g 5 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU g 4 " --> pdb=" O CYS g 116 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N TRP g 118 " --> pdb=" O LEU g 4 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU g 6 " --> pdb=" O TRP g 118 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N SER g 120 " --> pdb=" O LEU g 6 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE g 115 " --> pdb=" O SER g 204 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR h 63 " --> pdb=" O LEU h 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 66 through 69 removed outlier: 5.405A pdb=" N LEU h 67 " --> pdb=" O TYR h 63 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TYR h 63 " --> pdb=" O LEU h 67 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'h' and resid 174 through 176 removed outlier: 5.704A pdb=" N PHE h 228 " --> pdb=" O ASN h 244 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN h 244 " --> pdb=" O PHE h 228 " (cutoff:3.500A) 2992 hydrogen bonds defined for protein. 8472 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: 22.95 Time building geometry restraints manager: 12.33 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: 17965 1.34 - 1.47: 13083 1.47 - 1.59: 24756 1.59 - 1.72: 0 1.72 - 1.84: 314 Bond restraints: 56118 Sorted by residual: bond pdb=" N MET f 1 " pdb=" CA MET f 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N MET O 1 " pdb=" CA MET O 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LYS T 100 " pdb=" CA LYS T 100 " ideal model delta sigma weight residual 1.458 1.480 -0.023 1.33e-02 5.65e+03 2.98e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N MET W 1 " pdb=" CA MET W 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 ... (remaining 56113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 74870 1.52 - 3.03: 735 3.03 - 4.55: 263 4.55 - 6.07: 22 6.07 - 7.58: 6 Bond angle restraints: 75896 Sorted by residual: angle pdb=" N ARG Z 217 " pdb=" CA ARG Z 217 " pdb=" C ARG Z 217 " ideal model delta sigma weight residual 110.43 105.90 4.53 1.31e+00 5.83e-01 1.20e+01 angle pdb=" N ARG I 217 " pdb=" CA ARG I 217 " pdb=" C ARG I 217 " ideal model delta sigma weight residual 110.43 105.93 4.50 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N LYS C 100 " pdb=" CA LYS C 100 " pdb=" C LYS C 100 " ideal model delta sigma weight residual 112.54 108.56 3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" N LYS T 100 " pdb=" CA LYS T 100 " pdb=" C LYS T 100 " ideal model delta sigma weight residual 112.54 108.63 3.91 1.22e+00 6.72e-01 1.03e+01 angle pdb=" CA ARG I 217 " pdb=" C ARG I 217 " pdb=" O ARG I 217 " ideal model delta sigma weight residual 121.87 118.65 3.22 1.10e+00 8.26e-01 8.59e+00 ... (remaining 75891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 31194 17.90 - 35.81: 2019 35.81 - 53.71: 304 53.71 - 71.61: 78 71.61 - 89.52: 56 Dihedral angle restraints: 33651 sinusoidal: 13335 harmonic: 20316 Sorted by residual: dihedral pdb=" CB CYS F 66 " pdb=" SG CYS F 66 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 134.65 -41.65 1 1.00e+01 1.00e-02 2.43e+01 dihedral pdb=" CA LEU I 4 " pdb=" C LEU I 4 " pdb=" N SER I 5 " pdb=" CA SER I 5 " ideal model delta harmonic sigma weight residual -180.00 -159.06 -20.94 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA LEU Z 4 " pdb=" C LEU Z 4 " pdb=" N SER Z 5 " pdb=" CA SER Z 5 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 33648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 8595 0.154 - 0.307: 5 0.307 - 0.461: 0 0.461 - 0.614: 4 0.614 - 0.768: 2 Chirality restraints: 8606 Sorted by residual: chirality pdb=" CG LEU Z 220 " pdb=" CB LEU Z 220 " pdb=" CD1 LEU Z 220 " pdb=" CD2 LEU Z 220 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" CG LEU I 220 " pdb=" CB LEU I 220 " pdb=" CD1 LEU I 220 " pdb=" CD2 LEU I 220 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" CB THR b 53 " pdb=" CA THR b 53 " pdb=" OG1 THR b 53 " pdb=" CG2 THR b 53 " both_signs ideal model delta sigma weight residual False 2.55 2.04 0.51 2.00e-01 2.50e+01 6.58e+00 ... (remaining 8603 not shown) Planarity restraints: 9712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 129 " -0.028 2.00e-02 2.50e+03 2.80e-02 1.38e+01 pdb=" CG PHE L 129 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE L 129 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE L 129 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE L 129 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE L 129 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE L 129 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 129 " -0.028 2.00e-02 2.50e+03 2.79e-02 1.37e+01 pdb=" CG PHE c 129 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE c 129 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE c 129 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE c 129 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE c 129 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE c 129 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 117 " -0.015 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR d 117 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR d 117 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR d 117 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR d 117 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR d 117 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR d 117 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR d 117 " -0.003 2.00e-02 2.50e+03 ... (remaining 9709 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 587 2.59 - 3.17: 48882 3.17 - 3.75: 84263 3.75 - 4.32: 124313 4.32 - 4.90: 210933 Nonbonded interactions: 468978 Sorted by model distance: nonbonded pdb=" OG SER N 166 " pdb=" OE1 GLU N 169 " model vdw 2.014 3.040 nonbonded pdb=" OG SER e 166 " pdb=" OE1 GLU e 169 " model vdw 2.015 3.040 nonbonded pdb=" O PRO P 172 " pdb=" OG1 THR P 173 " model vdw 2.034 3.040 nonbonded pdb=" O PRO g 172 " pdb=" OG1 THR g 173 " model vdw 2.035 3.040 nonbonded pdb=" SG CYS W 66 " pdb=" SG CYS W 92 " model vdw 2.038 3.760 ... (remaining 468973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'R' } ncs_group { reference = chain 'B' selection = chain 'S' } ncs_group { reference = chain 'C' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'V' } ncs_group { reference = chain 'F' selection = chain 'W' } ncs_group { reference = chain 'G' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'Y' } ncs_group { reference = chain 'I' selection = chain 'Z' } ncs_group { reference = chain 'J' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'b' } ncs_group { reference = chain 'L' selection = chain 'c' } ncs_group { reference = chain 'M' selection = chain 'd' } ncs_group { reference = chain 'N' selection = chain 'e' } ncs_group { reference = chain 'O' selection = chain 'f' } ncs_group { reference = chain 'P' selection = chain 'g' } ncs_group { reference = chain 'Q' selection = chain 'h' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.900 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: 0.070 Extract box with map and model: 1.620 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 97.560 Find NCS groups from input model: 3.250 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.003 0.048 56118 Z= 0.174 Angle : 0.465 7.584 75896 Z= 0.251 Chirality : 0.043 0.768 8606 Planarity : 0.004 0.121 9712 Dihedral : 12.796 89.516 20616 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.07 % Allowed : 0.15 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.10), residues: 6864 helix: 1.75 (0.11), residues: 2434 sheet: 0.40 (0.12), residues: 1734 loop : 0.13 (0.12), residues: 2696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 261 HIS 0.003 0.001 HIS Q 95 PHE 0.063 0.001 PHE L 129 TYR 0.049 0.001 TYR d 117 ARG 0.008 0.000 ARG D 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1013 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8546 (tp30) cc_final: 0.8251 (tp30) REVERT: C 28 SER cc_start: 0.8959 (t) cc_final: 0.8664 (p) REVERT: C 152 ASN cc_start: 0.8111 (m-40) cc_final: 0.7863 (m-40) REVERT: C 156 ASN cc_start: 0.8380 (p0) cc_final: 0.8029 (p0) REVERT: C 165 VAL cc_start: 0.8395 (p) cc_final: 0.8140 (m) REVERT: C 191 GLU cc_start: 0.7271 (mp0) cc_final: 0.7031 (mp0) REVERT: C 236 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7853 (ptpt) REVERT: C 237 ASP cc_start: 0.7785 (m-30) cc_final: 0.7583 (m-30) REVERT: D 6 ARG cc_start: 0.8258 (pmt-80) cc_final: 0.7595 (mtt180) REVERT: H 35 GLN cc_start: 0.8029 (tt0) cc_final: 0.7617 (pt0) REVERT: H 133 MET cc_start: 0.4405 (mmp) cc_final: 0.3776 (mmp) REVERT: I 178 GLU cc_start: 0.8058 (mp0) cc_final: 0.7795 (mp0) REVERT: I 214 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7388 (mm-30) REVERT: I 218 ASN cc_start: 0.7478 (m-40) cc_final: 0.7251 (m110) REVERT: K 148 TYR cc_start: 0.7621 (t80) cc_final: 0.7351 (t80) REVERT: K 156 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7118 (mt-10) REVERT: K 167 GLU cc_start: 0.7892 (mp0) cc_final: 0.7045 (mp0) REVERT: L 148 ARG cc_start: 0.6746 (tpt-90) cc_final: 0.6238 (ttt180) REVERT: M 22 ASN cc_start: 0.7024 (t0) cc_final: 0.6571 (p0) REVERT: M 234 GLU cc_start: 0.7443 (mm-30) cc_final: 0.7188 (mm-30) REVERT: Q 157 ASP cc_start: 0.7422 (m-30) cc_final: 0.7065 (m-30) REVERT: Q 161 ARG cc_start: 0.8749 (mmm160) cc_final: 0.8489 (mtp85) REVERT: Q 190 