Starting phenix.real_space_refine on Tue Sep 24 01:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qm8_4591/09_2024/6qm8_4591.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.018 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 328 5.16 5 C 30870 2.51 5 N 8468 2.21 5 O 9458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 516 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49124 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "B" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "C" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "D" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "E" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "F" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "G" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "I" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "J" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "K" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "L" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "M" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "N" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "O" Number of atoms: 1857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1857 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain: "P" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "Q" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2195 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "R" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1873 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 4, 'TRANS': 234} Chain: "S" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1756 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Chain: "T" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 8, 'TRANS': 229} Chain: "U" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "V" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 220} Chain: "W" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1659 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 10, 'TRANS': 208} Chain: "X" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1557 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 196} Chain: "Y" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1612 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain: "Z" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1579 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 2, 'TRANS': 199} Chain: "a" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1702 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 205} Chain: "b" Number of atoms: 1712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1712 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Time building chain proxies: 21.83, per 1000 atoms: 0.44 Number of scatterers: 49124 At special positions: 0 Unit cell: (149.8, 203.3, 139.1, 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 328 16.00 O 9458 8.00 N 8468 7.00 C 30870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 102 " - pdb=" SG CYS b 104 " distance=2.96 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.41 Conformation dependent library (CDL) restraints added in 4.7 seconds 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11708 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 70 sheets defined 38.0% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.97 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.785A pdb=" N THR A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 103 Processing helix chain 'A' and resid 107 through 125 removed outlier: 3.627A pdb=" N ARG A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 188 removed outlier: 3.543A pdb=" N LYS A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 235 through 249 removed outlier: 3.693A pdb=" N TRP A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 245 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 removed outlier: 3.642A pdb=" N ALA B 23 " --> pdb=" O GLN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 100 removed outlier: 3.860A pdb=" N VAL B 83 " --> pdb=" O PRO B 79 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 86 " --> pdb=" O ARG B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 122 removed outlier: 3.506A pdb=" N ILE B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.589A pdb=" N ALA B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS B 174 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 3.584A pdb=" N HIS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLY B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 229 removed outlier: 3.677A pdb=" N TYR B 227 " --> pdb=" O GLN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 85 through 108 Processing helix chain 'C' and resid 112 through 130 removed outlier: 3.536A pdb=" N LEU C 116 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 185 removed outlier: 3.553A pdb=" N LYS C 183 " --> pdb=" O ALA C 179 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 184 " --> pdb=" O LEU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 206 Processing helix chain 'C' and resid 230 through 234 removed outlier: 3.518A pdb=" N ASP C 234 " --> pdb=" O GLN C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 270 Proline residue: C 256 - end of helix removed outlier: 3.511A pdb=" N GLN C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 268 " --> pdb=" O ALA C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.900A pdb=" N GLN C 276 " --> pdb=" O GLU C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 29 Processing helix chain 'D' and resid 76 through 98 Processing helix chain 'D' and resid 103 through 118 removed outlier: 3.675A pdb=" N ARG D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 4.116A pdb=" N LYS D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER D 175 " --> pdb=" O TYR D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 218 through 231 removed outlier: 3.685A pdb=" N GLN D 223 " --> pdb=" O GLU D 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 224 " --> pdb=" O GLU D 220 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 4.033A pdb=" N LYS D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 130 removed outlier: 3.598A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 204 removed outlier: 3.739A pdb=" N ILE E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 215 Processing helix chain 'E' and resid 273 through 285 removed outlier: 3.550A pdb=" N SER E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU E 283 " --> pdb=" O SER E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 306 Processing helix chain 'E' and resid 331 through 341 removed outlier: 3.981A pdb=" N ARG E 341 " --> pdb=" O ALA E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 removed outlier: 3.576A pdb=" N GLU F 187 " --> pdb=" O LEU F 183 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 192 " --> pdb=" O TYR F 188 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 193 " --> pdb=" O ALA F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 265 Processing helix chain 'F' and resid 269 through 285 removed outlier: 4.000A pdb=" N HIS F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 341 removed outlier: 3.985A pdb=" N SER F 333 " --> pdb=" O ARG F 329 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N HIS F 340 " --> pdb=" O TYR F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 345 removed outlier: 4.267A pdb=" N SER F 345 " --> pdb=" O GLU F 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 342 through 345' Processing helix chain 'F' and resid 348 through 363 removed outlier: 3.612A pdb=" N ALA F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 391 through 399 removed outlier: 4.470A pdb=" N LYS F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TYR F 397 " --> pdb=" O SER F 393 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 10 removed outlier: 4.040A pdb=" N ASP G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN G 10 " --> pdb=" O GLY G 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 6 through 10' Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.568A pdb=" N GLU G 25 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL G 31 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 102 Processing helix chain 'G' and resid 108 through 123 removed outlier: 3.847A pdb=" N TYR G 123 " --> pdb=" O PHE G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 178 removed outlier: 3.601A pdb=" N LYS G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 201 removed outlier: 3.608A pdb=" N VAL G 190 " --> pdb=" O CYS G 186 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 125 Processing helix chain 'H' and resid 129 through 144 removed outlier: 3.539A pdb=" N ASN H 144 " --> pdb=" O MET H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 197 removed outlier: 4.057A pdb=" N LEU H 189 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER H 191 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N PHE H 192 " --> pdb=" O PHE H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 219 Processing helix chain 'H' and resid 244 through 248 Processing helix chain 'H' and resid 255 through 259 removed outlier: 3.575A pdb=" N VAL H 259 " --> pdb=" O PRO H 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 Processing helix chain 'I' and resid 104 through 119 removed outlier: 3.628A pdb=" N TYR I 119 " --> pdb=" O HIS I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 195 removed outlier: 3.567A pdb=" N GLY I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 78 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.535A pdb=" N ALA J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 176 Processing helix chain 'K' and resid 50 through 72 removed outlier: 3.557A pdb=" N TYR K 60 " --> pdb=" O ASN K 56 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN K 68 " --> pdb=" O ASN K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 94 removed outlier: 3.513A pdb=" N THR K 82 " --> pdb=" O SER K 78 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE K 94 " --> pdb=" O LEU K 90 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 158 removed outlier: 3.536A pdb=" N ALA K 152 " --> pdb=" O CYS K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 182 Processing helix chain 'L' and resid 147 through 169 removed outlier: 3.631A pdb=" N ARG L 156 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 189 Processing helix chain 'L' and resid 230 through 242 removed outlier: 3.549A pdb=" N GLY L 236 " --> pdb=" O ILE L 232 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL L 237 " --> pdb=" O TYR L 233 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 240 " --> pdb=" O GLY L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 264 Processing helix chain 'L' and resid 291 through 299 removed outlier: 3.705A pdb=" N HIS L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 182 through 204 removed outlier: 3.809A pdb=" N TRP M 199 " --> pdb=" O TYR M 195 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 225 removed outlier: 3.859A pdb=" N ARG M 225 " --> pdb=" O MET M 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 281 Proline residue: M 273 - end of helix Processing helix chain 'M' and resid 293 through 310 Processing helix chain 'N' and resid 53 through 74 removed outlier: 3.509A pdb=" N HIS N 74 " --> pdb=" O GLN N 70 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 97 Processing helix chain 'N' and resid 136 through 140 Processing helix chain 'N' and resid 141 through 153 removed outlier: 4.147A pdb=" N LEU N 145 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN N 153 " --> pdb=" O ALA N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 177 Processing helix chain 'N' and resid 212 through 217 removed outlier: 3.589A pdb=" N THR N 216 " --> pdb=" O CYS N 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 31 removed outlier: 3.547A pdb=" N ALA O 28 " --> pdb=" O TYR O 24 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 80 through 103 Processing helix chain 'O' and resid 107 through 122 removed outlier: 3.641A pdb=" N ARG O 122 " --> pdb=" O LYS O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 188 removed outlier: 3.532A pdb=" N LYS O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N THR O 188 " --> pdb=" O ARG O 184 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 211 Processing helix chain 'O' and resid 235 through 249 removed outlier: 3.686A pdb=" N TRP O 242 " --> pdb=" O GLU O 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA O 245 " --> pdb=" O GLU O 241 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA O 249 " --> pdb=" O ALA O 245 " (cutoff:3.500A) Processing helix chain 'P' and resid 17 through 28 removed outlier: 3.584A pdb=" N ALA P 23 " --> pdb=" O GLN P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 100 removed outlier: 3.813A pdb=" N VAL P 83 " --> pdb=" O PRO P 79 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET P 98 " --> pdb=" O GLN P 94 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 122 Processing helix chain 'P' and resid 164 through 176 removed outlier: 3.516A pdb=" N ALA P 170 " --> pdb=" O PRO P 166 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS P 174 " --> pdb=" O ALA P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 181 through 197 removed outlier: 3.634A pdb=" N HIS P 187 " --> pdb=" O GLU P 183 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY P 196 " --> pdb=" O THR P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 220 through 229 removed outlier: 3.691A pdb=" N TYR P 227 " --> pdb=" O GLN P 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 