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7960 (mtmt) REVERT: R 242 GLU cc_start: 0.8489 (tp30) cc_final: 0.8198 (tp30) REVERT: T 28 SER cc_start: 0.8961 (t) cc_final: 0.8664 (p) REVERT: T 152 ASN cc_start: 0.8105 (m-40) cc_final: 0.7851 (m-40) REVERT: T 156 ASN cc_start: 0.8373 (p0) cc_final: 0.8018 (p0) REVERT: T 165 VAL cc_start: 0.8405 (p) cc_final: 0.8147 (m) REVERT: T 191 GLU cc_start: 0.7272 (mp0) cc_final: 0.7011 (mp0) REVERT: T 236 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7849 (ptpt) REVERT: T 237 ASP cc_start: 0.7799 (m-30) cc_final: 0.7576 (m-30) REVERT: U 6 ARG cc_start: 0.8257 (pmt-80) cc_final: 0.7591 (mtt180) REVERT: V 185 ASN cc_start: 0.7919 (m110) cc_final: 0.7716 (m110) REVERT: Y 35 GLN cc_start: 0.8051 (tt0) cc_final: 0.7623 (pt0) REVERT: Y 133 MET cc_start: 0.4402 (mmp) cc_final: 0.3779 (mmp) REVERT: Z 178 GLU cc_start: 0.8111 (mp0) cc_final: 0.7844 (mp0) REVERT: Z 214 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7417 (mm-30) REVERT: Z 218 ASN cc_start: 0.7581 (m-40) cc_final: 0.7357 (m110) REVERT: b 148 TYR cc_start: 0.7546 (t80) cc_final: 0.7284 (t80) REVERT: b 156 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7067 (mt-10) REVERT: b 167 GLU cc_start: 0.7903 (mp0) cc_final: 0.7053 (mp0) REVERT: c 148 ARG cc_start: 0.6756 (tpt-90) cc_final: 0.6229 (ttt180) REVERT: d 22 ASN cc_start: 0.6998 (t0) cc_final: 0.6641 (p0) REVERT: d 234 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7110 (mm-30) REVERT: d 241 ASP cc_start: 0.6376 (p0) cc_final: 0.5712 (p0) REVERT: h 95 HIS cc_start: 0.7767 (t-90) cc_final: 0.7542 (t-90) REVERT: h 157 ASP cc_start: 0.7392 (m-30) cc_final: 0.6917 (m-30) REVERT: h 161 ARG cc_start: 0.8733 (mmm160) cc_final: 0.8474 (mtp85) REVERT: h 190 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7903 (mtmt) outliers start: 4 outliers final: 6 residues processed: 1013 average time/residue: 1.4366 time to fit residues: 1820.1304 Evaluate side-chains 686 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 680 time to evaluate : 4.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain Q residue 70 ASN Chi-restraints excluded: chain S residue 220 ASP Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain h residue 70 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 584 optimal weight: 5.9990 chunk 524 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 179 optimal weight: 0.9980 chunk 353 optimal weight: 0.0670 chunk 280 optimal weight: 0.4980 chunk 542 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 403 optimal weight: 0.9990 chunk 628 optimal weight: 6.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 123 GLN C 21 GLN E 100 ASN E 147 HIS E 185 ASN E 218 GLN F 31 GLN F 166 GLN G 21 ASN G 183 HIS H 112 ASN I 86 GLN I 170 HIS J 145 GLN K 78 GLN M 74 ASN N 108 ASN O 225 ASN Q 227 ASN R 209 HIS S 123 GLN T 21 GLN V 147 HIS V 185 ASN W 31 GLN W 166 GLN X 21 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 86 GLN Z 170 HIS a 145 GLN b 78 GLN c 137 GLN d 74 ASN e 108 ASN f 225 ASN h 227 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56118 Z= 0.200 Angle : 0.587 9.008 75896 Z= 0.314 Chirality : 0.045 0.166 8606 Planarity : 0.004 0.059 9712 Dihedral : 4.840 84.000 7614 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.52 % Allowed : 9.36 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.10), residues: 6864 helix: 1.67 (0.10), residues: 2540 sheet: 0.33 (0.12), residues: 1738 loop : 0.22 (0.13), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 158 HIS 0.009 0.001 HIS X 183 PHE 0.039 0.002 PHE L 129 TYR 0.020 0.001 TYR g 32 ARG 0.008 0.001 ARG X 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 845 time to evaluate : 4.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8355 (t0) cc_final: 0.8145 (t0) REVERT: A 121 MET cc_start: 0.9093 (mmm) cc_final: 0.8876 (mmm) REVERT: B 103 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8211 (pm20) REVERT: C 156 ASN cc_start: 0.8459 (p0) cc_final: 0.8229 (p0) REVERT: C 165 VAL cc_start: 0.8405 (p) cc_final: 0.8174 (m) REVERT: C 194 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 6 ARG cc_start: 0.8256 (pmt-80) cc_final: 0.7567 (mtt-85) REVERT: D 220 ASP cc_start: 0.8258 (t0) cc_final: 0.8055 (t0) REVERT: E 209 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6459 (pp20) REVERT: F 93 ASN cc_start: 0.7363 (t0) cc_final: 0.7087 (t0) REVERT: H 35 GLN cc_start: 0.8205 (tt0) cc_final: 0.7833 (pt0) REVERT: H 73 ARG cc_start: 0.8609 (ttp80) cc_final: 0.8398 (ttp80) REVERT: I 110 GLN cc_start: 0.8741 (mm110) cc_final: 0.8455 (mm-40) REVERT: I 214 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7430 (mm-30) REVERT: K 148 TYR cc_start: 0.7556 (t80) cc_final: 0.7344 (t80) REVERT: K 156 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7614 (mt-10) REVERT: K 167 GLU cc_start: 0.7911 (mp0) cc_final: 0.6726 (mp0) REVERT: L 145 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: L 148 ARG cc_start: 0.6713 (tpt-90) cc_final: 0.6265 (ttt180) REVERT: L 200 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.6019 (t0) REVERT: M 22 ASN cc_start: 0.7111 (t0) cc_final: 0.6615 (p0) REVERT: M 166 MET cc_start: 0.5197 (mmm) cc_final: 0.4816 (mmm) REVERT: Q 137 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7972 (ttt90) REVERT: Q 157 ASP cc_start: 0.7829 (m-30) cc_final: 0.7489 (m-30) REVERT: R 39 ASN cc_start: 0.8352 (t0) cc_final: 0.8140 (t0) REVERT: R 89 ASP cc_start: 0.8679 (m-30) cc_final: 0.8390 (m-30) REVERT: R 121 MET cc_start: 0.9089 (mmm) cc_final: 0.8787 (mmm) REVERT: S 103 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8185 (pm20) REVERT: T 156 ASN cc_start: 0.8458 (p0) cc_final: 0.8224 (p0) REVERT: T 165 VAL cc_start: 0.8414 (p) cc_final: 0.8183 (m) REVERT: T 194 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8060 (mm) REVERT: T 236 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7652 (ptmt) REVERT: U 6 ARG cc_start: 0.8257 (pmt-80) cc_final: 0.7566 (mtt-85) REVERT: U 220 ASP cc_start: 0.8253 (t0) cc_final: 0.8043 (t0) REVERT: V 209 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6427 (pp20) REVERT: Y 35 GLN cc_start: 0.8199 (tt0) cc_final: 0.7827 (pt0) REVERT: Z 110 GLN cc_start: 0.8786 (mm110) cc_final: 0.8506 (mm-40) REVERT: Z 214 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7452 (mm-30) REVERT: b 148 TYR cc_start: 0.7595 (t80) cc_final: 0.7372 (t80) REVERT: b 156 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7622 (mt-10) REVERT: b 167 GLU cc_start: 0.7913 (mp0) cc_final: 0.6730 (mp0) REVERT: c 145 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: c 148 ARG cc_start: 0.6718 (tpt-90) cc_final: 0.6233 (ttt180) REVERT: c 200 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.6010 (t0) REVERT: d 22 ASN cc_start: 0.7026 (t0) cc_final: 0.6597 (p0) REVERT: d 166 MET cc_start: 0.5132 (mmm) cc_final: 0.4745 (mmm) REVERT: d 201 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8422 (ttpp) REVERT: d 241 ASP cc_start: 0.6750 (p0) cc_final: 0.6473 (p0) REVERT: e 47 ASN cc_start: 0.8161 (t0) cc_final: 0.7943 (t0) REVERT: e 162 ARG cc_start: 0.7880 (mtm110) cc_final: 0.6964 (mtm110) REVERT: h 157 ASP cc_start: 0.7767 (m-30) cc_final: 0.7429 (m-30) REVERT: h 190 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8065 (mtmt) outliers start: 91 outliers final: 29 residues processed: 890 average time/residue: 1.3424 time to fit residues: 1511.4112 Evaluate side-chains 720 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 679 time to evaluate : 4.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 46 CYS Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 200 ASP Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain S residue 103 GLU Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 186 VAL Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 209 GLU Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain c residue 200 ASP Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain f residue 31 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 349 optimal weight: 0.9990 chunk 195 optimal weight: 9.9990 chunk 523 optimal weight: 1.9990 chunk 427 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 629 optimal weight: 7.9990 chunk 680 optimal weight: 4.9990 chunk 560 optimal weight: 9.9990 chunk 624 optimal weight: 7.9990 chunk 214 optimal weight: 9.9990 chunk 505 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 218 ASN E 114 GLN E 185 ASN F 60 GLN F 166 GLN F 199 GLN G 90 ASN G 123 HIS G 183 HIS G 195 GLN H 112 ASN I 86 GLN I 170 HIS I 194 ASN K 101 ASN K 118 GLN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN O 225 ASN Q 95 HIS Q 212 ASN S 30 GLN S 218 ASN V 114 GLN V 185 ASN W 60 GLN W 166 GLN W 199 GLN X 90 ASN X 123 HIS X 183 HIS Y 112 ASN Z 170 HIS Z 194 ASN a 169 GLN b 101 ASN b 118 GLN c 137 GLN ** e 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN f 225 ASN ** f 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 95 HIS h 212 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 56118 Z= 0.447 Angle : 0.674 8.480 75896 Z= 0.354 Chirality : 0.049 0.181 8606 Planarity : 0.005 0.080 9712 Dihedral : 4.995 45.087 7606 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.01 % Allowed : 11.51 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.10), residues: 6864 helix: 1.38 (0.10), residues: 2540 sheet: 0.10 (0.12), residues: 1732 loop : -0.09 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 199 HIS 0.011 0.002 HIS X 123 PHE 0.036 0.002 PHE J 124 TYR 0.028 0.002 TYR J 69 ARG 0.016 0.001 ARG b 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 744 time to evaluate : 4.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7487 (p0) REVERT: A 48 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6801 (mttp) REVERT: A 121 MET cc_start: 0.9253 (mmm) cc_final: 0.8828 (mmm) REVERT: A 148 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: A 158 ASP cc_start: 0.8596 (p0) cc_final: 0.8388 (p0) REVERT: A 222 ASP cc_start: 0.8452 (t0) cc_final: 0.8034 (t0) REVERT: C 39 MET cc_start: 0.8984 (ttp) cc_final: 0.8770 (ttp) REVERT: C 70 ASN cc_start: 0.8301 (t0) cc_final: 0.8043 (t0) REVERT: C 152 ASN cc_start: 0.8416 (m-40) cc_final: 0.8154 (m-40) REVERT: C 194 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8095 (mm) REVERT: C 233 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7768 (tm-30) REVERT: D 6 ARG cc_start: 0.8336 (pmt-80) cc_final: 0.7517 (mtt-85) REVERT: E 134 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6900 (mtm) REVERT: G 68 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: G 184 PRO cc_start: 0.7724 (Cg_endo) cc_final: 0.7303 (Cg_exo) REVERT: H 35 GLN cc_start: 0.8245 (tt0) cc_final: 0.7989 (pt0) REVERT: H 118 ASP cc_start: 0.8124 (t0) cc_final: 0.7898 (t0) REVERT: I 214 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7391 (mm-30) REVERT: J 126 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8097 (tp) REVERT: J 169 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7576 (tp40) REVERT: K 148 TYR cc_start: 0.7623 (t80) cc_final: 0.7384 (t80) REVERT: K 156 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7615 (mt-10) REVERT: K 167 GLU cc_start: 0.7236 (mp0) cc_final: 0.6756 (mp0) REVERT: K 195 PHE cc_start: 0.4828 (m-10) cc_final: 0.4272 (m-80) REVERT: L 145 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: M 241 ASP cc_start: 0.7211 (p0) cc_final: 0.6983 (p0) REVERT: O 47 TYR cc_start: 0.5677 (m-80) cc_final: 0.5401 (m-80) REVERT: Q 157 ASP cc_start: 0.8021 (m-30) cc_final: 0.7611 (m-30) REVERT: R 41 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7493 (p0) REVERT: R 48 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6780 (mttp) REVERT: R 121 MET cc_start: 0.9252 (mmm) cc_final: 0.8830 (mmm) REVERT: R 148 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7555 (pt0) REVERT: R 158 ASP cc_start: 0.8623 (p0) cc_final: 0.8415 (p0) REVERT: R 222 ASP cc_start: 0.8298 (t0) cc_final: 0.8076 (t0) REVERT: T 39 MET cc_start: 0.8995 (ttp) cc_final: 0.8787 (ttp) REVERT: T 70 ASN cc_start: 0.8304 (t0) cc_final: 0.8057 (t0) REVERT: T 152 ASN cc_start: 0.8387 (m-40) cc_final: 0.8140 (m-40) REVERT: T 194 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8089 (mm) REVERT: T 233 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7624 (tm-30) REVERT: U 6 ARG cc_start: 0.8342 (pmt-80) cc_final: 0.7525 (mtt-85) REVERT: V 134 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6941 (mtm) REVERT: X 68 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: X 184 PRO cc_start: 0.7711 (Cg_endo) cc_final: 0.7249 (Cg_exo) REVERT: X 195 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7512 (mm-40) REVERT: Y 35 GLN cc_start: 0.8242 (tt0) cc_final: 0.7977 (pt0) REVERT: Y 70 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7888 (tp30) REVERT: Y 118 ASP cc_start: 0.8095 (t0) cc_final: 0.7880 (t0) REVERT: Z 214 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7377 (mm-30) REVERT: a 103 TYR cc_start: 0.8728 (m-80) cc_final: 0.8503 (m-80) REVERT: a 126 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8103 (tp) REVERT: a 169 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7535 (tp-100) REVERT: b 156 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7537 (mt-10) REVERT: b 167 GLU cc_start: 0.7235 (mp0) cc_final: 0.6763 (mp0) REVERT: b 195 PHE cc_start: 0.4828 (m-10) cc_final: 0.4271 (m-80) REVERT: c 145 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6670 (mp0) REVERT: d 241 ASP cc_start: 0.7131 (p0) cc_final: 0.6862 (p0) REVERT: f 47 TYR cc_start: 0.5848 (m-80) cc_final: 0.5607 (m-80) REVERT: h 137 ARG cc_start: 0.8350 (OUTLIER) cc_final: 0.8107 (ttt90) REVERT: h 157 ASP cc_start: 0.8083 (m-30) cc_final: 0.7669 (m-30) outliers start: 181 outliers final: 70 residues processed: 860 average time/residue: 1.3457 time to fit residues: 1465.6693 Evaluate side-chains 739 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 649 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 134 MET Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain G residue 68 GLN Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 109 VAL Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 169 GLN Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 149 ARG Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 171 ARG Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 226 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 243 LYS Chi-restraints excluded: chain R residue 41 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 134 MET Chi-restraints excluded: chain V residue 218 GLN Chi-restraints excluded: chain X residue 68 GLN Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain Z residue 221 THR Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 109 VAL Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 169 GLN Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 149 ARG Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 171 ARG Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 226 VAL Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 243 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 621 optimal weight: 0.8980 chunk 473 optimal weight: 3.9990 chunk 326 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 300 optimal weight: 9.9990 chunk 422 optimal weight: 0.6980 chunk 631 optimal weight: 6.9990 chunk 668 optimal weight: 8.9990 chunk 330 optimal weight: 0.9990 chunk 598 optimal weight: 0.5980 chunk 180 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 123 GLN E 154 GLN E 180 GLN E 185 ASN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 112 ASN I 86 GLN I 194 ASN K 10 GLN K 37 GLN K 101 ASN L 137 GLN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN O 225 ASN O 271 GLN S 30 GLN S 123 GLN V 180 GLN V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 183 HIS Y 112 ASN Z 86 GLN Z 194 ASN b 37 GLN b 101 ASN c 137 GLN e 108 ASN ** f 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 225 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56118 Z= 0.187 Angle : 0.555 8.140 75896 Z= 0.293 Chirality : 0.044 0.152 8606 Planarity : 0.004 0.058 9712 Dihedral : 4.658 39.173 7606 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.60 % Allowed : 13.95 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.93 (0.10), residues: 6864 helix: 1.66 (0.10), residues: 2528 sheet: 0.25 (0.12), residues: 1674 loop : -0.05 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 133 HIS 0.004 0.001 HIS b 133 PHE 0.028 0.001 PHE E 164 TYR 0.022 0.001 TYR G 201 ARG 0.005 0.000 ARG X 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 733 time to evaluate : 5.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7423 (p0) REVERT: A 48 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6698 (mttp) REVERT: A 148 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: A 158 ASP cc_start: 0.8553 (p0) cc_final: 0.8330 (p0) REVERT: A 222 ASP cc_start: 0.8406 (t0) cc_final: 0.8020 (t0) REVERT: B 57 MET cc_start: 0.8146 (mtp) cc_final: 0.7834 (mtp) REVERT: C 114 ARG cc_start: 0.8798 (tpp80) cc_final: 0.8523 (tpp-160) REVERT: C 152 ASN cc_start: 0.8313 (m-40) cc_final: 0.8046 (m-40) REVERT: C 194 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8076 (mm) REVERT: C 233 GLN cc_start: 0.7952 (tm-30) cc_final: 0.7691 (tm-30) REVERT: C 237 ASP cc_start: 0.7694 (m-30) cc_final: 0.7415 (m-30) REVERT: D 6 ARG cc_start: 0.8030 (pmt-80) cc_final: 0.7154 (mtt180) REVERT: G 184 PRO cc_start: 0.7774 (Cg_endo) cc_final: 0.7368 (Cg_exo) REVERT: G 195 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7330 (mm-40) REVERT: H 31 ASP cc_start: 0.8352 (t0) cc_final: 0.8065 (t0) REVERT: H 35 GLN cc_start: 0.8227 (tt0) cc_final: 0.8009 (pt0) REVERT: H 86 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8197 (mmt) REVERT: H 118 ASP cc_start: 0.7898 (t0) cc_final: 0.7687 (t0) REVERT: H 120 GLU cc_start: 0.8516 (mp0) cc_final: 0.8299 (mp0) REVERT: H 133 MET cc_start: 0.4594 (mmp) cc_final: 0.4321 (mmp) REVERT: H 141 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8370 (mttp) REVERT: I 93 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8242 (tt0) REVERT: I 214 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7372 (mm-30) REVERT: J 126 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8107 (tp) REVERT: K 148 TYR cc_start: 0.7552 (t80) cc_final: 0.7330 (t80) REVERT: K 156 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7523 (mt-10) REVERT: K 167 GLU cc_start: 0.7235 (mp0) cc_final: 0.6860 (mp0) REVERT: K 195 PHE cc_start: 0.4837 (m-10) cc_final: 0.4232 (m-80) REVERT: L 145 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: M 37 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: M 234 GLU cc_start: 0.7269 (mm-30) cc_final: 0.6962 (mm-30) REVERT: M 241 ASP cc_start: 0.7037 (p0) cc_final: 0.6775 (p0) REVERT: Q 