18 through 29 Processing helix chain 'Q' and resid 85 through 108 removed outlier: 3.608A pdb=" N GLN Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 130 removed outlier: 3.712A pdb=" N LYS Q 124 " --> pdb=" O LEU Q 120 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR Q 128 " --> pdb=" O LYS Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 185 removed outlier: 3.629A pdb=" N LYS Q 183 " --> pdb=" O ALA Q 179 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP Q 184 " --> pdb=" O LEU Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 206 Processing helix chain 'Q' and resid 230 through 234 removed outlier: 3.509A pdb=" N ASP Q 234 " --> pdb=" O GLN Q 231 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 270 removed outlier: 3.511A pdb=" N GLN Q 263 " --> pdb=" O GLU Q 259 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU Q 268 " --> pdb=" O ALA Q 264 " (cutoff:3.500A) Processing helix chain 'Q' and resid 271 through 276 removed outlier: 3.925A pdb=" N GLN Q 276 " --> pdb=" O GLU Q 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 Processing helix chain 'R' and resid 76 through 98 removed outlier: 3.585A pdb=" N GLN R 92 " --> pdb=" O GLN R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 119 removed outlier: 3.726A pdb=" N ARG R 109 " --> pdb=" O ASP R 105 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR R 119 " --> pdb=" O GLN R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 176 removed outlier: 4.116A pdb=" N LYS R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER R 175 " --> pdb=" O TYR R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 194 Processing helix chain 'R' and resid 218 through 231 removed outlier: 3.702A pdb=" N GLN R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS R 224 " --> pdb=" O GLU R 220 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE R 225 " --> pdb=" O GLU R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 234 through 240 removed outlier: 3.996A pdb=" N LYS R 240 " --> pdb=" O GLU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 130 removed outlier: 3.623A pdb=" N GLU S 129 " --> pdb=" O GLU S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 181 through 204 removed outlier: 3.746A pdb=" N ILE S 187 " --> pdb=" O ALA S 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 215 removed outlier: 3.503A pdb=" N CYS S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing helix chain 'S' and resid 273 through 285 removed outlier: 3.528A pdb=" N SER S 279 " --> pdb=" O GLU S 275 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL S 280 " --> pdb=" O ALA S 276 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU S 283 " --> pdb=" O SER S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 290 through 306 Processing helix chain 'S' and resid 331 through 341 removed outlier: 3.974A pdb=" N ARG S 341 " --> pdb=" O ALA S 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 195 removed outlier: 3.528A pdb=" N GLU T 187 " --> pdb=" O LEU T 183 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA T 192 " --> pdb=" O TYR T 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL T 193 " --> pdb=" O ALA T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 242 through 265 Processing helix chain 'T' and resid 269 through 285 removed outlier: 3.990A pdb=" N HIS T 284 " --> pdb=" O LYS T 280 " (cutoff:3.500A) Processing helix chain 'T' and resid 329 through 341 removed outlier: 3.993A pdb=" N SER T 333 " --> pdb=" O ARG T 329 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG T 339 " --> pdb=" O THR T 335 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS T 340 " --> pdb=" O TYR T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 342 through 345 removed outlier: 4.247A pdb=" N SER T 345 " --> pdb=" O GLU T 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 342 through 345' Processing helix chain 'T' and resid 348 through 363 removed outlier: 3.584A pdb=" N ALA T 363 " --> pdb=" O ALA T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 391 through 399 removed outlier: 4.475A pdb=" N LYS T 396 " --> pdb=" O GLU T 392 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR T 397 " --> pdb=" O SER T 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 6 through 10 removed outlier: 4.075A pdb=" N ASP U 9 " --> pdb=" O SER U 6 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN U 10 " --> pdb=" O GLY U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 6 through 10' Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.511A pdb=" N GLU U 25 " --> pdb=" O VAL U 21 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL U 31 " --> pdb=" O ALA U 27 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP U 32 " --> pdb=" O GLY U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 102 Processing helix chain 'U' and resid 108 through 122 Processing helix chain 'U' and resid 168 through 178 removed outlier: 3.601A pdb=" N LYS U 178 " --> pdb=" O SER U 174 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.630A pdb=" N VAL U 190 " --> pdb=" O CYS U 186 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY U 191 " --> pdb=" O ASP U 187 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS U 201 " --> pdb=" O LEU U 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 102 through 125 Processing helix chain 'V' and resid 129 through 144 removed outlier: 3.508A pdb=" N ALA V 133 " --> pdb=" O ASN V 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN V 144 " --> pdb=" O MET V 140 " (cutoff:3.500A) Processing helix chain 'V' and resid 185 through 197 removed outlier: 4.034A pdb=" N LEU V 189 " --> pdb=" O GLY V 185 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N SER V 191 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE V 192 " --> pdb=" O PHE V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 202 through 219 Processing helix chain 'V' and resid 244 through 248 Processing helix chain 'V' and resid 255 through 259 removed outlier: 3.576A pdb=" N VAL V 259 " --> pdb=" O PRO V 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 77 through 100 Processing helix chain 'W' and resid 104 through 119 removed outlier: 3.633A pdb=" N TYR W 119 " --> pdb=" O HIS W 115 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 171 Processing helix chain 'W' and resid 176 through 195 removed outlier: 3.588A pdb=" N GLY W 191 " --> pdb=" O ALA W 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 78 Processing helix chain 'X' and resid 83 through 97 Processing helix chain 'X' and resid 142 through 154 removed outlier: 3.542A pdb=" N ALA X 152 " --> pdb=" O GLY X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 159 through 176 Processing helix chain 'Y' and resid 50 through 72 removed outlier: 3.650A pdb=" N TYR Y 60 " --> pdb=" O ASN Y 56 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN Y 68 " --> pdb=" O ASN Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 78 through 94 removed outlier: 3.508A pdb=" N THR Y 82 " --> pdb=" O SER Y 78 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 146 through 158 removed outlier: 3.525A pdb=" N ALA Y 152 " --> pdb=" O CYS Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 163 through 182 removed outlier: 3.509A pdb=" N VAL Y 178 " --> pdb=" O CYS Y 174 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 169 removed outlier: 3.600A pdb=" N ARG Z 156 " --> pdb=" O GLN Z 152 " (cutoff:3.500A) Processing helix chain 'Z' and resid 174 through 189 Processing helix chain 'Z' and resid 230 through 242 removed outlier: 3.504A pdb=" N GLY Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Z 240 " --> pdb=" O GLY Z 236 " (cutoff:3.500A) Processing helix chain 'Z' and resid 247 through 264 Processing helix chain 'Z' and resid 291 through 299 removed outlier: 3.711A pdb=" N HIS Z 296 " --> pdb=" O THR Z 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 182 through 204 removed outlier: 3.859A pdb=" N TRP a 199 " --> pdb=" O TYR a 195 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR a 202 " --> pdb=" O LYS a 198 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 225 removed outlier: 3.908A pdb=" N ARG a 225 " --> pdb=" O MET a 221 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 281 Proline residue: a 273 - end of helix Processing helix chain 'a' and resid 293 through 310 Processing helix chain 'b' and resid 53 through 74 Processing helix chain 'b' and resid 80 through 97 Processing helix chain 'b' and resid 136 through 140 Processing helix chain 'b' and resid 141 through 153 removed outlier: 4.152A pdb=" N LEU b 145 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN b 153 " --> pdb=" O ALA b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 177 removed outlier: 3.551A pdb=" N LEU b 166 " --> pdb=" O ALA b 162 " (cutoff:3.500A) Processing helix chain 'b' and resid 212 through 217 removed outlier: 3.598A pdb=" N THR b 216 " --> pdb=" O CYS b 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 170 Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 70 removed outlier: 6.762A pdb=" N ILE A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 67 removed outlier: 5.351A pdb=" N VAL B 65 " --> pdb=" O CYS B 72 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N CYS B 72 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 73 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 144 " --> pdb=" O TRP B 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 75 removed outlier: 6.621A pdb=" N MET C 71 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL C 82 " --> pdb=" O MET C 71 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS C 73 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS C 80 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 143 " --> pdb=" O GLY C 79 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 81 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 146 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU C 153 " --> pdb=" O TRP C 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AA8, first strand: chain 'D' and resid 158 through 161 Processing sheet with id=AA9, first strand: chain 'D' and resid 63 through 66 removed outlier: 6.692A pdb=" N ILE D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 267 through 270 Processing sheet with id=AB2, first strand: chain 'E' and resid 167 through 171 removed outlier: 6.436A pdb=" N ILE E 174 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E 253 " --> pdb=" O TYR E 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 323 through 326 removed outlier: 3.524A pdb=" N ILE F 377 " --> pdb=" O PHE F 389 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY F 381 " --> pdb=" O PRO F 385 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 228 through 232 removed outlier: 6.612A pdb=" N VAL F 235 " --> pdb=" O ILE F 231 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 297 " --> pdb=" O THR F 312 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU F 309 " --> pdb=" O TYR F 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 162 through 165 Processing sheet with id=AB6, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.847A pdb=" N ALA G 142 " --> pdb=" O GLY G 145 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU G 148 " --> pdb=" O TYR G 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 179 through 182 removed outlier: 3.587A pdb=" N GLN H 241 " --> pdb=" O THR H 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 74 through 76 removed outlier: 6.573A pdb=" N SER H 76 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 88 through 92 removed outlier: 6.660A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP H 158 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL H 165 " --> pdb=" O LEU H 177 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 153 through 156 removed outlier: 6.700A pdb=" N VAL I 202 " --> pdb=" O GLY I 217 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY I 217 " --> pdb=" O VAL I 202 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 49 through 50 Processing sheet with id=AC3, first strand: chain 'I' and resid 63 through 67 removed outlier: 6.335A pdb=" N ILE I 63 " --> pdb=" O GLY I 74 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLY I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N TYR I 65 " --> pdb=" O CYS I 72 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N CYS I 72 " --> pdb=" O TYR I 65 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP I 133 " --> pdb=" O GLY I 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 240 through 247 removed outlier: 3.578A pdb=" N LYS I 242 " --> pdb=" O LEU J 199 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA J 185 " --> pdb=" O ILE J 200 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 28 through 30 removed outlier: 6.938A pdb=" N LEU J 28 " --> pdb=" O ILE J 35 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 42 through 46 removed outlier: 6.953A pdb=" N ILE J 49 " --> pdb=" O VAL J 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR J 54 " --> pdb=" O GLU J 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 140 through 143 removed outlier: 4.261A pdb=" N VAL K 191 " --> pdb=" O ILE K 202 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 22 through 24 removed outlier: 7.075A pdb=" N ASN K 22 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'K' and resid 36 through 38 removed outlier: 3.515A pdb=" N THR K 37 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN K 104 " --> pdb=" O THR K 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 224 through 227 removed outlier: 3.651A pdb=" N VAL L 275 " --> pdb=" O