137 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8189 (ttt90) REVERT: Q 157 ASP cc_start: 0.8004 (m-30) cc_final: 0.7630 (m-30) REVERT: R 41 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7409 (p0) REVERT: R 48 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6620 (mttp) REVERT: R 111 ASP cc_start: 0.8551 (m-30) cc_final: 0.8347 (m-30) REVERT: R 148 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: R 158 ASP cc_start: 0.8568 (p0) cc_final: 0.8356 (p0) REVERT: R 222 ASP cc_start: 0.8336 (t0) cc_final: 0.8024 (t0) REVERT: S 57 MET cc_start: 0.8145 (mtp) cc_final: 0.7828 (mtp) REVERT: S 78 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8156 (mtt) REVERT: T 114 ARG cc_start: 0.8801 (tpp80) cc_final: 0.8528 (tpp-160) REVERT: T 152 ASN cc_start: 0.8365 (m-40) cc_final: 0.8083 (m-40) REVERT: T 194 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8073 (mm) REVERT: U 6 ARG cc_start: 0.8044 (pmt-80) cc_final: 0.7130 (mtt-85) REVERT: V 53 ARG cc_start: 0.7653 (ttm-80) cc_final: 0.7411 (ttm170) REVERT: V 209 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6472 (pp20) REVERT: X 184 PRO cc_start: 0.7742 (Cg_endo) cc_final: 0.7337 (Cg_exo) REVERT: Y 35 GLN cc_start: 0.8217 (tt0) cc_final: 0.8001 (pt0) REVERT: Y 70 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7850 (tp30) REVERT: Y 120 GLU cc_start: 0.8515 (mp0) cc_final: 0.8295 (mp0) REVERT: Y 133 MET cc_start: 0.4501 (mmp) cc_final: 0.4170 (mmp) REVERT: Y 141 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8375 (mttp) REVERT: Z 93 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8238 (tt0) REVERT: Z 214 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7339 (mm-30) REVERT: a 126 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8106 (tp) REVERT: a 169 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7303 (mm-40) REVERT: b 156 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7531 (mt-10) REVERT: b 167 GLU cc_start: 0.7160 (mp0) cc_final: 0.6708 (mp0) REVERT: b 195 PHE cc_start: 0.4828 (m-10) cc_final: 0.4232 (m-80) REVERT: c 145 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6527 (mp0) REVERT: d 201 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8597 (mttp) REVERT: d 234 GLU cc_start: 0.7255 (mm-30) cc_final: 0.6961 (mm-30) REVERT: d 241 ASP cc_start: 0.6943 (p0) cc_final: 0.6734 (p0) REVERT: f 57 MET cc_start: 0.7881 (mmm) cc_final: 0.7265 (mmp) REVERT: h 157 ASP cc_start: 0.8062 (m-30) cc_final: 0.7670 (m-30) outliers start: 156 outliers final: 54 residues processed: 826 average time/residue: 1.3540 time to fit residues: 1419.9915 Evaluate side-chains 732 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 654 time to evaluate : 4.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 104 ASP Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 93 GLU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 186 LYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain R residue 41 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain V residue 209 GLU Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 93 GLU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 169 GLN Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 186 LYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 196 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 557 optimal weight: 5.9990 chunk 379 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 498 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 570 optimal weight: 0.8980 chunk 462 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 341 optimal weight: 0.0970 chunk 600 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS B 30 GLN C 70 ASN E 185 ASN F 166 GLN G 90 ASN G 183 HIS H 102 ASN H 112 ASN I 86 GLN L 137 GLN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 271 GLN R 209 HIS S 123 GLN T 70 ASN V 154 GLN V 185 ASN W 166 GLN X 90 ASN X 183 HIS Y 102 ASN Y 112 ASN Z 59 ASN Z 86 GLN Z 218 ASN b 101 ASN c 137 GLN f 271 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 56118 Z= 0.243 Angle : 0.567 8.999 75896 Z= 0.297 Chirality : 0.044 0.204 8606 Planarity : 0.004 0.074 9712 Dihedral : 4.545 29.116 7602 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.90 % Allowed : 14.82 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.94 (0.10), residues: 6864 helix: 1.69 (0.10), residues: 2536 sheet: 0.26 (0.12), residues: 1662 loop : -0.06 (0.12), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 133 HIS 0.005 0.001 HIS X 183 PHE 0.029 0.002 PHE E 164 TYR 0.025 0.001 TYR X 201 ARG 0.007 0.001 ARG W 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 706 time to evaluate : 4.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7692 (OUTLIER) cc_final: 0.7480 (p0) REVERT: A 48 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6548 (mttp) REVERT: A 148 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7480 (pt0) REVERT: A 158 ASP cc_start: 0.8592 (p0) cc_final: 0.8364 (p0) REVERT: A 222 ASP cc_start: 0.8460 (t0) cc_final: 0.7984 (t0) REVERT: C 114 ARG cc_start: 0.8852 (tpp80) cc_final: 0.8584 (tpp-160) REVERT: C 152 ASN cc_start: 0.8319 (m-40) cc_final: 0.8038 (m-40) REVERT: C 194 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8026 (mm) REVERT: C 233 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 6 ARG cc_start: 0.8060 (pmt-80) cc_final: 0.7142 (mtt180) REVERT: G 184 PRO cc_start: 0.7771 (Cg_endo) cc_final: 0.7363 (Cg_exo) REVERT: H 31 ASP cc_start: 0.8375 (t0) cc_final: 0.8137 (t0) REVERT: H 133 MET cc_start: 0.4566 (mmp) cc_final: 0.4273 (mmp) REVERT: H 141 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8460 (mttp) REVERT: I 214 GLU cc_start: 0.7644 (mt-10) cc_final: 0.7355 (mm-30) REVERT: J 126 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (tp) REVERT: K 148 TYR cc_start: 0.7540 (t80) cc_final: 0.7311 (t80) REVERT: K 156 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7498 (mt-10) REVERT: K 167 GLU cc_start: 0.7117 (mp0) cc_final: 0.6733 (mp0) REVERT: K 170 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7228 (tmmt) REVERT: K 195 PHE cc_start: 0.4745 (m-10) cc_final: 0.4152 (m-80) REVERT: L 145 GLU cc_start: 0.7145 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: M 234 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6953 (mm-30) REVERT: M 241 ASP cc_start: 0.6860 (p0) cc_final: 0.6622 (p0) REVERT: O 177 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6224 (ttp) REVERT: Q 157 ASP cc_start: 0.8071 (m-30) cc_final: 0.7759 (m-30) REVERT: R 41 ASN cc_start: 0.7684 (OUTLIER) cc_final: 0.7466 (p0) REVERT: R 48 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6553 (mttp) REVERT: R 61 ASP cc_start: 0.6547 (t0) cc_final: 0.5972 (p0) REVERT: R 148 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: R 158 ASP cc_start: 0.8590 (p0) cc_final: 0.8352 (p0) REVERT: S 78 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8226 (mtt) REVERT: T 114 ARG cc_start: 0.8856 (tpp80) cc_final: 0.8576 (tpp-160) REVERT: T 152 ASN cc_start: 0.8348 (m-40) cc_final: 0.8076 (m-40) REVERT: T 194 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8022 (mm) REVERT: T 233 GLN cc_start: 0.7979 (tm-30) cc_final: 0.7565 (tm-30) REVERT: T 237 ASP cc_start: 0.7695 (m-30) cc_final: 0.7203 (m-30) REVERT: U 6 ARG cc_start: 0.8072 (pmt-80) cc_final: 0.7113 (mtt180) REVERT: X 184 PRO cc_start: 0.7778 (Cg_endo) cc_final: 0.7374 (Cg_exo) REVERT: Y 31 ASP cc_start: 0.8365 (t0) cc_final: 0.8064 (t0) REVERT: Y 70 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7854 (tp30) REVERT: Y 120 GLU cc_start: 0.8527 (mp0) cc_final: 0.8293 (mp0) REVERT: Y 133 MET cc_start: 0.4563 (mmp) cc_final: 0.4268 (mmp) REVERT: Y 141 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8461 (mttp) REVERT: Z 214 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7334 (mm-30) REVERT: a 126 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8126 (tp) REVERT: b 156 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7554 (mt-10) REVERT: b 167 GLU cc_start: 0.7111 (mp0) cc_final: 0.6729 (mp0) REVERT: b 170 LYS cc_start: 0.7535 (mtmm) cc_final: 0.7163 (tmmt) REVERT: b 195 PHE cc_start: 0.4585 (m-10) cc_final: 0.4047 (m-80) REVERT: c 145 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6455 (mp0) REVERT: d 201 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8567 (mttp) REVERT: d 234 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7139 (mm-30) REVERT: d 241 ASP cc_start: 0.6808 (p0) cc_final: 0.6592 (p0) REVERT: h 157 ASP cc_start: 0.8067 (m-30) cc_final: 0.7751 (m-30) outliers start: 174 outliers final: 71 residues processed: 809 average time/residue: 1.3542 time to fit residues: 1389.5237 Evaluate side-chains 734 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 645 time to evaluate : 4.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain O residue 177 MET Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain R residue 41 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 25 GLU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain V residue 104 ASP Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain d residue 212 GLU Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 225 optimal weight: 8.9990 chunk 602 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 392 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 669 optimal weight: 2.9990 chunk 555 optimal weight: 6.9990 chunk 309 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 221 optimal weight: 3.9990 chunk 351 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 218 GLN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 112 ASN H 139 HIS I 86 GLN J 169 GLN K 118 GLN L 137 GLN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN N 164 ASN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN V 218 GLN W 60 GLN W 166 GLN X 90 ASN X 183 HIS Y 112 ASN Y 139 HIS ** Z 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 86 GLN ** Z 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 GLN b 101 ASN b 118 GLN b 146 HIS c 137 GLN ** e 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN e 164 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 56118 Z= 0.388 Angle : 0.628 10.722 75896 Z= 0.327 Chirality : 0.046 0.214 8606 Planarity : 0.005 0.099 9712 Dihedral : 4.741 31.057 7602 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.18 % Allowed : 15.48 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.10), residues: 6864 helix: 1.51 (0.10), residues: 2550 sheet: 0.09 (0.12), residues: 1684 loop : -0.11 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP c 133 HIS 0.006 0.001 HIS Y 139 PHE 0.032 0.002 PHE E 164 TYR 0.024 0.002 TYR c 163 ARG 0.008 0.001 ARG N 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 671 time to evaluate : 4.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7613 (p0) REVERT: A 48 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6571 (mttp) REVERT: A 61 ASP cc_start: 0.6971 (t0) cc_final: 0.6493 (p0) REVERT: A 121 MET cc_start: 0.9175 (mmm) cc_final: 0.8910 (mmm) REVERT: A 148 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7476 (pt0) REVERT: A 158 ASP cc_start: 0.8583 (p0) cc_final: 0.8329 (p0) REVERT: A 221 ASN cc_start: 0.7862 (m110) cc_final: 0.7385 (p0) REVERT: A 222 ASP cc_start: 0.8472 (t0) cc_final: 0.8054 (t0) REVERT: C 114 ARG cc_start: 0.8899 (tpp80) cc_final: 0.8624 (tpp-160) REVERT: C 152 ASN cc_start: 0.8385 (m-40) cc_final: 0.8122 (m-40) REVERT: C 194 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8100 (mm) REVERT: C 233 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7775 (tm-30) REVERT: D 6 ARG cc_start: 0.8104 (pmt-80) cc_final: 0.7168 (mtt180) REVERT: D 107 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: G 44 ASP cc_start: 0.7135 (p0) cc_final: 0.6713 (p0) REVERT: G 184 PRO cc_start: 0.7741 (Cg_endo) cc_final: 0.7346 (Cg_exo) REVERT: G 237 GLN cc_start: 0.8686 (mm-40) cc_final: 0.7607 (pt0) REVERT: H 35 GLN cc_start: 0.8440 (pt0) cc_final: 0.8134 (pt0) REVERT: H 120 GLU cc_start: 0.8627 (mp0) cc_final: 0.8372 (mp0) REVERT: H 133 MET cc_start: 0.4771 (mmp) cc_final: 0.4505 (mmp) REVERT: H 141 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8640 (mttp) REVERT: I 51 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.5602 (tm-30) REVERT: I 214 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7328 (mm-30) REVERT: J 126 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8192 (tp) REVERT: K 156 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7644 (mt-10) REVERT: K 195 PHE cc_start: 0.4936 (m-10) cc_final: 0.4405 (m-80) REVERT: L 145 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: M 241 ASP cc_start: 0.6885 (p0) cc_final: 0.6628 (p0) REVERT: Q 137 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.8049 (ttt90) REVERT: Q 157 ASP cc_start: 0.8095 (m-30) cc_final: 0.7806 (m-30) REVERT: R 41 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7615 (p0) REVERT: R 48 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6569 (mttp) REVERT: R 61 ASP cc_start: 0.6867 (t0) cc_final: 0.6327 (p0) REVERT: R 121 MET cc_start: 0.9175 (mmm) cc_final: 0.8916 (mmm) REVERT: R 158 ASP cc_start: 0.8591 (p0) cc_final: 0.8322 (p0) REVERT: S 78 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8216 (mtt) REVERT: T 114 ARG cc_start: 0.8891 (tpp80) cc_final: 0.8626 (tpp-160) REVERT: T 152 ASN cc_start: 0.8401 (m-40) cc_final: 0.8105 (m-40) REVERT: T 194 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8098 (mm) REVERT: U 6 ARG cc_start: 0.8109 (pmt-80) cc_final: 0.7140 (mtt180) REVERT: U 107 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8300 (tm-30) REVERT: X 44 ASP cc_start: 0.7133 (p0) cc_final: 0.6701 (p0) REVERT: X 184 PRO cc_start: 0.7747 (Cg_endo) cc_final: 0.7354 (Cg_exo) REVERT: X 237 GLN cc_start: 0.8788 (mm-40) cc_final: 0.7830 (pt0) REVERT: X 241 ASP cc_start: 0.8128 (m-30) cc_final: 0.7636 (p0) REVERT: Y 31 ASP cc_start: 0.8452 (t0) cc_final: 0.8140 (t0) REVERT: Y 35 GLN cc_start: 0.8451 (pt0) cc_final: 0.8158 (pt0) REVERT: Y 70 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: Y 133 MET cc_start: 0.4708 (mmp) cc_final: 0.4404 (mmp) REVERT: Y 141 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8636 (mttp) REVERT: Z 51 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.5597 (tm-30) REVERT: Z 214 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7324 (mm-30) REVERT: a 126 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (tp) REVERT: a 169 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7601 (tp-100) REVERT: b 156 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7614 (mt-10) REVERT: b 195 PHE cc_start: 0.4996 (m-10) cc_final: 0.4439 (m-80) REVERT: c 145 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: d 201 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8566 (mttp) REVERT: f 122 PHE cc_start: 0.6839 (m-80) cc_final: 0.6048 (m-80) REVERT: h 137 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8112 (ttt90) REVERT: h 157 ASP cc_start: 0.8169 (m-30) cc_final: 0.7860 (m-30) outliers start: 191 outliers final: 95 residues processed: 800 average time/residue: 1.3418 time to fit residues: 1364.0100 Evaluate side-chains 733 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 615 time to evaluate : 4.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ASN Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain E residue 218 GLN Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 51 GLN Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 30 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 136 ASP Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 122 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 41 ASN Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 78 MET Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 70 ASN Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 107 GLU Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain V residue 78 MET Chi-restraints excluded: chain W residue 77 LEU Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 70 GLU Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 51 GLN Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 54 THR Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain a residue 169 GLN Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 103 LEU Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 137 GLN Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 30 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 199 VAL Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 645 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 381 optimal weight: 0.6980 chunk 488 optimal weight: 3.9990 chunk 378 optimal weight: 0.0170 chunk 563 optimal weight: 0.6980 chunk 373 optimal weight: 0.8980 chunk 666 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 chunk 406 optimal weight: 0.8980 chunk 307 optimal weight: 5.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN E 218 GLN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 112 ASN I 86 GLN K 118 GLN K 146 HIS L 137 GLN N 47 ASN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 ASN S 123 GLN T 233 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN V 218 GLN W 166 GLN X 90 ASN X 147 HIS X 183 HIS Y 112 ASN Z 86 GLN b 101 ASN b 118 GLN b 146 HIS c 137 GLN e 108 ASN e 164 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56118 Z= 0.174 Angle : 0.548 9.610 75896 Z= 0.288 Chirality : 0.043 0.176 8606 Planarity : 0.004 0.069 9712 Dihedral : 4.479 27.555 7602 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.83 % Allowed : 16.42 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.92 (0.10), residues: 6864 helix: 1.72 (0.10), residues: 2558 sheet: 0.14 (0.12), residues: 1654 loop : -0.06 (0.12), residues: 2652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 133 HIS 0.005 0.001 HIS G 183 PHE 0.030 0.001 PHE E 164 TYR 0.036 0.001 TYR c 163 ARG 0.008 0.000 ARG N 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 711 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6555 (mttp) REVERT: A 148 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7439 (pt0) REVERT: A 158 ASP cc_start: 0.8502 (p0) cc_final: 0.8267 (p0) REVERT: A 221 ASN cc_start: 0.7897 (m110) cc_final: 0.7371 (p0) REVERT: A 222 ASP cc_start: 0.8480 (t0) cc_final: 0.8062 (t0) REVERT: C 114 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8541 (tpp-160) REVERT: C 194 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8128 (mm) REVERT: C 233 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7536 (tm-30) REVERT: C 234 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7496 (pt0) REVERT: C 237 ASP cc_start: 0.7755 (m-30) cc_final: 0.7293 (m-30) REVERT: D 6 ARG cc_start: 0.8016 (pmt-80) cc_final: 0.7129 (mtt180) REVERT: G 44 ASP cc_start: 0.7169 (p0) cc_final: 0.6744 (p0) REVERT: G 184 PRO cc_start: 