SER L 287 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER L 287 " --> pdb=" O VAL L 275 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N HIS L 277 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LYS L 285 " --> pdb=" O HIS L 277 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS L 279 " --> pdb=" O TRP L 283 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N TRP L 283 " --> pdb=" O HIS L 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'L' and resid 119 through 121 removed outlier: 3.705A pdb=" N SER L 127 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR L 121 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE L 125 " --> pdb=" O THR L 121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 133 through 135 removed outlier: 3.585A pdb=" N MET L 199 " --> pdb=" O THR L 143 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP L 204 " --> pdb=" O GLY L 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY L 207 " --> pdb=" O ASP L 204 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU L 210 " --> pdb=" O GLN L 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 261 through 265 removed outlier: 5.437A pdb=" N THR M 135 " --> pdb=" O ASP M 150 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE M 321 " --> pdb=" O GLU M 332 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 175 through 179 removed outlier: 3.972A pdb=" N CYS M 247 " --> pdb=" O PHE M 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 24 through 25 removed outlier: 3.526A pdb=" N SER N 45 " --> pdb=" O LEU N 41 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 24 through 25 Processing sheet with id=AD8, first strand: chain 'N' and resid 132 through 134 removed outlier: 3.504A pdb=" N GLY N 15 " --> pdb=" O TYR N 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'O' and resid 167 through 170 Processing sheet with id=AE1, first strand: chain 'O' and resid 68 through 70 removed outlier: 6.774A pdb=" N ILE O 73 " --> pdb=" O VAL O 69 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'P' and resid 158 through 161 Processing sheet with id=AE3, first strand: chain 'P' and resid 63 through 67 removed outlier: 5.351A pdb=" N VAL P 65 " --> pdb=" O CYS P 72 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS P 72 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU P 144 " --> pdb=" O TRP P 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 167 through 170 Processing sheet with id=AE5, first strand: chain 'Q' and resid 71 through 75 removed outlier: 6.613A pdb=" N MET Q 71 " --> pdb=" O VAL Q 82 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N VAL Q 82 " --> pdb=" O MET Q 71 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS Q 73 " --> pdb=" O CYS Q 80 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS Q 80 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL Q 143 " --> pdb=" O GLY Q 79 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER Q 81 " --> pdb=" O LEU Q 141 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP Q 146 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU Q 153 " --> pdb=" O TRP Q 165 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 223 through 225 Processing sheet with id=AE7, first strand: chain 'R' and resid 158 through 161 Processing sheet with id=AE8, first strand: chain 'R' and resid 63 through 66 removed outlier: 6.693A pdb=" N ILE R 69 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'S' and resid 267 through 270 Processing sheet with id=AF1, first strand: chain 'S' and resid 167 through 171 removed outlier: 6.497A pdb=" N ILE S 174 " --> pdb=" O VAL S 170 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU S 253 " --> pdb=" O TYR S 265 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'T' and resid 323 through 326 removed outlier: 3.523A pdb=" N ILE T 377 " --> pdb=" O PHE T 389 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLY T 381 " --> pdb=" O PRO T 385 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T' and resid 228 through 232 removed outlier: 6.663A pdb=" N VAL T 235 " --> pdb=" O ILE T 231 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU T 297 " --> pdb=" O THR T 312 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU T 309 " --> pdb=" O TYR T 321 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 162 through 165 Processing sheet with id=AF5, first strand: chain 'U' and resid 67 through 69 removed outlier: 3.855A pdb=" N ALA U 142 " --> pdb=" O GLY U 145 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU U 148 " --> pdb=" O TYR U 160 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 179 through 182 removed outlier: 3.612A pdb=" N GLN V 241 " --> pdb=" O THR V 230 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'V' and resid 74 through 76 removed outlier: 7.025A pdb=" N THR V 74 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TYR V 79 " --> pdb=" O SER V 76 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 88 through 92 removed outlier: 6.703A pdb=" N ILE V 95 " --> pdb=" O LEU V 91 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP V 158 " --> pdb=" O GLY V 162 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL V 165 " --> pdb=" O LEU V 177 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 153 through 156 removed outlier: 6.678A pdb=" N VAL W 202 " --> pdb=" O GLY W 217 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY W 217 " --> pdb=" O VAL W 202 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 49 through 50 Processing sheet with id=AG2, first strand: chain 'W' and resid 63 through 67 removed outlier: 6.404A pdb=" N ILE W 63 " --> pdb=" O GLY W 74 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY W 74 " --> pdb=" O ILE W 63 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N TYR W 65 " --> pdb=" O CYS W 72 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N CYS W 72 " --> pdb=" O TYR W 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP W 133 " --> pdb=" O GLY W 136 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 240 through 247 removed outlier: 3.549A pdb=" N LYS W 242 " --> pdb=" O LEU X 199 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS X 194 " --> pdb=" O THR X 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA X 185 " --> pdb=" O ILE X 200 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 28 through 30 removed outlier: 7.003A pdb=" N LEU X 28 " --> pdb=" O ILE X 35 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 42 through 46 removed outlier: 6.946A pdb=" N ILE X 49 " --> pdb=" O VAL X 45 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Y' and resid 140 through 143 removed outlier: 4.326A pdb=" N VAL Y 191 " --> pdb=" O ILE Y 202 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Y' and resid 22 through 24 removed outlier: 7.073A pdb=" N ASN Y 22 " --> pdb=" O ILE Y 29 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Y' and resid 36 through 38 removed outlier: 3.541A pdb=" N ASN Y 104 " --> pdb=" O THR Y 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Z' and resid 224 through 227 removed outlier: 3.514A pdb=" N ASP Z 289 " --> pdb=" O VAL Z 273 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL Z 275 " --> pdb=" O SER Z 287 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER Z 287 " --> pdb=" O VAL Z 275 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N HIS Z 277 " --> pdb=" O LYS Z 285 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LYS Z 285 " --> pdb=" O HIS Z 277 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS Z 279 " --> pdb=" O TRP Z 283 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N TRP Z 283 " --> pdb=" O HIS Z 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 119 through 121 removed outlier: 3.706A pdb=" N SER Z 127 " --> pdb=" O ALA Z 119 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR Z 121 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE Z 125 " --> pdb=" O THR Z 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 133 through 135 removed outlier: 3.561A pdb=" N MET Z 199 " --> pdb=" O THR Z 143 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY Z 207 " --> pdb=" O ASP Z 204 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU Z 210 " --> pdb=" O GLN Z 222 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'a' and resid 261 through 265 removed outlier: 5.471A pdb=" N THR a 135 " --> pdb=" O ASP a 150 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE a 321 " --> pdb=" O GLU a 332 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'a' and resid 175 through 179 removed outlier: 3.933A pdb=" N CYS a 247 " --> pdb=" O PHE a 259 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'b' and resid 24 through 25 Processing sheet with id=AH6, first strand: chain 'b' and resid 24 through 25 Processing sheet with id=AH7, first strand: chain 'b' and resid 132 through 134 removed outlier: 3.553A pdb=" N GLY b 15 " --> pdb=" O TYR b 12 " (cutoff:3.500A) 2596 hydrogen bonds defined for protein. 7419 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: 17.60 Time building geometry restraints manager: 10.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 8629 1.32 - 1.45: 12934 1.45 - 1.58: 27975 1.58 - 1.71: 0 1.71 - 1.85: 516 Bond restraints: 50054 Sorted by residual: bond pdb=" N ARG E 235 " pdb=" CA ARG E 235 " ideal model delta sigma weight residual 1.455 1.488 -0.033 7.00e-03 2.04e+04 2.25e+01 bond pdb=" N THR M 172 " pdb=" CA THR M 172 " ideal model delta sigma weight residual 1.455 1.488 -0.033 7.00e-03 2.04e+04 2.19e+01 bond pdb=" N THR a 172 " pdb=" CA THR a 172 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.07e+01 bond pdb=" N SER S 311 " pdb=" CA SER S 311 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.03e+01 bond pdb=" N ASP A 157 " pdb=" CA ASP A 157 " ideal model delta sigma weight residual 1.455 1.486 -0.031 7.00e-03 2.04e+04 2.00e+01 ... (remaining 50049 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 64358 3.71 - 7.42: 3329 7.42 - 11.12: 24 11.12 - 14.83: 1 14.83 - 18.54: 2 Bond angle restraints: 67714 Sorted by residual: angle pdb=" CA ASN L 137 " pdb=" CB ASN L 137 " pdb=" CG ASN L 137 " ideal model delta sigma weight residual 112.60 122.55 -9.95 1.00e+00 1.00e+00 9.90e+01 angle pdb=" CA ASN Z 137 " pdb=" CB ASN Z 137 " pdb=" CG ASN Z 137 " ideal model delta sigma weight residual 112.60 122.28 -9.68 1.00e+00 1.00e+00 9.38e+01 angle pdb=" C ASN Z 137 " pdb=" CA ASN Z 137 " pdb=" CB ASN Z 137 " ideal model delta sigma weight residual 110.42 128.96 -18.54 1.99e+00 2.53e-01 8.68e+01 angle pdb=" C ASN L 137 " pdb=" CA ASN L 137 " pdb=" CB ASN L 137 " ideal model delta sigma weight residual 110.42 127.72 -17.30 1.99e+00 2.53e-01 7.56e+01 angle pdb=" CA ASP J 135 " pdb=" CB ASP J 135 " pdb=" CG ASP J 135 " ideal model delta sigma weight residual 112.60 119.44 -6.84 1.00e+00 1.00e+00 4.68e+01 ... (remaining 67709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 25736 17.99 - 35.97: 2971 35.97 - 53.96: 997 53.96 - 71.94: 285 71.94 - 89.93: 92 Dihedral angle restraints: 30081 sinusoidal: 11755 harmonic: 18326 Sorted by residual: dihedral pdb=" CB CYS b 102 " pdb=" SG CYS b 102 " pdb=" SG CYS b 104 " pdb=" CB CYS b 104 " ideal model delta sinusoidal sigma weight residual 93.00 14.39 78.61 1 1.00e+01 1.00e-02 7.70e+01 dihedral pdb=" CA ALA b 49 " pdb=" C ALA b 49 " pdb=" N THR b 50 " pdb=" CA THR b 50 " ideal model delta harmonic sigma weight residual 180.00 143.95 36.05 0 5.00e+00 4.00e-02 5.20e+01 dihedral pdb=" CA SER R 124 " pdb=" C SER R 124 " pdb=" N ARG R 125 " pdb=" CA ARG R 125 " ideal model delta harmonic sigma weight residual 180.00 145.54 34.46 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 30078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3085 0.061 - 0.122: 2921 0.122 - 0.184: 1269 0.184 - 0.245: 248 0.245 - 0.306: 21 Chirality restraints: 7544 Sorted by residual: chirality pdb=" CA ILE K 6 " pdb=" N ILE K 6 " pdb=" C ILE K 6 " pdb=" CB ILE K 6 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE Y 6 " pdb=" N ILE Y 6 " pdb=" C ILE Y 6 " pdb=" CB ILE Y 6 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA MET F 237 " pdb=" N MET F 237 " pdb=" C MET F 237 " pdb=" CB MET F 237 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 7541 not shown) Planarity restraints: 8784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL T 235 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C VAL T 235 " -0.058 2.00e-02 2.50e+03 pdb=" O VAL T 235 " 0.022 2.00e-02 2.50e+03 pdb=" N GLY T 236 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE Z 260 " 0.034 2.00e-02 2.50e+03 2.36e-02 9.79e+00 pdb=" CG PHE Z 260 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE Z 260 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE Z 260 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE Z 260 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE Z 260 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE Z 260 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 250 " -0.040 2.00e-02 2.50e+03 2.19e-02 9.60e+00 pdb=" CG TYR a 250 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR a 250 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR a 250 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR a 250 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR a 250 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR a 250 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR a 250 " -0.011 2.00e-02 2.50e+03 ... (remaining 8781 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5429 2.78 - 3.31: 48333 3.31 - 3.84: 78797 3.84 - 4.37: 110577 4.37 - 4.90: 177674 Nonbonded