0.7560 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: G 237 GLN cc_start: 0.8692 (mm-40) cc_final: 0.7671 (pt0) REVERT: H 31 ASP cc_start: 0.8324 (t0) cc_final: 0.7996 (t0) REVERT: H 35 GLN cc_start: 0.8338 (pt0) cc_final: 0.8048 (pt0) REVERT: H 120 GLU cc_start: 0.8540 (mp0) cc_final: 0.8291 (mp0) REVERT: H 141 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8482 (mttp) REVERT: I 148 THR cc_start: 0.9020 (p) cc_final: 0.8817 (t) REVERT: I 214 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7276 (mm-30) REVERT: J 11 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8675 (tp) REVERT: J 126 LEU cc_start: 0.8322 (mp) cc_final: 0.8100 (tp) REVERT: K 156 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7538 (mt-10) REVERT: K 167 GLU cc_start: 0.7181 (mp0) cc_final: 0.6689 (mp0) REVERT: K 195 PHE cc_start: 0.4836 (m-10) cc_final: 0.4294 (m-80) REVERT: L 145 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: M 72 SER cc_start: 0.8436 (m) cc_final: 0.7840 (t) REVERT: M 241 ASP cc_start: 0.6734 (p0) cc_final: 0.6470 (p0) REVERT: O 122 PHE cc_start: 0.6762 (m-80) cc_final: 0.5873 (m-80) REVERT: Q 137 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.8010 (ttt90) REVERT: Q 157 ASP cc_start: 0.7971 (m-30) cc_final: 0.7705 (m-30) REVERT: R 48 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6552 (mttp) REVERT: R 61 ASP cc_start: 0.6863 (t0) cc_final: 0.6283 (p0) REVERT: R 148 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: R 158 ASP cc_start: 0.8494 (p0) cc_final: 0.8236 (p0) REVERT: R 221 ASN cc_start: 0.7903 (m110) cc_final: 0.7364 (p0) REVERT: T 114 ARG cc_start: 0.8829 (tpp80) cc_final: 0.8562 (tpp-160) REVERT: T 194 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8124 (mm) REVERT: T 233 GLN cc_start: 0.7970 (tp40) cc_final: 0.7692 (tm-30) REVERT: T 237 ASP cc_start: 0.7839 (m-30) cc_final: 0.7594 (m-30) REVERT: U 6 ARG cc_start: 0.8022 (pmt-80) cc_final: 0.7131 (mtt180) REVERT: U 46 CYS cc_start: 0.7789 (t) cc_final: 0.7470 (m) REVERT: X 44 ASP cc_start: 0.7138 (p0) cc_final: 0.6737 (p0) REVERT: X 184 PRO cc_start: 0.7562 (Cg_endo) cc_final: 0.7203 (Cg_exo) REVERT: X 237 GLN cc_start: 0.8718 (mm-40) cc_final: 0.7738 (pt0) REVERT: Y 31 ASP cc_start: 0.8323 (t0) cc_final: 0.8041 (t0) REVERT: Y 35 GLN cc_start: 0.8346 (pt0) cc_final: 0.8061 (pt0) REVERT: Y 141 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8483 (mttp) REVERT: Z 214 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7258 (mm-30) REVERT: a 11 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8705 (tp) REVERT: a 15 MET cc_start: 0.9178 (ttm) cc_final: 0.8936 (mtt) REVERT: a 126 LEU cc_start: 0.8322 (mp) cc_final: 0.8106 (tp) REVERT: b 156 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7602 (mt-10) REVERT: b 167 GLU cc_start: 0.7167 (mp0) cc_final: 0.6687 (mp0) REVERT: b 195 PHE cc_start: 0.4923 (m-10) cc_final: 0.4343 (m-80) REVERT: c 145 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: d 72 SER cc_start: 0.8503 (m) cc_final: 0.7906 (t) REVERT: d 201 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8583 (mttp) REVERT: f 122 PHE cc_start: 0.6769 (m-80) cc_final: 0.5945 (m-80) REVERT: h 137 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.8039 (ttt90) REVERT: h 157 ASP cc_start: 0.7999 (m-30) cc_final: 0.7734 (m-30) outliers start: 170 outliers final: 66 residues processed: 835 average time/residue: 1.3577 time to fit residues: 1436.7674 Evaluate side-chains 740 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 658 time to evaluate : 4.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 137 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 131 ASP Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 137 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 412 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 398 optimal weight: 0.0370 chunk 200 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 424 optimal weight: 4.9990 chunk 454 optimal weight: 9.9990 chunk 329 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 524 optimal weight: 6.9990 overall best weight: 1.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 41 ASN B 30 GLN C 177 GLN ** D 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 ASN F 166 GLN G 90 ASN G 147 HIS G 183 HIS I 86 GLN I 194 ASN J 169 GLN K 118 GLN K 146 HIS L 137 GLN M 171 ASN ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 108 ASN N 164 ASN R 27 GLN R 41 ASN S 30 GLN S 123 GLN T 177 GLN ** U 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 185 ASN W 60 GLN W 166 GLN X 90 ASN X 183 HIS ** Z 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 86 GLN ** Z 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 GLN b 101 ASN b 118 GLN b 146 HIS c 137 GLN ** e 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN e 164 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 56118 Z= 0.265 Angle : 0.585 10.864 75896 Z= 0.305 Chirality : 0.044 0.202 8606 Planarity : 0.004 0.062 9712 Dihedral : 4.519 27.868 7602 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.61 % Allowed : 17.35 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % 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: 0.91 (0.10), residues: 6864 helix: 1.70 (0.10), residues: 2558 sheet: 0.18 (0.12), residues: 1644 loop : -0.08 (0.12), residues: 2662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 133 HIS 0.006 0.001 HIS G 183 PHE 0.032 0.002 PHE V 164 TYR 0.046 0.001 TYR c 163 ARG 0.011 0.000 ARG J 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 667 time to evaluate : 4.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6542 (mttp) REVERT: A 61 ASP cc_start: 0.6725 (t0) cc_final: 0.6281 (p0) REVERT: A 63 LEU cc_start: 0.8366 (mt) cc_final: 0.8159 (mt) REVERT: A 148 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: A 158 ASP cc_start: 0.8538 (p0) cc_final: 0.8275 (p0) REVERT: A 221 ASN cc_start: 0.7996 (m110) cc_final: 0.7404 (p0) REVERT: B 150 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8779 (t) REVERT: C 114 ARG cc_start: 0.8861 (tpp80) cc_final: 0.8587 (tpp-160) REVERT: C 152 ASN cc_start: 0.8156 (m-40) cc_final: 0.7921 (m-40) REVERT: C 194 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8083 (mm) REVERT: C 233 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 234 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7527 (pt0) REVERT: C 237 ASP cc_start: 0.7831 (m-30) cc_final: 0.7365 (m-30) REVERT: D 6 ARG cc_start: 0.8072 (pmt-80) cc_final: 0.7111 (mtt180) REVERT: G 184 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7201 (Cg_exo) REVERT: H 31 ASP cc_start: 0.8349 (t0) cc_final: 0.8023 (t0) REVERT: H 35 GLN cc_start: 0.8448 (pt0) cc_final: 0.8209 (pt0) REVERT: H 141 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8535 (mttp) REVERT: I 214 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7303 (mm-30) REVERT: J 11 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8738 (tp) REVERT: J 126 LEU cc_start: 0.8282 (mp) cc_final: 0.8019 (tp) REVERT: K 107 TYR cc_start: 0.8933 (t80) cc_final: 0.8650 (t80) REVERT: K 156 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7552 (mt-10) REVERT: K 195 PHE cc_start: 0.4732 (m-10) cc_final: 0.4222 (m-80) REVERT: L 145 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: M 72 SER cc_start: 0.8442 (m) cc_final: 0.7857 (t) REVERT: M 241 ASP cc_start: 0.6818 (p0) cc_final: 0.6578 (p0) REVERT: N 110 ASP cc_start: 0.8138 (OUTLIER) cc_final: 0.7695 (t0) REVERT: Q 157 ASP cc_start: 0.7953 (m-30) cc_final: 0.7695 (m-30) REVERT: R 48 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6540 (mttp) REVERT: R 61 ASP cc_start: 0.6952 (t70) cc_final: 0.6398 (p0) REVERT: R 148 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7564 (pt0) REVERT: R 158 ASP cc_start: 0.8544 (p0) cc_final: 0.8273 (p0) REVERT: R 221 ASN cc_start: 0.7964 (m110) cc_final: 0.7353 (p0) REVERT: R 222 ASP cc_start: 0.8466 (t0) cc_final: 0.8036 (t0) REVERT: S 150 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8783 (t) REVERT: T 114 ARG cc_start: 0.8870 (tpp80) cc_final: 0.8588 (tpp-160) REVERT: T 152 ASN cc_start: 0.8183 (m-40) cc_final: 0.7953 (m-40) REVERT: T 194 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8078 (mm) REVERT: T 237 ASP cc_start: 0.7895 (m-30) cc_final: 0.7575 (m-30) REVERT: U 6 ARG cc_start: 0.8094 (pmt-80) cc_final: 0.7123 (mtt180) REVERT: X 184 PRO cc_start: 0.7561 (Cg_endo) cc_final: 0.7207 (Cg_exo) REVERT: X 237 GLN cc_start: 0.8738 (mm-40) cc_final: 0.7910 (pt0) REVERT: X 241 ASP cc_start: 0.8115 (m-30) cc_final: 0.7657 (p0) REVERT: Y 31 ASP cc_start: 0.8382 (t0) cc_final: 0.8132 (t0) REVERT: Y 35 GLN cc_start: 0.8451 (pt0) cc_final: 0.8213 (pt0) REVERT: Y 141 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8534 (mttp) REVERT: Z 214 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7300 (mm-30) REVERT: a 11 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8756 (tp) REVERT: a 126 LEU cc_start: 0.8283 (mp) cc_final: 0.8015 (tp) REVERT: b 156 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7574 (mt-10) REVERT: b 195 PHE cc_start: 0.4823 (m-10) cc_final: 0.4275 (m-80) REVERT: c 145 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: d 72 SER cc_start: 0.8523 (m) cc_final: 0.7940 (t) REVERT: d 201 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8598 (mttp) REVERT: h 157 ASP cc_start: 0.7956 (m-30) cc_final: 0.7688 (m-30) outliers start: 157 outliers final: 89 residues processed: 785 average time/residue: 1.3235 time to fit residues: 1321.5380 Evaluate side-chains 757 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 651 time to evaluate : 5.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 143 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 154 THR Chi-restraints excluded: chain L residue 137 GLN Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 147 VAL Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain N residue 110 ASP Chi-restraints excluded: chain N residue 131 THR Chi-restraints excluded: chain O residue 8 ASP Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 98 ARG Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 150 VAL Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 56 THR Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 92 ILE Chi-restraints excluded: chain b residue 103 LEU Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 151 ASP Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain b residue 154 THR Chi-restraints excluded: chain c residue 137 GLN Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 175 MET Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 136 ASP Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain e residue 122 ASP Chi-restraints excluded: chain e residue 131 THR Chi-restraints excluded: chain e residue 178 LEU Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 606 optimal weight: 8.9990 chunk 638 optimal weight: 5.9990 chunk 582 optimal weight: 5.9990 chunk 621 optimal weight: 0.0970 chunk 374 optimal weight: 0.0030 chunk 270 optimal weight: 0.8980 chunk 488 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 561 optimal weight: 4.9990 chunk 587 optimal weight: 0.9990 chunk 619 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS E 185 ASN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 112 ASN I 86 GLN I 110 GLN I 194 ASN J 169 GLN K 118 GLN K 146 HIS L 137 GLN L 164 GLN M 171 ASN N 164 ASN R 41 ASN R 209 HIS V 185 ASN W 166 GLN X 183 HIS Y 112 ASN Z 59 ASN Z 86 GLN Z 110 GLN Z 218 ASN b 101 ASN b 118 GLN b 146 HIS c 137 GLN d 68 ASN e 164 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56118 Z= 0.169 Angle : 0.558 11.692 75896 Z= 0.291 Chirality : 0.043 0.205 8606 Planarity : 0.004 0.062 9712 Dihedral : 4.382 28.212 7602 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.05 % Allowed : 18.12 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.10), residues: 6864 helix: 1.87 (0.10), residues: 2528 sheet: 0.22 (0.12), residues: 1652 loop : -0.06 (0.12), residues: 2684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 133 HIS 0.006 0.001 HIS X 183 PHE 0.044 0.001 PHE L 129 TYR 0.041 0.001 TYR L 163 ARG 0.015 0.000 ARG b 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 705 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6488 (mttp) REVERT: A 61 ASP cc_start: 0.6693 (t0) cc_final: 0.6174 (p0) REVERT: A 148 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: A 158 ASP cc_start: 0.8477 (p0) cc_final: 0.8232 (p0) REVERT: A 221 ASN cc_start: 0.7982 (m110) cc_final: 0.7370 (p0) REVERT: A 222 ASP cc_start: 0.8537 (t0) cc_final: 0.8102 (t0) REVERT: C 114 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8533 (tpp-160) REVERT: C 194 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8035 (mm) REVERT: C 233 GLN cc_start: 0.7891 (tm-30) cc_final: 0.7449 (tm-30) REVERT: C 237 ASP cc_start: 0.7780 (m-30) cc_final: 0.7229 (m-30) REVERT: D 6 ARG cc_start: 0.8001 (pmt-80) cc_final: 0.7071 (mtt180) REVERT: F 118 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8271 (tptp) REVERT: G 44 ASP cc_start: 0.7308 (p0) cc_final: 0.6843 (p0) REVERT: G 184 PRO cc_start: 0.7536 (Cg_endo) cc_final: 0.7236 (Cg_exo) REVERT: G 190 ARG cc_start: 0.8232 (mmm160) cc_final: 0.8001 (mmm160) REVERT: G 237 GLN cc_start: 0.8672 (mm-40) cc_final: 0.7875 (pt0) REVERT: G 241 ASP cc_start: 0.8180 (m-30) cc_final: 0.7710 (p0) REVERT: H 31 ASP cc_start: 0.8255 (t0) cc_final: 0.8044 (t0) REVERT: H 133 MET cc_start: 0.4750 (mmp) cc_final: 0.4359 (mmp) REVERT: H 141 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: I 214 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7296 (mm-30) REVERT: J 11 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8711 (tp) REVERT: J 126 LEU cc_start: 0.8276 (mp) cc_final: 0.8067 (tp) REVERT: K 58 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7771 (mm-30) REVERT: K 85 ARG cc_start: 0.8977 (ttp80) cc_final: 0.8718 (ttt-90) REVERT: K 107 TYR cc_start: 0.8888 (t80) cc_final: 0.8645 (t80) REVERT: K 156 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7532 (mt-10) REVERT: K 167 GLU cc_start: 0.7156 (mp0) cc_final: 0.6674 (mp0) REVERT: K 195 PHE cc_start: 0.4711 (m-10) cc_final: 0.4068 (m-80) REVERT: L 145 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6209 (mp0) REVERT: M 72 SER cc_start: 0.8375 (m) cc_final: 0.7783 (t) REVERT: M 240 ARG cc_start: 0.8698 (ttt90) cc_final: 0.8478 (tpt-90) REVERT: M 241 ASP cc_start: 0.6850 (p0) cc_final: 0.6616 (p0) REVERT: Q 106 GLU cc_start: 0.7256 (pp20) cc_final: 0.6978 (tm-30) REVERT: Q 157 ASP cc_start: 0.7889 (m-30) cc_final: 0.7655 (m-30) REVERT: R 48 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.6487 (mttp) REVERT: R 61 ASP cc_start: 0.7043 (t70) cc_final: 0.6476 (p0) REVERT: R 148 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7497 (pt0) REVERT: R 158 ASP cc_start: 0.8480 (p0) cc_final: 0.8228 (p0) REVERT: R 221 ASN cc_start: 0.7985 (m110) cc_final: 0.7358 (p0) REVERT: R 222 ASP cc_start: 0.8492 (t0) cc_final: 0.8040 (t0) REVERT: T 114 ARG cc_start: 0.8821 (tpp80) cc_final: 0.8533 (tpp-160) REVERT: T 178 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7549 (ppp) REVERT: T 194 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8032 (mm) REVERT: T 237 ASP cc_start: 0.7892 (m-30) cc_final: 0.7676 (m-30) REVERT: U 6 ARG cc_start: 0.8040 (pmt-80) cc_final: 0.7113 (mtt180) REVERT: W 118 LYS cc_start: 0.8542 (mtmm) cc_final: 0.8260 (tptp) REVERT: X 44 ASP cc_start: 0.7244 (p0) cc_final: 0.6855 (p0) REVERT: X 184 PRO cc_start: 0.7537 (Cg_endo) cc_final: 0.7236 (Cg_exo) REVERT: X 190 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7975 (mmm160) REVERT: X 241 ASP cc_start: 0.8097 (m-30) cc_final: 0.7695 (p0) REVERT: Y 133 MET cc_start: 0.4767 (mmp) cc_final: 0.4372 (mmp) REVERT: Y 141 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8453 (mttp) REVERT: Z 214 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7282 (mm-30) REVERT: a 11 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8798 (tp) REVERT: a 15 MET cc_start: 0.9179 (ttm) cc_final: 0.8928 (mtt) REVERT: a 126 LEU cc_start: 0.8287 (mp) cc_final: 0.8064 (tp) REVERT: b 58 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7778 (mm-30) REVERT: b 156 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7664 (mt-10) REVERT: b 195 PHE cc_start: 0.4691 (m-10) cc_final: 0.4054 (m-80) REVERT: c 145 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6580 (mp0) REVERT: d 72 SER cc_start: 0.8407 (m) cc_final: 0.7829 (t) REVERT: d 201 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8587 (mttp) REVERT: h 47 MET cc_start: 0.9197 (ptm) cc_final: 0.8945 (ttp) REVERT: h 157 ASP cc_start: 0.7888 (m-30) cc_final: 0.7644 (m-30) outliers start: 123 outliers final: 69 residues processed: 789 average time/residue: 1.3486 time to fit residues: 1353.3477 Evaluate side-chains 728 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 645 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain J residue 11 ILE Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 131 ASP Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 138 CYS Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain P residue 124 MET Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 11 ILE Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 151 ASP Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 197 GLU Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain g residue 124 MET Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 408 optimal weight: 0.9990 chunk 657 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 311 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 689 optimal weight: 2.9990 chunk 634 optimal weight: 10.0000 chunk 548 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 424 optimal weight: 4.9990 chunk 336 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS E 185 ASN F 166 GLN G 90 ASN G 183 HIS I 86 GLN I 194 ASN K 118 GLN K 146 HIS L 137 GLN M 68 ASN M 171 ASN N 164 ASN ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS V 185 ASN W 60 GLN W 166 GLN X 183 HIS Z 86 GLN Z 194 ASN b 101 ASN b 118 GLN b 146 HIS c 137 GLN c 164 GLN e 108 ASN e 164 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 56118 Z= 0.225 Angle : 0.578 12.175 75896 Z= 0.301 Chirality : 0.044 0.199 8606 Planarity : 0.004 0.059 9712 Dihedral : 4.398 27.702 7602 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.91 % Allowed : 18.76 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 6864 helix: 1.85 (0.10), residues: 2524 sheet: 0.22 (0.12), residues: 1650 loop : -0.05 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 133 HIS 0.006 0.001 HIS G 183 PHE 0.049 0.001 PHE L 129 TYR 0.030 0.001 TYR c 163 ARG 0.012 0.000 ARG b 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13728 Ramachandran restraints generated. 