interactions: 420810 Sorted by model distance: nonbonded pdb=" O PHE Z 260 " pdb=" OG1 THR Z 263 " model vdw 2.250 3.040 nonbonded pdb=" O THR A 123 " pdb=" NH1 ARG B 126 " model vdw 2.257 3.120 nonbonded pdb=" O PHE L 260 " pdb=" OG1 THR L 263 " model vdw 2.269 3.040 nonbonded pdb=" NH2 ARG G 100 " pdb=" O SER V 269 " model vdw 2.278 3.120 nonbonded pdb=" OE2 GLU S 205 " pdb=" OH TYR a 200 " model vdw 2.315 3.040 ... (remaining 420805 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 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.360 Check model and map are aligned: 0.280 Set scattering table: 0.350 Process input model: 83.630 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 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 : 0.013 0.058 50054 Z= 0.852 Angle : 1.896 18.539 67714 Z= 1.381 Chirality : 0.095 0.306 7544 Planarity : 0.005 0.034 8784 Dihedral : 18.727 89.929 18370 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.94 % Allowed : 7.33 % Favored : 91.73 % Rotamer: Outliers : 11.34 % Allowed : 12.10 % Favored : 76.56 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.29 (0.08), residues: 6290 helix: -3.48 (0.07), residues: 2264 sheet: -2.27 (0.12), residues: 1414 loop : -2.33 (0.10), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.005 TRP L 165 HIS 0.017 0.003 HIS H 216 PHE 0.050 0.005 PHE Z 260 TYR 0.046 0.005 TYR N 137 ARG 0.009 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2187 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 594 poor density : 1593 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6694 (pm20) REVERT: A 61 ASP cc_start: 0.8174 (t70) cc_final: 0.7759 (m-30) REVERT: A 63 VAL cc_start: 0.8728 (t) cc_final: 0.8495 (m) REVERT: A 70 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8685 (p) REVERT: A 83 ASP cc_start: 0.8968 (m-30) cc_final: 0.8745 (m-30) REVERT: A 101 ARG cc_start: 0.8463 (ttm110) cc_final: 0.8237 (mtp85) REVERT: A 150 LYS cc_start: 0.9220 (tttt) cc_final: 0.8947 (ttpt) REVERT: A 178 MET cc_start: 0.8917 (mmt) cc_final: 0.8404 (mmp) REVERT: A 182 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6919 (mt-10) REVERT: B 29 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7998 (mtpt) REVERT: B 87 SER cc_start: 0.8915 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 96 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8325 (mmmt) REVERT: B 110 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8539 (mmt90) REVERT: B 117 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8046 (tp-100) REVERT: B 126 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8612 (ptt90) REVERT: B 148 ASP cc_start: 0.8485 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: B 167 ASP cc_start: 0.6952 (m-30) cc_final: 0.6554 (m-30) REVERT: B 180 MET cc_start: 0.7149 (ttm) cc_final: 0.6942 (ttm) REVERT: B 182 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8421 (tt) REVERT: B 184 ASP cc_start: 0.7774 (t0) cc_final: 0.7529 (t0) REVERT: B 197 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.5419 (t80) REVERT: B 202 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8704 (p) REVERT: B 205 ASN cc_start: 0.8275 (t0) cc_final: 0.7486 (t0) REVERT: B 214 ASN cc_start: 0.8194 (p0) cc_final: 0.7913 (m110) REVERT: C 29 GLN cc_start: 0.8256 (mt0) cc_final: 0.7846 (mm110) REVERT: C 60 SER cc_start: 0.8524 (m) cc_final: 0.8323 (t) REVERT: C 88 ASP cc_start: 0.8773 (m-30) cc_final: 0.8482 (m-30) REVERT: C 97 ARG cc_start: 0.9179 (OUTLIER) cc_final: 0.8965 (mtt90) REVERT: C 115 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8701 (m-30) REVERT: C 117 CYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8294 (t) REVERT: C 119 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8474 (mt) REVERT: C 120 LEU cc_start: 0.8965 (tp) cc_final: 0.8692 (tp) REVERT: C 126 LEU cc_start: 0.8435 (mt) cc_final: 0.8232 (mp) REVERT: C 138 VAL cc_start: 0.9153 (OUTLIER) cc_final: 0.8866 (p) REVERT: C 174 ASP cc_start: 0.7709 (p0) cc_final: 0.6628 (p0) REVERT: C 195 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7594 (tpp) REVERT: C 204 LYS cc_start: 0.8452 (tptt) cc_final: 0.8071 (tptp) REVERT: C 206 MET cc_start: 0.8041 (ptt) cc_final: 0.7412 (ptt) REVERT: C 234 ASP cc_start: 0.7903 (t0) cc_final: 0.7597 (p0) REVERT: C 241 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7447 (mttm) REVERT: C 245 ARG cc_start: 0.8137 (ttp80) cc_final: 0.7812 (ttp-170) REVERT: D 4 ASP cc_start: 0.8065 (p0) cc_final: 0.7399 (m-30) REVERT: D 5 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7252 (ttm-80) REVERT: D 17 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: D 28 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8038 (mmtp) REVERT: D 46 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: D 47 LYS cc_start: 0.8290 (mttt) cc_final: 0.7960 (mtmm) REVERT: D 61 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7127 (mtpt) REVERT: D 117 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8051 (mtmm) REVERT: D 121 SER cc_start: 0.8358 (t) cc_final: 0.8134 (p) REVERT: D 141 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7942 (tttp) REVERT: D 143 HIS cc_start: 0.8641 (m-70) cc_final: 0.8373 (m90) REVERT: D 148 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (p0) REVERT: D 170 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7064 (mm-30) REVERT: D 178 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7453 (t70) REVERT: D 197 VAL cc_start: 0.8011 (p) cc_final: 0.7520 (t) REVERT: D 203 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7455 (p0) REVERT: D 213 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7359 (tt0) REVERT: D 235 GLU cc_start: 0.5169 (OUTLIER) cc_final: 0.4499 (tp30) REVERT: E 138 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8282 (pp) REVERT: E 164 MET cc_start: 0.7758 (ptp) cc_final: 0.7416 (ptm) REVERT: E 181 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: E 204 ASN cc_start: 0.8891 (t0) cc_final: 0.8424 (t0) REVERT: E 220 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8686 (t) REVERT: E 233 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.7491 (mtt) REVERT: E 241 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8706 (mp) REVERT: E 249 LYS cc_start: 0.8696 (mmtm) cc_final: 0.8492 (mptt) REVERT: E 252 GLN cc_start: 0.8134 (mt0) cc_final: 0.7682 (mt0) REVERT: E 259 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8339 (p) REVERT: E 286 HIS cc_start: 0.7584 (p-80) cc_final: 0.6796 (p-80) REVERT: E 290 THR cc_start: 0.8235 (p) cc_final: 0.8031 (t) REVERT: E 342 MET cc_start: 0.5630 (ttm) cc_final: 0.5182 (mtp) REVERT: F 170 TYR cc_start: 0.9042 (m-80) cc_final: 0.8701 (m-80) REVERT: F 173 ASP cc_start: 0.8383 (t0) cc_final: 0.7879 (m-30) REVERT: F 190 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8312 (m-40) REVERT: F 230 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: F 237 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8398 (ttp) REVERT: F 276 MET cc_start: 0.7684 (mtt) cc_final: 0.7432 (mtm) REVERT: F 283 ARG cc_start: 0.8507 (mtm180) cc_final: 0.8167 (mtp-110) REVERT: F 287 CYS cc_start: 0.8113 (m) cc_final: 0.7856 (t) REVERT: F 351 GLU cc_start: 0.6673 (mt-10) cc_final: 0.6178 (mt-10) REVERT: F 354 THR cc_start: 0.8451 (OUTLIER) cc_final: 0.7960 (p) REVERT: F 387 THR cc_start: 0.8574 (p) cc_final: 0.8304 (p) REVERT: G 73 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: G 141 TYR cc_start: 0.9193 (t80) cc_final: 0.8985 (t80) REVERT: G 167 LYS cc_start: 0.8194 (pttt) cc_final: 0.7962 (ptmm) REVERT: G 192 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7414 (mmmt) REVERT: G 203 LYS cc_start: 0.7210 (mttt) cc_final: 0.7006 (mtpt) REVERT: G 206 ASP cc_start: 0.6958 (m-30) cc_final: 0.6744 (m-30) REVERT: G 210 GLU cc_start: 0.8495 (pt0) cc_final: 0.7991 (pt0) REVERT: G 222 ARG cc_start: 0.8828 (mtp180) cc_final: 0.8576 (mtm110) REVERT: H 72 SER cc_start: 0.9186 (p) cc_final: 0.8866 (p) REVERT: H 114 SER cc_start: 0.9075 (t) cc_final: 0.8659 (p) REVERT: H 137 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.9131 (t80) REVERT: H 140 MET cc_start: 0.8570 (mtp) cc_final: 0.8130 (mtp) REVERT: H 201 MET cc_start: 0.7884 (mtt) cc_final: 0.7667 (mtt) REVERT: H 203 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8331 (tttt) REVERT: H 237 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7658 (tm-30) REVERT: H 240 ASP cc_start: 0.8663 (p0) cc_final: 0.8275 (p0) REVERT: I 59 ARG cc_start: 0.7234 (mtm-85) cc_final: 0.6621 (mtm110) REVERT: I 60 CYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8558 (p) REVERT: I 61 ARG cc_start: 0.8045 (mtp85) cc_final: 0.7792 (mtm180) REVERT: I 80 ASP cc_start: 0.9316 (m-30) cc_final: 0.9079 (m-30) REVERT: I 87 MET cc_start: 0.8578 (ttm) cc_final: 0.8316 (ttp) REVERT: I 172 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8324 (pptt) REVERT: I 179 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8206 (mt-10) REVERT: I 197 TYR cc_start: 0.8470 (m-80) cc_final: 0.8229 (m-80) REVERT: I 208 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8910 (p) REVERT: I 209 LYS cc_start: 0.8665 (tptt) cc_final: 0.8172 (tptp) REVERT: I 213 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: I 241 LEU cc_start: 0.8665 (mt) cc_final: 0.8359 (mt) REVERT: J 4 MET cc_start: 0.8701 (mmm) cc_final: 0.8224 (mmm) REVERT: J 12 MET cc_start: 0.8883 (tmm) cc_final: 0.8437 (ttp) REVERT: J 30 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7626 (mm-30) REVERT: J 72 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8319 (mm-30) REVERT: J 80 ARG cc_start: 0.9063 (ptt180) cc_final: 0.8730 (ptt90) REVERT: J 96 TYR cc_start: 0.8836 (t80) cc_final: 0.8593 (t80) REVERT: J 158 MET cc_start: 0.8082 (mtp) cc_final: 0.7670 (mtp) REVERT: J 161 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8061 (mm-30) REVERT: J 193 ASP cc_start: 0.7598 (t70) cc_final: 0.7356 (t70) REVERT: J 203 ARG cc_start: 0.8487 (mtt-85) cc_final: 0.8223 (mmm160) REVERT: K 62 LYS cc_start: 0.8697 (tttm) cc_final: 0.8464 (ttpt) REVERT: K 75 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7225 (mtm180) REVERT: K 80 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7775 (mp0) REVERT: K 121 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8241 (p) REVERT: K 131 TYR cc_start: 0.8743 (p90) cc_final: 0.8297 (p90) REVERT: K 151 THR cc_start: 0.8914 (m) cc_final: 0.8656 (m) REVERT: K 159 ARG cc_start: 0.8473 (mtm110) cc_final: 0.8017 (mtm-85) REVERT: K 177 GLU cc_start: 0.8848 (tp30) cc_final: 0.8374 (tp30) REVERT: K 180 ARG cc_start: 0.8355 (ttm110) cc_final: 0.7447 (tpt-90) REVERT: L 123 GLN cc_start: 0.8117 (tt0) cc_final: 0.7894 (tt0) REVERT: L 137 ASN cc_start: 0.6368 (OUTLIER) cc_final: 0.6061 (t0) REVERT: L 209 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8498 (p) REVERT: L 216 LYS cc_start: 0.8377 (mmtp) cc_final: 0.8157 (mmmm) REVERT: L 227 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8865 (t) REVERT: M 143 ASP cc_start: 0.8149 (t70) cc_final: 0.7913 (t70) REVERT: M 167 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8376 (tppt) REVERT: M 168 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8965 (mp) REVERT: M 186 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8408 (ttm170) REVERT: M 198 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8361 (tttt) REVERT: M 257 GLU cc_start: 0.8594 (pt0) cc_final: 0.8289 (pt0) REVERT: M 315 THR cc_start: 0.8924 (m) cc_final: 0.8433 (p) REVERT: M 335 GLU cc_start: 0.8261 (mm-30) cc_final: 0.8056 (mm-30) REVERT: M 338 LYS cc_start: 0.6530 (OUTLIER) cc_final: 0.5685 (mmmm) REVERT: N 68 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: N 152 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8220 (mmtt) REVERT: N 153 ASN cc_start: 0.8921 (m-40) cc_final: 0.8709 (m-40) REVERT: N 205 HIS cc_start: 0.8203 (t70) cc_final: 0.7393 (m90) REVERT: O 23 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7935 (tt0) REVERT: O 94 GLU cc_start: 0.8072 (tp30) cc_final: 0.7669 (tp30) REVERT: O 101 ARG cc_start: 0.8374 (ttm110) cc_final: 0.8052 (mtp-110) REVERT: O 143 SER cc_start: 0.9077 (t) cc_final: 0.8840 (t) REVERT: O 150 LYS cc_start: 0.8884 (tttt) cc_final: 0.8455 (tppt) REVERT: O 190 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8248 (mp) REVERT: O 196 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8291 (tptp) REVERT: O 223 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8432 (ttp-170) REVERT: O 238 GLU cc_start: 0.7336 (tt0) cc_final: 0.6982 (tt0) REVERT: P 16 LYS cc_start: 0.8663 (ptmt) cc_final: 0.7849 (mmtm) REVERT: P 29 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7900 (mtpp) REVERT: P 49 LYS cc_start: 0.8430 (ttpp) cc_final: 0.7647 (mmmt) REVERT: P 89 ARG cc_start: 0.9208 (mtt180) cc_final: 0.8941 (mtt180) REVERT: P 117 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7787 (tp-100) REVERT: P 175 ARG cc_start: 0.7686 (mmt-90) cc_final: 0.7470 (mtp85) REVERT: P 177 THR cc_start: 0.8182 (p) cc_final: 0.7896 (t) REVERT: P 201 MET cc_start: 0.8348 (mtm) cc_final: 0.8137 (mtm) REVERT: P 202 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8613 (t) REVERT: Q 3 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7084 (m-70) REVERT: Q 8 ARG cc_start: 0.8128 (mtp180) cc_final: 0.7846 (mtm180) REVERT: Q 10 THR cc_start: 0.8804 (p) cc_final: 0.8549 (p) REVERT: Q 56 PHE cc_start: 0.8965 (m-10) cc_final: 0.8672 (m-80) REVERT: Q 102 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8380 (mtm-85) REVERT: Q 138 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8669 (m) REVERT: Q 147 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8170 (mtm-85) REVERT: Q 161 ASP cc_start: 0.8326 (p0) cc_final: 0.7596 (t0) REVERT: Q 172 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: Q 182 LYS cc_start: 0.7655 (mtmm) cc_final: 0.7235 (mttm) REVERT: Q 214 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8263 (m-30) REVERT: Q 237 LYS cc_start: 0.8667 (tttp) cc_final: 0.8233 (ttpt) REVERT: Q 243 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8710 (p) REVERT: Q 270 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.6934 (tptp) REVERT: R 11 SER cc_start: 0.8955 (m) cc_final: 0.8562 (p) REVERT: R 17 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: R 24 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: R 90 GLU cc_start: 0.8138 (tp30) cc_final: 0.7893 (tp30) REVERT: R 103 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8499 (p0) REVERT: R 148 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8209 (p0) REVERT: R 177 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7460 (mmmt) REVERT: R 180 MET cc_start: 0.8319 (mtt) cc_final: 0.8001 (mtt) REVERT: R 185 CYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8177 (m) REVERT: R 194 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7877 (mt) REVERT: R 202 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5082 (ptp-170) REVERT: R 203 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7556 (p0) REVERT: R 212 LYS cc_start: 0.8510 (mptp) cc_final: 0.8231 (mmmt) REVERT: R 215 ARG cc_start: 0.8355 (ttp-170) cc_final: 0.7812 (ttm110) REVERT: S 140 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8767 (mm) REVERT: S 152 LYS cc_start: 0.7773 (mttm) cc_final: 0.7371 (mtpp) REVERT: S 164 MET cc_start: 0.8184 (ptp) cc_final: 0.7483 (ppp) REVERT: S 166 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8600 (mptt) REVERT: S 186 ARG cc_start: 0.8783 (mmt90) cc_final: 0.8380 (mpt-90) REVERT: S 220 SER cc_start: 0.8878 (OUTLIER) cc_final: 0.8596 (m) REVERT: S 247 ASP cc_start: 0.7577 (p0) cc_final: 0.7355 (t70) REVERT: S 311 SER cc_start: 0.8750 (m) cc_final: 0.8481 (m) REVERT: T 190 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7409 (m-40) REVERT: T 230 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: T 270 MET cc_start: 0.9124 (mmm) cc_final: 0.8856 (mmm) REVERT: T 315 SER cc_start: 0.8762 (p) cc_final: 0.8485 (t) REVERT: T 320 ASP cc_start: 0.8650 (t0) cc_final: 0.8435 (t0) REVERT: T 326 MET cc_start: 0.8703 (ttp) cc_final: 0.8358 (ttp) REVERT: T 368 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8100 (tt) REVERT: T 391 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6957 (tp30) REVERT: T 404 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.4951 (ptp-170) REVERT: U 10 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8675 (mm-40) REVERT: U 81 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8517 (tp) REVERT: U 115 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7580 (tpp80) REVERT: U 129 TYR cc_start: 0.8517 (m-80) cc_final: 0.7830 (m-80) REVERT: U 152 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7930 (p0) REVERT: U 210 GLU cc_start: 0.7866 (pt0) cc_final: 0.7618 (pt0) REVERT: U 221 ASP cc_start: 0.8277 (t0) cc_final: 0.7920 (m-30) REVERT: V 137 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.9010 (t80) REVERT: V 187 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8707 (tp) REVERT: V 203 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: V 212 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8065 (ttp80) REVERT: W 59 ARG cc_start: 0.8121 (mtm-85) cc_final: 0.7788 (mtm110) REVERT: W 60 CYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8248 (t) REVERT: W 80 ASP cc_start: 0.9089 (m-30) cc_final: 0.8852 (m-30) REVERT: W 89 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8567 (m) REVERT: W 124 SER cc_start: 0.9127 (t) cc_final: 0.8920 (t) REVERT: W 172 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8395 (pptt) REVERT: W 173 ASP cc_start: 0.7755 (m-30) cc_final: 0.7499 (m-30) REVERT: W 186 SER cc_start: 0.9050 (t) cc_final: 0.8781 (m) REVERT: W 222 ASN cc_start: 0.8784 (m-40) cc_final: 0.8398 (m110) REVERT: W 225 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6239 (mpp) REVERT: W 228 ARG cc_start: 0.7274 (ttp-170) cc_final: 0.6775 (mtm110) REVERT: W 244 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7122 (tt0) REVERT: W 247 GLN cc_start: 0.7326 (mm110) cc_final: 0.7104 (tp40) REVERT: X 54 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8885 (m) REVERT: X 66 LYS cc_start: 0.8605 (mttp) cc_final: 0.8358 (mttt) REVERT: X 72 GLU cc_start: 0.8301 (mm-30) cc_final: 0.8050 (mm-30) REVERT: X 85 LYS cc_start: 0.8793 (mptt) cc_final: 0.8299 (mtpp) REVERT: X 97 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7711 (mt-10) REVERT: X 106 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8296 (mt-10) REVERT: X 125 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.8304 (p0) REVERT: X 188 MET cc_start: 0.8625 (ttt) cc_final: 0.8389 (ttt) REVERT: X 194 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7896 (pttm) REVERT: Y 12 ASP cc_start: 0.8292 (p0) cc_final: 0.7986 (p0) REVERT: Y 29 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8091 (mm) REVERT: Y 31 ASP cc_start: 0.8836 (m-30) cc_final: 0.8544 (m-30) REVERT: Y 76 HIS cc_start: 0.7779 (m170) cc_final: 0.7526 (m-70) REVERT: Y 88 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.7514 (m110) REVERT: Y 129 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8078 (mtm) REVERT: Y 200 GLU cc_start: 0.7916 (pt0) cc_final: 0.7670 (tp30) REVERT: Z 137 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.7405 (t0) REVERT: Z 139 TYR cc_start: 0.7353 (m-80) cc_final: 0.6924 (m-80) REVERT: Z 155 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8667 (mt-10) REVERT: Z 160 MET cc_start: 0.8683 (ttp) cc_final: 0.8426 (ttp) REVERT: Z 186 THR cc_start: 0.8916 (p) cc_final: 0.8579 (p) REVERT: Z 194 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7389 (mp) REVERT: a 126 TRP cc_start: 0.7930 (t60) cc_final: 0.7710 (t60) REVERT: a 142 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7572 (tptp) REVERT: a 157 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: a 182 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8622 (ttt) REVERT: a 186 ARG cc_start: 0.9143 (OUTLIER) cc_final: 0.8841 (ttm170) REVERT: a 249 SER cc_start: 0.9014 (OUTLIER) cc_final: 0.8746 (p) REVERT: a 251 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8084 (p0) REVERT: a 284 MET cc_start: 0.8191 (mtt) cc_final: 0.7847 (mtt) REVERT: a 331 GLN cc_start: 0.7930 (pt0) cc_final: 0.7296 (tt0) REVERT: a 337 ARG cc_start: 0.8103 (mtt-85) cc_final: 0.7739 (mtm180) REVERT: b 3 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8525 (p) REVERT: b 53 TYR cc_start: 0.9124 (t80) cc_final: 0.8764 (t80) REVERT: b 65 ASP cc_start: 0.8595 (m-30) cc_final: 0.8291 (m-30) REVERT: b 69 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7941 (mmt90) REVERT: b 106 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7597 (mpt) REVERT: b 151 GLU cc_start: 0.8191 (tt0) cc_final: 0.7926 (mm-30) REVERT: b 152 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7493 (mtpt) REVERT: b 155 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: b 171 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8593 (ttm110) REVERT: b 179 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8121 (mpt90) REVERT: b 183 LYS cc_start: 0.8420 (ttpt) cc_final: 0.8100 (ttmm) REVERT: b 198 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8345 (mp0) REVERT: b 205 HIS cc_start: 0.8158 (t70) cc_final: 0.7936 (m-70) outliers start: 594 outliers final: 156 residues processed: 1978 average time/residue: 0.5584 time to fit residues: 1756.8764 Evaluate side-chains 1354 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1076 time to evaluate : 4.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 29 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 126 ARG Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 117 CYS Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 214 ASP Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 46 GLU Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 141 LYS Chi-restraints excluded: chain D residue 148 ASP Chi-restraints excluded: chain D residue 154 SER Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 235 GLU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 241 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain F residue 190 ASN Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 277 ILE Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 362 SER Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 192 LYS Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 203 LYS Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 236 ASP Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 274 ILE Chi-restraints excluded: chain I residue 32 ILE Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 172 LYS Chi-restraints excluded: chain I residue 192 ILE Chi-restraints excluded: chain I residue 204 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 213 GLU Chi-restraints excluded: chain J residue 30 GLU Chi-restraints excluded: chain J residue 73 MET Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 131 CYS Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 121 VAL Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 209 SER Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 186 ARG Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 226 ARG Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 338 LYS Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 21 ASP Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 123 ASP Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 45 VAL Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 78 THR Chi-restraints excluded: chain O residue 190 LEU Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain O residue 215 LYS Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 29 LYS Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 117 GLN Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain P residue 202 THR Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 3 HIS Chi-restraints excluded: chain Q residue 20 GLN Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 102 ARG Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 138 VAL Chi-restraints excluded: chain Q residue 147 ARG Chi-restraints excluded: chain Q residue 152 GLN Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain Q residue 243 THR Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain Q residue 270 LYS Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 18 GLN Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain R residue 154 SER Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 185 CYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 128 VAL Chi-restraints excluded: chain S residue 140 ILE Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 194 VAL Chi-restraints excluded: chain S residue 220 SER Chi-restraints excluded: chain S residue 259 SER Chi-restraints excluded: chain T residue 190 ASN Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 277 ILE Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 404 ARG Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 152 ASP Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 122 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 144 ASN Chi-restraints excluded: chain V residue 164 SER Chi-restraints excluded: chain V residue 181 LEU Chi-restraints excluded: chain V residue 187 ILE Chi-restraints excluded: chain V residue 203 LYS Chi-restraints excluded: chain V residue 206 CYS Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 60 CYS Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 89 SER Chi-restraints excluded: chain W residue 172 LYS Chi-restraints excluded: chain W residue 225 MET Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 73 MET Chi-restraints excluded: chain X residue 125 ASP Chi-restraints excluded: chain X residue 131 CYS Chi-restraints excluded: chain X residue 156 PRO Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain X residue 194 LYS Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 29 ILE Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 82 THR Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 88 ASN Chi-restraints excluded: chain Y residue 89 CYS Chi-restraints excluded: chain Y residue 97 ARG Chi-restraints excluded: chain Y residue 129 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Z residue 120 SER Chi-restraints excluded: chain Z residue 137 ASN Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 157 PHE Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 186 ARG Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 235 MET Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 251 ASP Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 69 ARG Chi-restraints excluded: chain b residue 106 MET Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 152 LYS Chi-restraints excluded: chain b residue 155 ASP Chi-restraints excluded: chain b residue 171 ARG Chi-restraints excluded: chain b residue 179 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 520 optimal weight: 0.7980 chunk 466 optimal weight: 0.8980 chunk 259 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 314 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 482 optimal weight: 0.6980 chunk 186 optimal weight: 0.7980 chunk 293 optimal weight: 1.9990 chunk 359 optimal weight: 0.0060 chunk 559 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 207 GLN A 232 GLN A 236 ASN B 94 GLN B 117 GLN B 187 HIS B 223 GLN C 263 GLN D 88 GLN D 115 GLN D 187 HIS F 225 GLN F 286 GLN G 64 ASN G 68 HIS H 129 ASN H 264 GLN I 115 HIS I 247 GLN J 26 ASN J 65 ASN K 64 ASN K 186 ASN K 197 ASN L 128 GLN L 152 GLN L 291 GLN M 170 GLN M 180 ASN M 188 GLN M 224 HIS N 62 GLN N 148 GLN O 21 GLN O 207 GLN O 236 ASN P 19 GLN P 61 GLN P 93 GLN P 117 GLN P 121 GLN P 140 ASN P 207 GLN P 230 GLN Q 29 GLN Q 175 GLN Q 186 HIS Q 263 GLN R 115 GLN S 255 GLN T 206 ASN T 305 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 129 ASN V 161 ASN V 241 GLN W 102 GLN W 115 HIS W 247 GLN X 26 ASN X 65 ASN X 169 GLN Y 64 ASN Y 72 GLN Y 73 HIS ** Y 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 186 ASN Z 108 ASN Z 128 GLN Z 205 GLN Z 291 GLN Z 296 HIS a 132 ASN a 154 ASN a 170 GLN a 280 ASN a 282 GLN b 44 HIS b 62 GLN b 70 GLN b 148 GLN b 185 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.040 50054 Z= 0.199 Angle : 0.631 9.897 67714 Z= 0.341 Chirality : 0.044 0.242 7544 Planarity : 0.005 0.048 8784 Dihedral : 10.656 94.805 7575 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 1.76 % Favored : 98.04 % Rotamer: Outliers : 6.01 % Allowed : 16.91 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.10), residues: 6290 helix: -0.35 (0.10), residues: 2296 sheet: -1.49 (0.12), residues: 1506 loop : -1.35 (0.11), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.006 0.001 HIS G 201 PHE 0.027 0.002 PHE M 157 TYR 0.021 0.002 TYR b 175 ARG 0.008 0.001 ARG P 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1208 time to evaluate : 4.