6864 Oldfield, 0 Emsley, 6864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 669 time to evaluate : 4.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6512 (mttp) REVERT: A 61 ASP cc_start: 0.6758 (t0) cc_final: 0.6228 (p0) REVERT: A 148 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: A 158 ASP cc_start: 0.8510 (p0) cc_final: 0.8249 (p0) REVERT: A 221 ASN cc_start: 0.8021 (m110) cc_final: 0.7405 (p0) REVERT: C 114 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8563 (tpp-160) REVERT: C 194 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8062 (mm) REVERT: C 233 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7616 (tp-100) REVERT: D 6 ARG cc_start: 0.8036 (pmt-80) cc_final: 0.7105 (mtt180) REVERT: D 46 CYS cc_start: 0.7832 (t) cc_final: 0.7544 (m) REVERT: F 118 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8273 (tptp) REVERT: G 44 ASP cc_start: 0.7285 (p0) cc_final: 0.6888 (p0) REVERT: G 184 PRO cc_start: 0.7489 (Cg_endo) cc_final: 0.7206 (Cg_exo) REVERT: G 190 ARG cc_start: 0.8248 (mmm160) cc_final: 0.8019 (mmm160) REVERT: H 31 ASP cc_start: 0.8274 (t0) cc_final: 0.8049 (t0) REVERT: H 133 MET cc_start: 0.4761 (mmp) cc_final: 0.4395 (mmp) REVERT: H 141 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8466 (mttp) REVERT: I 214 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7289 (mm-30) REVERT: J 126 LEU cc_start: 0.8293 (mp) cc_final: 0.8064 (tp) REVERT: K 58 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7778 (mm-30) REVERT: K 156 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7595 (mt-10) REVERT: K 161 LEU cc_start: 0.8563 (tp) cc_final: 0.8319 (tm) REVERT: K 167 GLU cc_start: 0.7388 (mp0) cc_final: 0.6937 (mp0) REVERT: K 195 PHE cc_start: 0.4593 (m-10) cc_final: 0.4100 (m-80) REVERT: L 145 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6153 (mp0) REVERT: M 72 SER cc_start: 0.8369 (m) cc_final: 0.7784 (t) REVERT: M 156 ARG cc_start: 0.7811 (tpt170) cc_final: 0.7560 (tpt170) REVERT: M 241 ASP cc_start: 0.6886 (p0) cc_final: 0.6657 (p0) REVERT: P 133 ARG cc_start: 0.7332 (ptp-170) cc_final: 0.7112 (ptp-170) REVERT: Q 106 GLU cc_start: 0.7276 (pp20) cc_final: 0.6982 (tm-30) REVERT: Q 157 ASP cc_start: 0.7826 (m-30) cc_final: 0.7577 (m-30) REVERT: R 48 LYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6479 (mttp) REVERT: R 61 ASP cc_start: 0.7082 (t70) cc_final: 0.6480 (p0) REVERT: R 148 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7521 (pt0) REVERT: R 158 ASP cc_start: 0.8519 (p0) cc_final: 0.8245 (p0) REVERT: R 221 ASN cc_start: 0.7988 (m110) cc_final: 0.7363 (p0) REVERT: T 114 ARG cc_start: 0.8842 (tpp80) cc_final: 0.8563 (tpp-160) REVERT: T 152 ASN cc_start: 0.8117 (m-40) cc_final: 0.7914 (m-40) REVERT: T 178 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7561 (ppp) REVERT: T 194 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8039 (mm) REVERT: U 6 ARG cc_start: 0.8065 (pmt-80) cc_final: 0.7133 (mtt180) REVERT: W 118 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8268 (tptp) REVERT: X 44 ASP cc_start: 0.7323 (p0) cc_final: 0.6896 (p0) REVERT: X 184 PRO cc_start: 0.7487 (Cg_endo) cc_final: 0.7207 (Cg_exo) REVERT: X 190 ARG cc_start: 0.8229 (mmm160) cc_final: 0.7985 (mmm160) REVERT: X 237 GLN cc_start: 0.8709 (mm-40) cc_final: 0.7835 (pt0) REVERT: X 241 ASP cc_start: 0.8116 (m-30) cc_final: 0.7651 (p0) REVERT: Y 133 MET cc_start: 0.4766 (mmp) cc_final: 0.4405 (mmp) REVERT: Y 141 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8464 (mttp) REVERT: Z 214 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7295 (mm-30) REVERT: a 126 LEU cc_start: 0.8309 (mp) cc_final: 0.8061 (tp) REVERT: b 58 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7783 (mm-30) REVERT: b 156 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7678 (mt-10) REVERT: b 161 LEU cc_start: 0.8572 (tp) cc_final: 0.8325 (tm) REVERT: b 195 PHE cc_start: 0.4526 (m-10) cc_final: 0.4066 (m-80) REVERT: c 145 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: d 72 SER cc_start: 0.8426 (m) cc_final: 0.7851 (t) REVERT: d 201 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8594 (mttp) REVERT: h 47 MET cc_start: 0.9207 (ptm) cc_final: 0.8958 (ttp) REVERT: h 157 ASP cc_start: 0.7875 (m-30) cc_final: 0.7631 (m-30) outliers start: 115 outliers final: 74 residues processed: 750 average time/residue: 1.3382 time to fit residues: 1277.1585 Evaluate side-chains 721 residues out of total 6006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 635 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LYS Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 231 LYS Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain D residue 32 CYS Chi-restraints excluded: chain D residue 150 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain G residue 76 CYS Chi-restraints excluded: chain H residue 21 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 141 LYS Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 35 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain L residue 145 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 161 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 128 THR Chi-restraints excluded: chain M residue 197 GLU Chi-restraints excluded: chain N residue 63 CYS Chi-restraints excluded: chain O residue 31 CYS Chi-restraints excluded: chain Q residue 82 THR Chi-restraints excluded: chain Q residue 169 THR Chi-restraints excluded: chain Q residue 196 SER Chi-restraints excluded: chain Q residue 208 GLU Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 148 GLU Chi-restraints excluded: chain S residue 169 VAL Chi-restraints excluded: chain S residue 200 VAL Chi-restraints excluded: chain S residue 216 ASP Chi-restraints excluded: chain S residue 227 ILE Chi-restraints excluded: chain S residue 231 LYS Chi-restraints excluded: chain T residue 34 THR Chi-restraints excluded: chain T residue 55 THR Chi-restraints excluded: chain T residue 57 LEU Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 178 MET Chi-restraints excluded: chain T residue 194 LEU Chi-restraints excluded: chain U residue 32 CYS Chi-restraints excluded: chain U residue 150 THR Chi-restraints excluded: chain U residue 215 VAL Chi-restraints excluded: chain X residue 76 CYS Chi-restraints excluded: chain Y residue 21 VAL Chi-restraints excluded: chain Y residue 55 SER Chi-restraints excluded: chain Y residue 86 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain Z residue 148 THR Chi-restraints excluded: chain a residue 49 VAL Chi-restraints excluded: chain a residue 58 THR Chi-restraints excluded: chain a residue 114 SER Chi-restraints excluded: chain a residue 131 ASP Chi-restraints excluded: chain a residue 138 VAL Chi-restraints excluded: chain b residue 35 THR Chi-restraints excluded: chain b residue 103 LEU Chi-restraints excluded: chain b residue 151 ASP Chi-restraints excluded: chain b residue 153 THR Chi-restraints excluded: chain c residue 137 GLN Chi-restraints excluded: chain c residue 138 CYS Chi-restraints excluded: chain c residue 145 GLU Chi-restraints excluded: chain c residue 151 VAL Chi-restraints excluded: chain c residue 161 LEU Chi-restraints excluded: chain c residue 180 THR Chi-restraints excluded: chain d residue 128 THR Chi-restraints excluded: chain d residue 201 LYS Chi-restraints excluded: chain e residue 63 CYS Chi-restraints excluded: chain f residue 8 ASP Chi-restraints excluded: chain f residue 31 CYS Chi-restraints excluded: chain h residue 82 THR Chi-restraints excluded: chain h residue 98 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 196 SER Chi-restraints excluded: chain h residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 692 random chunks: chunk 436 optimal weight: 0.6980 chunk 584 optimal weight: 10.0000 chunk 168 optimal weight: 0.9980 chunk 506 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 549 optimal weight: 0.9980 chunk 230 optimal weight: 0.9990 chunk 564 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 101 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS E 185 ASN F 60 GLN F 166 GLN G 90 ASN G 183 HIS H 112 ASN I 86 GLN I 120 GLN I 194 ASN ** J 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 GLN K 146 HIS L 137 GLN M 171 ASN N 108 ASN N 164 ASN ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 209 HIS V 185 ASN W 166 GLN X 183 HIS Y 112 ASN Z 86 GLN Z 120 GLN Z 194 ASN b 101 ASN b 118 GLN b 146 HIS c 164 GLN e 108 ASN e 164 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.143268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101502 restraints weight = 80379.773| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.08 r_work: 0.3183 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 56118 Z= 0.246 Angle : 0.699 59.199 75896 Z= 0.371 Chirality : 0.044 0.567 8606 Planarity : 0.004 0.059 9712 Dihedral : 4.403 27.708 7602 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.85 % Allowed : 18.96 % Favored : 79.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.10), residues: 6864 helix: 1.84 (0.10), residues: 2532 sheet: 0.22 (0.12), residues: 1650 loop : -0.06 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP c 133 HIS 0.006 0.001 HIS G 183 PHE 0.040 0.001 PHE L 129 TYR 0.026 0.001 TYR c 163 ARG 0.010 0.000 ARG b 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20363.73 seconds wall clock time: 352 minutes 40.48 seconds (21160.48 seconds total)