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8770 (m-30) cc_final: 0.8536 (m-30) REVERT: A 101 ARG cc_start: 0.8478 (ttm110) cc_final: 0.8220 (mtp85) REVERT: A 150 LYS cc_start: 0.8832 (tttt) cc_final: 0.8628 (ttpt) REVERT: A 223 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7614 (ttm-80) REVERT: A 228 ASN cc_start: 0.8382 (t0) cc_final: 0.8127 (t0) REVERT: A 232 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7679 (mp10) REVERT: B 96 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8337 (mmmt) REVERT: B 110 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8620 (mtt-85) REVERT: B 117 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7569 (tp40) REVERT: B 148 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: B 167 ASP cc_start: 0.7009 (m-30) cc_final: 0.6551 (m-30) REVERT: B 182 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8505 (tt) REVERT: B 197 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.5675 (t80) REVERT: B 202 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8714 (p) REVERT: B 205 ASN cc_start: 0.8292 (t0) cc_final: 0.7556 (t0) REVERT: B 214 ASN cc_start: 0.8458 (p0) cc_final: 0.8219 (m110) REVERT: B 222 ASP cc_start: 0.7144 (m-30) cc_final: 0.6821 (p0) REVERT: B 226 ASP cc_start: 0.7777 (m-30) cc_final: 0.7550 (m-30) REVERT: C 20 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7255 (mp-120) REVERT: C 29 GLN cc_start: 0.8165 (mt0) cc_final: 0.7930 (mm-40) REVERT: C 60 SER cc_start: 0.8510 (m) cc_final: 0.8103 (t) REVERT: C 76 GLU cc_start: 0.8574 (tt0) cc_final: 0.8330 (pm20) REVERT: C 123 GLU cc_start: 0.8031 (tp30) cc_final: 0.7661 (tp30) REVERT: C 138 VAL cc_start: 0.9200 (OUTLIER) cc_final: 0.8911 (p) REVERT: C 193 ASP cc_start: 0.7733 (t0) cc_final: 0.7175 (m-30) REVERT: C 204 LYS cc_start: 0.8596 (tptt) cc_final: 0.8374 (tptp) REVERT: C 241 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7433 (mttm) REVERT: D 4 ASP cc_start: 0.8273 (p0) cc_final: 0.8066 (p0) REVERT: D 5 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7324 (ttm-80) REVERT: D 11 SER cc_start: 0.8860 (m) cc_final: 0.8464 (p) REVERT: D 17 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.8139 (m-80) REVERT: D 28 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7707 (mmtp) REVERT: D 47 LYS cc_start: 0.8291 (mttt) cc_final: 0.7898 (mtmm) REVERT: D 57 ARG cc_start: 0.6599 (tmm-80) cc_final: 0.6001 (tmt170) REVERT: D 61 LYS cc_start: 0.7732 (mptp) cc_final: 0.7316 (mtpp) REVERT: D 92 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8266 (mm110) REVERT: D 117 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.8066 (mtpp) REVERT: D 121 SER cc_start: 0.8517 (t) cc_final: 0.8130 (p) REVERT: D 143 HIS cc_start: 0.8568 (m-70) cc_final: 0.8262 (m90) REVERT: D 166 GLN cc_start: 0.7235 (mm110) cc_final: 0.7035 (mm-40) REVERT: D 170 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7297 (tm-30) REVERT: D 203 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7274 (p0) REVERT: D 205 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: D 207 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8619 (tp) REVERT: D 213 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7472 (tt0) REVERT: E 138 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8110 (pp) REVERT: E 164 MET cc_start: 0.7794 (ptp) cc_final: 0.7553 (ptm) REVERT: E 204 ASN cc_start: 0.8805 (t0) cc_final: 0.8278 (t0) REVERT: E 249 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8269 (mptt) REVERT: E 252 GLN cc_start: 0.8170 (mt0) cc_final: 0.7498 (mt0) REVERT: E 257 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8274 (t0) REVERT: E 286 HIS cc_start: 0.7677 (p-80) cc_final: 0.7456 (p-80) REVERT: E 290 THR cc_start: 0.7943 (p) cc_final: 0.7570 (t) REVERT: E 300 ASP cc_start: 0.7561 (m-30) cc_final: 0.7214 (m-30) REVERT: E 329 MET cc_start: 0.8290 (mmt) cc_final: 0.7970 (mmt) REVERT: F 171 ASP cc_start: 0.8443 (p0) cc_final: 0.7967 (p0) REVERT: F 173 ASP cc_start: 0.8495 (t0) cc_final: 0.8024 (m-30) REVERT: F 276 MET cc_start: 0.7553 (mtt) cc_final: 0.7114 (mtp) REVERT: F 350 ASP cc_start: 0.8126 (m-30) cc_final: 0.7726 (m-30) REVERT: F 354 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.7855 (p) REVERT: G 129 TYR cc_start: 0.8986 (m-80) cc_final: 0.8716 (m-80) REVERT: G 199 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7437 (tt0) REVERT: G 201 HIS cc_start: 0.5839 (t-170) cc_final: 0.5493 (t-170) REVERT: G 206 ASP cc_start: 0.6773 (m-30) cc_final: 0.6341 (m-30) REVERT: G 231 MET cc_start: 0.6040 (mtt) cc_final: 0.5801 (mtp) REVERT: H 139 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8146 (mptt) REVERT: H 140 MET cc_start: 0.8358 (mtp) cc_final: 0.8050 (mtp) REVERT: H 203 LYS cc_start: 0.8483 (ttmm) cc_final: 0.8156 (tttt) REVERT: H 240 ASP cc_start: 0.8605 (p0) cc_final: 0.8373 (p0) REVERT: H 254 LYS cc_start: 0.8319 (mttp) cc_final: 0.7998 (mtpt) REVERT: I 59 ARG cc_start: 0.7241 (mtm-85) cc_final: 0.6783 (mtm110) REVERT: I 60 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8587 (p) REVERT: I 66 MET cc_start: 0.8687 (mmm) cc_final: 0.8475 (ttm) REVERT: I 87 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8324 (ttp) REVERT: I 94 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8427 (mt) REVERT: I 117 TYR cc_start: 0.9032 (t80) cc_final: 0.8721 (t80) REVERT: I 173 ASP cc_start: 0.8333 (m-30) cc_final: 0.7905 (m-30) REVERT: I 209 LYS cc_start: 0.8607 (tptt) cc_final: 0.8265 (tppt) REVERT: I 211 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7934 (pttp) REVERT: I 225 MET cc_start: 0.6350 (mmm) cc_final: 0.5591 (mtm) REVERT: J 12 MET cc_start: 0.8783 (tmm) cc_final: 0.8301 (ttp) REVERT: J 65 ASN cc_start: 0.8026 (m-40) cc_final: 0.7822 (m-40) REVERT: J 72 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8027 (mm-30) REVERT: J 74 TYR cc_start: 0.9055 (t80) cc_final: 0.8526 (t80) REVERT: J 80 ARG cc_start: 0.9116 (ptt180) cc_final: 0.8801 (ptt90) REVERT: J 144 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7346 (mm-30) REVERT: J 203 ARG cc_start: 0.8403 (mtt-85) cc_final: 0.8069 (mmm160) REVERT: K 1 MET cc_start: 0.6909 (mmm) cc_final: 0.6623 (tpt) REVERT: K 62 LYS cc_start: 0.8663 (tttm) cc_final: 0.8430 (ttpp) REVERT: K 80 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7859 (mp0) REVERT: K 131 TYR cc_start: 0.8663 (p90) cc_final: 0.8272 (p90) REVERT: K 159 ARG cc_start: 0.8447 (mtm110) cc_final: 0.7952 (mtm-85) REVERT: K 176 ASP cc_start: 0.8022 (m-30) cc_final: 0.7720 (m-30) REVERT: K 180 ARG cc_start: 0.8549 (ttm110) cc_final: 0.7738 (tpt170) REVERT: L 123 GLN cc_start: 0.8160 (tt0) cc_final: 0.7942 (tt0) REVERT: L 160 MET cc_start: 0.8982 (ttm) cc_final: 0.8741 (ttt) REVERT: M 142 LYS cc_start: 0.8446 (mmtt) cc_final: 0.8204 (mmmt) REVERT: M 143 ASP cc_start: 0.8420 (t70) cc_final: 0.8061 (t0) REVERT: M 198 LYS cc_start: 0.8445 (ttmm) cc_final: 0.8133 (tttt) REVERT: M 296 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7689 (mm-30) REVERT: M 315 THR cc_start: 0.8889 (m) cc_final: 0.8454 (p) REVERT: M 338 LYS cc_start: 0.6270 (mmpt) cc_final: 0.5612 (mmmm) REVERT: N 21 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (p0) REVERT: N 152 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: N 153 ASN cc_start: 0.8884 (m-40) cc_final: 0.8475 (m-40) REVERT: N 155 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7108 (t0) REVERT: N 205 HIS cc_start: 0.8250 (t70) cc_final: 0.7429 (m-70) REVERT: O 10 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8814 (tt) REVERT: O 23 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7291 (tt0) REVERT: O 83 ASP cc_start: 0.8784 (m-30) cc_final: 0.8347 (m-30) REVERT: O 94 GLU cc_start: 0.7946 (tp30) cc_final: 0.7735 (tp30) REVERT: O 101 ARG cc_start: 0.8319 (ttm110) cc_final: 0.7962 (mtp-110) REVERT: O 122 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9044 (mtp85) REVERT: O 150 LYS cc_start: 0.8491 (tttt) cc_final: 0.8168 (tppt) REVERT: O 196 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7780 (ttmm) REVERT: O 201 ILE cc_start: 0.8506 (mt) cc_final: 0.8294 (tt) REVERT: O 223 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8589 (ttp-170) REVERT: P 16 LYS cc_start: 0.8582 (ptmt) cc_final: 0.7972 (mmtm) REVERT: P 154 TRP cc_start: 0.7698 (m100) cc_final: 0.7285 (m-90) REVERT: P 175 ARG cc_start: 0.7851 (mmt-90) cc_final: 0.7546 (mtp85) REVERT: P 177 THR cc_start: 0.7988 (p) cc_final: 0.7715 (t) REVERT: P 180 MET cc_start: 0.8182 (mtt) cc_final: 0.7852 (mtt) REVERT: P 181 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6911 (mp0) REVERT: P 204 GLU cc_start: 0.8526 (mp0) cc_final: 0.8077 (mp0) REVERT: P 225 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.6978 (mtp85) REVERT: Q 8 ARG cc_start: 0.8112 (mtp180) cc_final: 0.7748 (mtm180) REVERT: Q 161 ASP cc_start: 0.8319 (p0) cc_final: 0.7539 (t70) REVERT: Q 172 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8186 (mt0) REVERT: Q 175 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7674 (mm-40) REVERT: Q 188 SER cc_start: 0.8004 (t) cc_final: 0.7696 (p) REVERT: Q 195 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8005 (mtp) REVERT: Q 214 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: Q 237 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8184 (ttpt) REVERT: Q 265 ARG cc_start: 0.7544 (tpp-160) cc_final: 0.7284 (ttp-110) REVERT: R 11 SER cc_start: 0.8912 (m) cc_final: 0.8472 (p) REVERT: R 17 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: R 38 SER cc_start: 0.8250 (m) cc_final: 0.8021 (t) REVERT: R 177 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6799 (mmmt) REVERT: R 180 MET cc_start: 0.8174 (mtt) cc_final: 0.7929 (mtt) REVERT: R 191 LYS cc_start: 0.7801 (tttm) cc_final: 0.7587 (ttmt) REVERT: R 202 ARG cc_start: 0.5951 (OUTLIER) cc_final: 0.4839 (ptp-170) REVERT: R 203 ASN cc_start: 0.7507 (OUTLIER) cc_final: 0.7017 (p0) REVERT: R 205 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: R 206 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8251 (pp) REVERT: R 212 LYS cc_start: 0.8483 (mptp) cc_final: 0.8046 (tppt) REVERT: R 215 ARG cc_start: 0.8392 (ttp-170) cc_final: 0.7796 (ttm110) REVERT: R 216 TYR cc_start: 0.8949 (m-80) cc_final: 0.8630 (m-80) REVERT: S 164 MET cc_start: 0.8137 (ptp) cc_final: 0.7293 (ppp) REVERT: S 166 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8367 (mptt) REVERT: S 186 ARG cc_start: 0.8558 (mmt90) cc_final: 0.8298 (mpt-90) REVERT: S 283 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7859 (mt-10) REVERT: S 321 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.8096 (mmm-85) REVERT: T 230 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: T 326 MET cc_start: 0.8450 (ttp) cc_final: 0.8124 (ttp) REVERT: T 391 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6805 (tp30) REVERT: U 115 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7455 (tpp80) REVERT: U 129 TYR cc_start: 0.8383 (m-80) cc_final: 0.7739 (m-80) REVERT: U 141 TYR cc_start: 0.9073 (t80) cc_final: 0.8559 (t80) REVERT: U 221 ASP cc_start: 0.8224 (t0) cc_final: 0.7963 (t70) REVERT: V 140 MET cc_start: 0.8612 (mtp) cc_final: 0.8304 (mtt) REVERT: V 203 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8233 (ttpp) REVERT: V 212 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8312 (ttp80) REVERT: W 51 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7196 (pt0) REVERT: W 89 SER cc_start: 0.8685 (p) cc_final: 0.8475 (m) REVERT: W 186 SER cc_start: 0.8856 (t) cc_final: 0.8612 (p) REVERT: W 222 ASN cc_start: 0.8591 (m-40) cc_final: 0.8244 (m110) REVERT: W 226 TYR cc_start: 0.7164 (t80) cc_final: 0.6766 (t80) REVERT: X 12 MET cc_start: 0.8870 (tmm) cc_final: 0.8269 (ttp) REVERT: X 54 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8827 (m) REVERT: X 72 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8055 (mm-30) REVERT: X 106 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8338 (mt-10) REVERT: X 111 SER cc_start: 0.8955 (p) cc_final: 0.8596 (t) REVERT: X 135 ASP cc_start: 0.8992 (p0) cc_final: 0.8706 (p0) REVERT: X 188 MET cc_start: 0.8436 (ttt) cc_final: 0.8166 (ttt) REVERT: Y 31 ASP cc_start: 0.8960 (m-30) cc_final: 0.8357 (m-30) REVERT: Y 56 ASN cc_start: 0.8421 (m-40) cc_final: 0.8123 (m110) REVERT: Y 60 TYR cc_start: 0.9238 (t80) cc_final: 0.9033 (t80) REVERT: Y 70 MET cc_start: 0.8198 (mpp) cc_final: 0.7812 (mpp) REVERT: Y 168 LEU cc_start: 0.8341 (mm) cc_final: 0.7994 (mt) REVERT: Y 181 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.8229 (mmt180) REVERT: Z 137 ASN cc_start: 0.6683 (t0) cc_final: 0.6294 (t0) REVERT: Z 139 TYR cc_start: 0.7029 (m-80) cc_final: 0.6708 (m-80) REVERT: Z 194 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.6905 (mp) REVERT: Z 235 TYR cc_start: 0.8737 (m-80) cc_final: 0.7971 (m-80) REVERT: Z 244 LYS cc_start: 0.8831 (mtmt) cc_final: 0.7939 (mmtt) REVERT: Z 291 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7948 (pp30) REVERT: a 142 LYS cc_start: 0.7749 (pttm) cc_final: 0.7391 (tptp) REVERT: a 226 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7607 (ttt-90) REVERT: a 231 TYR cc_start: 0.8599 (t80) cc_final: 0.8338 (t80) REVERT: a 251 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.7967 (p0) REVERT: a 284 MET cc_start: 0.8094 (mtt) cc_final: 0.7700 (mtt) REVERT: a 331 GLN cc_start: 0.7918 (pt0) cc_final: 0.7406 (tt0) REVERT: b 3 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8624 (p) REVERT: b 61 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7996 (ttpt) REVERT: b 64 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7811 (mt-10) REVERT: b 65 ASP cc_start: 0.8521 (m-30) cc_final: 0.8077 (m-30) REVERT: b 152 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7465 (mtpt) REVERT: b 155 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: b 205 HIS cc_start: 0.8135 (t70) cc_final: 0.7842 (m90) outliers start: 315 outliers final: 131 residues processed: 1424 average time/residue: 0.5309 time to fit residues: 1214.4833 Evaluate side-chains 1240 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1051 time to evaluate : 4.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 232 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 110 ARG Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 92 GLN Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 354 THR Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 87 MET Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 128 GLN Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain N residue 21 ASP Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 152 LYS Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain O residue 10 ILE Chi-restraints excluded: chain O residue 66 LEU Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 191 ASP Chi-restraints excluded: chain O residue 196 LYS Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 197 PHE Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 117 CYS Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 172 GLN Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 214 ASP Chi-restraints excluded: chain Q residue 237 LYS Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 7 ILE Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain T residue 203 LYS Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 277 ILE Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 144 ASN Chi-restraints excluded: chain V residue 160 ILE Chi-restraints excluded: chain V residue 187 ILE Chi-restraints excluded: chain V residue 203 LYS Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 125 ASP Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 181 ARG Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain Z residue 291 GLN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 154 ASN Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 251 ASP Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 61 LYS Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 106 MET Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 152 LYS Chi-restraints excluded: chain b residue 155 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 310 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 465 optimal weight: 1.9990 chunk 380 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 560 optimal weight: 5.9990 chunk 605 optimal weight: 0.6980 chunk 499 optimal weight: 0.9990 chunk 555 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 chunk 449 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 125 GLN A 165 HIS B 19 GLN B 187 HIS C 3 HIS C 247 GLN D 92 GLN D 115 GLN E 278 GLN F 190 ASN F 259 ASN G 64 ASN H 241 GLN H 261 GLN H 264 GLN K 56 ASN K 143 HIS L 152 GLN M 180 ASN N 185 GLN O 72 ASN O 152 GLN P 61 GLN ** P 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 117 GLN P 121 GLN P 205 ASN Q 172 GLN R 18 GLN R 92 GLN S 262 HIS ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 241 GLN V 261 GLN Y 42 HIS Y 72 GLN Y 143 HIS Z 108 ASN Z 128 GLN Z 205 GLN Z 291 GLN a 130 GLN a 203 ASN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 50054 Z= 0.277 Angle : 0.587 11.364 67714 Z= 0.312 Chirality : 0.044 0.250 7544 Planarity : 0.004 0.054 8784 Dihedral : 8.460 89.535 7249 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 5.38 % Allowed : 18.00 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.10), residues: 6290 helix: 0.73 (0.11), residues: 2332 sheet: -1.09 (0.12), residues: 1514 loop : -0.94 (0.12), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 185 HIS 0.014 0.001 HIS S 262 PHE 0.020 0.002 PHE M 157 TYR 0.026 0.002 TYR b 12 ARG 0.011 0.001 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1077 time to evaluate : 4.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 CYS cc_start: 0.8200 (p) cc_final: 0.7930 (p) REVERT: A 75 CYS cc_start: 0.8526 (t) cc_final: 0.8282 (t) REVERT: A 83 ASP cc_start: 0.8813 (m-30) cc_final: 0.8601 (m-30) REVERT: A 101 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8115 (mtp85) REVERT: A 150 LYS cc_start: 0.8821 (tttt) cc_final: 0.8553 (ttpt) REVERT: A 223 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7683 (ttm-80) REVERT: B 117 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7716 (tp40) REVERT: B 118 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 167 ASP cc_start: 0.7233 (m-30) cc_final: 0.6919 (m-30) REVERT: B 175 ARG cc_start: 0.7608 (mmt-90) cc_final: 0.7186 (mmm160) REVERT: B 182 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8472 (tt) REVERT: B 197 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.5616 (t80) REVERT: B 205 ASN cc_start: 0.8499 (t0) cc_final: 0.7603 (t0) REVERT: B 222 ASP cc_start: 0.7217 (m-30) cc_final: 0.6835 (p0) REVERT: B 226 ASP cc_start: 0.7739 (m-30) cc_final: 0.7495 (m-30) REVERT: C 60 SER cc_start: 0.8517 (m) cc_final: 0.8264 (t) REVERT: C 76 GLU cc_start: 0.8708 (tt0) cc_final: 0.8281 (mm-30) REVERT: C 123 GLU cc_start: 0.8084 (tp30) cc_final: 0.7648 (tp30) REVERT: C 138 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8929 (p) REVERT: C 193 ASP cc_start: 0.7785 (t0) cc_final: 0.7236 (m-30) REVERT: C 204 LYS cc_start: 0.8645 (tptt) cc_final: 0.8393 (tptp) REVERT: C 211 ILE cc_start: 0.7877 (mp) cc_final: 0.7510 (tp) REVERT: C 217 GLU cc_start: 0.8679 (tt0) cc_final: 0.8429 (tt0) REVERT: C 234 ASP cc_start: 0.7894 (t0) cc_final: 0.7452 (m-30) REVERT: C 241 LYS cc_start: 0.7629 (mmtt) cc_final: 0.7341 (mttm) REVERT: D 4 ASP cc_start: 0.8276 (p0) cc_final: 0.8063 (p0) REVERT: D 5 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7378 (ttm-80) REVERT: D 11 SER cc_start: 0.8766 (m) cc_final: 0.8402 (p) REVERT: D 17 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: D 28 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7563 (mmtp) REVERT: D 46 GLU cc_start: 0.8289 (pt0) cc_final: 0.7481 (tt0) REVERT: D 47 LYS cc_start: 0.8303 (mttt) cc_final: 0.7855 (mtmm) REVERT: D 61 LYS cc_start: 0.7783 (mptp) cc_final: 0.7270 (mtpt) REVERT: D 117 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8046 (mtpp) REVERT: D 121 SER cc_start: 0.8564 (t) cc_final: 0.8195 (p) REVERT: D 143 HIS cc_start: 0.8624 (m-70) cc_final: 0.8259 (m90) REVERT: D 147 THR cc_start: 0.9169 (m) cc_final: 0.8929 (m) REVERT: D 148 ASP cc_start: 0.8144 (p0) cc_final: 0.7897 (p0) REVERT: D 170 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7430 (tm-30) REVERT: D 178 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7580 (t70) REVERT: D 203 ASN cc_start: 0.7786 (OUTLIER) cc_final: 0.7387 (p0) REVERT: D 205 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7918 (tp30) REVERT: D 207 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (tp) REVERT: D 213 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7576 (tt0) REVERT: D 232 GLU cc_start: 0.6850 (tt0) cc_final: 0.6287 (tm-30) REVERT: E 138 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8023 (pp) REVERT: E 164 MET cc_start: 0.7967 (ptp) cc_final: 0.7648 (ptm) REVERT: E 204 ASN cc_start: 0.8885 (t0) cc_final: 0.8421 (t0) REVERT: E 252 GLN cc_start: 0.8215 (mt0) cc_final: 0.7550 (mt0) REVERT: E 257 ASP cc_start: 0.8403 (OUTLIER) cc_final: 0.8190 (t0) REVERT: E 287 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7808 (ttm-80) REVERT: E 329 MET cc_start: 0.8132 (mmt) cc_final: 0.7846 (mmt) REVERT: E 339 MET cc_start: 0.7406 (mtm) cc_final: 0.7187 (mtm) REVERT: F 170 TYR cc_start: 0.9018 (m-80) cc_final: 0.8702 (m-80) REVERT: F 173 ASP cc_start: 0.8437 (t0) cc_final: 0.7839 (m-30) REVERT: F 276 MET cc_start: 0.7490 (mtt) cc_final: 0.7194 (mtm) REVERT: F 350 ASP cc_start: 0.8160 (m-30) cc_final: 0.7792 (m-30) REVERT: G 129 TYR cc_start: 0.9024 (m-80) cc_final: 0.8768 (m-80) REVERT: G 231 MET cc_start: 0.6043 (mtt) cc_final: 0.5425 (ttm) REVERT: H 140 MET cc_start: 0.8369 (mtp) cc_final: 0.8133 (mtp) REVERT: H 254 LYS cc_start: 0.8455 (mttp) cc_final: 0.8107 (mtpt) REVERT: I 59 ARG cc_start: 0.7398 (mtm-85) cc_final: 0.6922 (mtm110) REVERT: I 60 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8441 (t) REVERT: I 61 ARG cc_start: 0.8097 (ttm110) cc_final: 0.7770 (ttm-80) REVERT: I 66 MET cc_start: 0.8727 (mmm) cc_final: 0.8477 (ttm) REVERT: I 87 MET cc_start: 0.8609 (ttm) cc_final: 0.8385 (ttp) REVERT: I 117 TYR cc_start: 0.9095 (t80) cc_final: 0.8868 (t80) REVERT: I 173 ASP cc_start: 0.8363 (m-30) cc_final: 0.7943 (m-30) REVERT: I 225 MET cc_start: 0.5865 (mmm) cc_final: 0.5250 (mtt) REVERT: J 12 MET cc_start: 0.8808 (tmm) cc_final: 0.8339 (ttp) REVERT: J 72 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8087 (mm-30) REVERT: J 155 ARG cc_start: 0.8452 (mtm110) cc_final: 0.8145 (mtm110) REVERT: J 180 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8786 (mm) REVERT: J 203 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8200 (mmm160) REVERT: K 1 MET cc_start: 0.6843 (mmm) cc_final: 0.6513 (tpt) REVERT: K 70 MET cc_start: 0.7598 (mmp) cc_final: 0.7362 (mmt) REVERT: K 80 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7862 (mp0) REVERT: K 131 TYR cc_start: 0.8651 (p90) cc_final: 0.8242 (p90) REVERT: K 159 ARG cc_start: 0.8448 (mtm110) cc_final: 0.7971 (ttm110) REVERT: K 165 GLN cc_start: 0.8303 (tp40) cc_final: 0.7981 (tp-100) REVERT: K 176 ASP cc_start: 0.8024 (m-30) cc_final: 0.7671 (m-30) REVERT: K 180 ARG cc_start: 0.8689 (ttm110) cc_final: 0.7915 (tpt90) REVERT: L 129 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7899 (m) REVERT: L 160 MET cc_start: 0.9053 (ttm) cc_final: 0.8807 (ttt) REVERT: L 199 MET cc_start: 0.8597 (mtp) cc_final: 0.8367 (mtm) REVERT: L 293 LYS cc_start: 0.7988 (mmtm) cc_final: 0.7729 (mtmm) REVERT: M 143 ASP cc_start: 0.8430 (t70) cc_final: 0.8222 (t0) REVERT: M 315 THR cc_start: 0.8888 (m) cc_final: 0.8477 (p) REVERT: M 338 LYS cc_start: 0.6317 (mmpt) cc_final: 0.5728 (mtpt) REVERT: N 68 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: N 152 LYS cc_start: 0.8492 (mttt) cc_final: 0.8254 (mmtt) REVERT: N 153 ASN cc_start: 0.8879 (m-40) cc_final: 0.8406 (m-40) REVERT: N 155 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7242 (t0) REVERT: N 205 HIS cc_start: 0.8269 (t70) cc_final: 0.7365 (m-70) REVERT: O 23 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7406 (tt0) REVERT: O 83 ASP cc_start: 0.8824 (m-30) cc_final: 0.8416 (m-30) REVERT: O 94 GLU cc_start: 0.8010 (tp30) cc_final: 0.7682 (tp30) REVERT: O 101 ARG cc_start: 0.8377 (ttm110) cc_final: 0.8006 (mtp-110) REVERT: O 122 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.8958 (mtp85) REVERT: O 150 LYS cc_start: 0.8438 (tttt) cc_final: 0.8155 (tppt) REVERT: O 223 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8726 (ttp-170) REVERT: O 232 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7969 (mt0) REVERT: P 16 LYS cc_start: 0.8650 (ptmt) cc_final: 0.8101 (mmtm) REVERT: P 154 TRP cc_start: 0.7897 (m100) cc_final: 0.7331 (m-90) REVERT: P 175 ARG cc_start: 0.7845 (mmt-90) cc_final: 0.7548 (mtp85) REVERT: P 181 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6980 (mp0) REVERT: P 204 GLU cc_start: 0.8556 (mp0) cc_final: 0.8026 (mp0) REVERT: Q 8 ARG cc_start: 0.8046 (mtp180) cc_final: 0.7739 (mtm180) REVERT: Q 41 ASP cc_start: 0.7307 (m-30) cc_final: 0.6890 (t0) REVERT: Q 161 ASP cc_start: 0.8407 (p0) cc_final: 0.7556 (t70) REVERT: Q 175 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7781 (mm-40) REVERT: Q 188 SER cc_start: 0.7942 (t) cc_final: 0.7668 (p) REVERT: Q 195 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8241 (mtp) REVERT: Q 237 LYS cc_start: 0.8594 (tttp) cc_final: 0.8354 (ttpt) REVERT: Q 265 ARG cc_start: 0.7631 (tpp-160) cc_final: 0.7419 (ttp-110) REVERT: R 11 SER cc_start: 0.8738 (m) cc_final: 0.8266 (p) REVERT: R 17 PHE cc_start: 0.8654 (OUTLIER) cc_final: 0.7900 (m-80) REVERT: R 24 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7370 (mt-10) REVERT: R 27 LYS cc_start: 0.8411 (mmmm) cc_final: 0.8160 (mmmm) REVERT: R 38 SER cc_start: 0.8354 (m) cc_final: 0.8138 (t) REVERT: R 65 VAL cc_start: 0.9220 (t) cc_final: 0.9019 (m) REVERT: R 177 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.6881 (mmmt) REVERT: R 180 MET cc_start: 0.8077 (mtt) cc_final: 0.7837 (mtt) REVERT: R 202 ARG cc_start: 0.5968 (OUTLIER) cc_final: 0.4974 (ptp-170) REVERT: R 203 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.7055 (p0) REVERT: R 205 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: R 212 LYS cc_start: 0.8560 (mptp) cc_final: 0.7849 (tppt) REVERT: R 213 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6917 (mp0) REVERT: R 215 ARG cc_start: 0.8450 (ttp-170) cc_final: 0.7813 (ttm110) REVERT: R 216 TYR cc_start: 0.8937 (m-80) cc_final: 0.8621 (m-80) REVERT: S 164 MET cc_start: 0.8083 (ptp) cc_final: 0.7257 (ppp) REVERT: S 166 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8312 (mptt) REVERT: S 186 ARG cc_start: 0.8611 (mmt90) cc_final: 0.8241 (mpt-90) REVERT: S 195 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8111 (mm-30) REVERT: S 283 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7695 (mt-10) REVERT: S 321 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8082 (mmm-85) REVERT: T 221 LEU cc_start: 0.6728 (OUTLIER) cc_final: 0.6520 (tt) REVERT: T 230 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: T 389 PHE cc_start: 0.7868 (m-10) cc_final: 0.7664 (m-10) REVERT: T 391 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6674 (tp30) REVERT: U 34 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7985 (p) REVERT: U 51 GLU cc_start: 0.8311 (pt0) cc_final: 0.7961 (pt0) REVERT: U 115 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7227 (mtt90) REVERT: U 129 TYR cc_start: 0.8501 (m-80) cc_final: 0.7816 (m-80) REVERT: U 221 ASP cc_start: 0.8385 (t0) cc_final: 0.7778 (m-30) REVERT: V 203 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8330 (ttpp) REVERT: W 51 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7235 (pt0) REVERT: W 87 MET cc_start: 0.7747 (ttm) cc_final: 0.7493 (ttm) REVERT: W 89 SER cc_start: 0.8885 (p) cc_final: 0.8533 (m) REVERT: W 186 SER cc_start: 0.9128 (t) cc_final: 0.8814 (p) REVERT: W 222 ASN cc_start: 0.8515 (m-40) cc_final: 0.8135 (m110) REVERT: W 226 TYR cc_start: 0.7160 (t80) cc_final: 0.6790 (t80) REVERT: X 12 MET cc_start: 0.8899 (tmm) cc_final: 0.8199 (ttp) REVERT: X 33 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8254 (ptpp) REVERT: X 54 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8779 (m) REVERT: X 72 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8110 (mm-30) REVERT: X 106 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8218 (mt-10) REVERT: X 111 SER cc_start: 0.8976 (p) cc_final: 0.8693 (t) REVERT: Y 30 THR cc_start: 0.8559 (t) cc_final: 0.8135 (p) REVERT: Y 31 ASP cc_start: 0.8955 (m-30) cc_final: 0.8353 (m-30) REVERT: Y 56 ASN cc_start: 0.8489 (m-40) cc_final: 0.8170 (m110) REVERT: Y 69 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7583 (mtm-85) REVERT: Y 168 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8148 (mt) REVERT: Y 181 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8216 (mmt180) REVERT: Z 137 ASN cc_start: 0.6333 (t0) cc_final: 0.6123 (m-40) REVERT: Z 139 TYR cc_start: 0.7064 (m-80) cc_final: 0.6728 (m-80) REVERT: Z 160 MET cc_start: 0.8651 (ttp) cc_final: 0.8160 (ttp) REVERT: Z 161 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8261 (mm-30) REVERT: Z 190 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7633 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6994 (mp) REVERT: Z 235 TYR cc_start: 0.8728 (m-80) cc_final: 0.8006 (m-80) REVERT: a 142 LYS cc_start: 0.7806 (pttm) cc_final: 0.7335 (tptp) REVERT: a 193 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8330 (tt) REVERT: a 251 ASP cc_start: 0.8515 (p0) cc_final: 0.8092 (p0) REVERT: a 253 VAL cc_start: 0.8153 (t) cc_final: 0.7759 (p) REVERT: a 269 SER cc_start: 0.8966 (m) cc_final: 0.8719 (p) REVERT: a 284 MET cc_start: 0.8073 (mtt) cc_final: 0.7714 (mtt) REVERT: a 314 TYR cc_start: 0.8378 (m-80) cc_final: 0.8010 (m-80) REVERT: a 331 GLN cc_start: 0.7945 (pt0) cc_final: 0.7407 (tt0) REVERT: b 3 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8512 (p) REVERT: b 64 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7801 (mt-10) REVERT: b 155 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: b 157 LEU cc_start: 0.9273 (mt) cc_final: 0.9060 (mt) REVERT: b 183 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8023 (ttpt) REVERT: b 195 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8466 (ttm110) outliers start: 282 outliers final: 159 residues processed: 1270 average time/residue: 0.5116 time to fit residues: 1056.9156 Evaluate side-chains 1185 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 983 time to evaluate : 4.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 287 CYS Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 144 LEU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 191 ASP Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 205 ASN Chi-restraints excluded: chain Q residue 2 SER Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 117 CYS Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 195 MET Chi-restraints excluded: chain Q residue 247 GLN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 102 MET Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 205 GLU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 166 LYS Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 243 ILE Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 203 LYS Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 277 ILE Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain T residue 330 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 44 ASP Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain U residue 184 LEU Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 203 LYS Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 3 ILE Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 181 ARG Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 208 VAL Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 ILE Chi-restraints excluded: chain b residue 3 SER Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 155 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 553 optimal weight: 0.7980 chunk 421 optimal weight: 9.9990 chunk 290 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 267 optimal weight: 2.9990 chunk 376 optimal weight: 8.9990 chunk 562 optimal weight: 6.9990 chunk 595 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 533 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 165 HIS B 187 HIS D 203 ASN E 113 ASN F 206 ASN G 64 ASN K 56 ASN K 72 GLN L 291 GLN M 180 ASN N 185 GLN O 72 ASN P 61 GLN P 140 ASN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 211 GLN V 241 GLN Y 72 GLN Y 197 ASN a 132 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 50054 Z= 0.293 Angle : 0.569 8.741 67714 Z= 0.301 Chirality : 0.044 0.256 7544 Planarity : 0.004 0.058 8784 Dihedral : 7.644 89.403 7177 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.99 % Favored : 97.90 % Rotamer: Outliers : 5.54 % Allowed : 18.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.10), residues: 6290 helix: 1.10 (0.11), residues: 2334 sheet: -0.83 (0.12), residues: 1532 loop : -0.76 (0.12), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 165 HIS 0.028 0.001 HIS C 3 PHE 0.016 0.002 PHE K 8 TYR 0.027 0.001 TYR b 12 ARG 0.007 0.001 ARG K 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1323 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1033 time to evaluate : 4.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 CYS cc_start: 0.8181 (p) cc_final: 0.7937 (p) REVERT: A 61 ASP cc_start: 0.7890 (t70) cc_final: 0.7618 (t0) REVERT: A 83 ASP cc_start: 0.8806 (m-30) cc_final: 0.8586 (m-30) REVERT: A 87 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8549 (mt) REVERT: A 101 ARG cc_start: 0.8404 (ttm110) cc_final: 0.8183 (mtp85) REVERT: A 150 LYS cc_start: 0.8815 (tttt) cc_final: 0.8510 (ttpt) REVERT: A 223 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7588 (ttm-80) REVERT: B 118 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 167 ASP cc_start: 0.7252 (m-30) cc_final: 0.6865 (m-30) REVERT: B 175 ARG cc_start: 0.7626 (mmt-90) cc_final: 0.7156 (mmm160) REVERT: B 182 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8438 (tt) REVERT: B 197 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.5827 (t80) REVERT: B 205 ASN cc_start: 0.8471 (t0) cc_final: 0.7576 (t0) REVERT: B 222 ASP cc_start: 0.7290 (m-30) cc_final: 0.6853 (p0) REVERT: B 226 ASP cc_start: 0.7753 (m-30) cc_final: 0.7487 (m-30) REVERT: C 60 SER cc_start: 0.8482 (m) cc_final: 0.8097 (t) REVERT: C 76 GLU cc_start: 0.8801 (tt0) cc_final: 0.8355 (mm-30) REVERT: C 123 GLU cc_start: 0.8048 (tp30) cc_final: 0.7536 (tp30) REVERT: C 138 VAL cc_start: 0.9216 (OUTLIER) cc_final: 0.8972 (p) REVERT: C 193 ASP cc_start: 0.7649 (t0) cc_final: 0.7188 (m-30) REVERT: C 204 LYS cc_start: 0.8664 (tptt) cc_final: 0.8402 (tptp) REVERT: C 211 ILE cc_start: 0.8071 (mp) cc_final: 0.7709 (tp) REVERT: C 234 ASP cc_start: 0.7960 (t0) cc_final: 0.7550 (m-30) REVERT: D 4 ASP cc_start: 0.8306 (p0) cc_final: 0.7325 (m-30) REVERT: D 5 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7266 (ttm-80) REVERT: D 11 SER cc_start: 0.8710 (m) cc_final: 0.8464 (p) REVERT: D 28 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7566 (mmtp) REVERT: D 46 GLU cc_start: 0.8312 (pt0) cc_final: 0.7588 (tt0) REVERT: D 47 LYS cc_start: 0.8326 (mttt) cc_final: 0.7868 (mtmm) REVERT: D 61 LYS cc_start: 0.7780 (mptp) cc_final: 0.7245 (mttm) REVERT: D 121 SER cc_start: 0.8558 (t) cc_final: 0.8248 (p) REVERT: D 147 THR cc_start: 0.9182 (m) cc_final: 0.8930 (m) REVERT: D 148 ASP cc_start: 0.8189 (p0) cc_final: 0.7925 (p0) REVERT: D 170 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7369 (tm-30) REVERT: D 178 ASP cc_start: 0.7847 (OUTLIER) cc_final: 0.7557 (t70) REVERT: D 205 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: D 213 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7721 (tt0) REVERT: D 232 GLU cc_start: 0.6854 (tt0) cc_final: 0.6583 (tm-30) REVERT: E 138 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8069 (pp) REVERT: E 164 MET cc_start: 0.8008 (ptp) cc_final: 0.7619 (ptm) REVERT: E 204 ASN cc_start: 0.8844 (t0) cc_final: 0.8352 (t0) REVERT: E 287 ARG cc_start: 0.8098 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: E 314 ASN cc_start: 0.7949 (t0) cc_final: 0.7387 (t0) REVERT: E 329 MET cc_start: 0.8159 (mmt) cc_final: 0.7850 (mmt) REVERT: F 170 TYR cc_start: 0.9027 (m-80) cc_final: 0.8731 (m-80) REVERT: F 173 ASP cc_start: 0.8427 (t0) cc_final: 0.7834 (m-30) REVERT: F 276 MET cc_start: 0.7483 (mtt) cc_final: 0.7196 (mtm) REVERT: F 350 ASP cc_start: 0.8179 (m-30) cc_final: 0.7847 (m-30) REVERT: F 387 THR cc_start: 0.8464 (p) cc_final: 0.8246 (p) REVERT: G 129 TYR cc_start: 0.9028 (m-80) cc_final: 0.8757 (m-80) REVERT: G 208 LEU cc_start: 0.8134 (mt) cc_final: 0.7625 (mp) REVERT: G 231 MET cc_start: 0.6207 (mtt) cc_final: 0.5554 (ttm) REVERT: H 74 THR cc_start: 0.9268 (OUTLIER) cc_final: 0.9031 (t) REVERT: H 137 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8880 (t80) REVERT: H 139 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8113 (mptt) REVERT: H 140 MET cc_start: 0.8336 (mtp) cc_final: 0.8028 (mtp) REVERT: H 254 LYS cc_start: 0.8512 (mttp) cc_final: 0.8146 (mtpt) REVERT: I 59 ARG cc_start: 0.7476 (mtm-85) cc_final: 0.7021 (mtm110) REVERT: I 60 CYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8500 (t) REVERT: I 61 ARG cc_start: 0.8129 (ttm110) cc_final: 0.7848 (ttm170) REVERT: I 117 TYR cc_start: 0.9082 (t80) cc_final: 0.8844 (t80) REVERT: I 209 LYS cc_start: 0.8726 (tptt) cc_final: 0.8165 (tptp) REVERT: I 225 MET cc_start: 0.5837 (mmm) cc_final: 0.5617 (mtp) REVERT: J 12 MET cc_start: 0.8716 (tmm) cc_final: 0.8219 (ttp) REVERT: J 155 ARG cc_start: 0.8264 (mtm110) cc_final: 0.7962 (mtm110) REVERT: J 203 ARG cc_start: 0.8386 (mtt-85) cc_final: 0.8089 (mmm160) REVERT: K 1 MET cc_start: 0.6855 (mmm) cc_final: 0.6258 (mmm) REVERT: K 70 MET cc_start: 0.7667 (mmp) cc_final: 0.7448 (mmt) REVERT: K 80 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7758 (mp0) REVERT: K 131 TYR cc_start: 0.8655 (p90) cc_final: 0.8295 (p90) REVERT: K 159 ARG cc_start: 0.8397 (mtm110) cc_final: 0.7970 (ttm110) REVERT: K 165 GLN cc_start: 0.8245 (tp40) cc_final: 0.7904 (tp-100) REVERT: K 180 ARG cc_start: 0.8709 (ttm110) cc_final: 0.7923 (tpt90) REVERT: L 160 MET cc_start: 0.9097 (ttm) cc_final: 0.8808 (ttt) REVERT: L 196 MET cc_start: 0.8642 (ptm) cc_final: 0.8316 (ptm) REVERT: L 281 LYS cc_start: 0.8720 (tppt) cc_final: 0.8263 (mptt) REVERT: M 198 LYS cc_start: 0.8522 (tttp) cc_final: 0.8044 (ttpt) REVERT: M 338 LYS cc_start: 0.6312 (mmpt) cc_final: 0.5606 (mtpt) REVERT: N 68 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: N 153 ASN cc_start: 0.8862 (m-40) cc_final: 0.8449 (m110) REVERT: N 155 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7304 (t0) REVERT: N 205 HIS cc_start: 0.8269 (t70) cc_final: 0.7383 (m90) REVERT: O 23 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7413 (tt0) REVERT: O 83 ASP cc_start: 0.8850 (m-30) cc_final: 0.8493 (m-30) REVERT: O 101 ARG cc_start: 0.8376 (ttm110) cc_final: 0.7925 (mtp-110) REVERT: O 122 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8967 (mtp85) REVERT: O 150 LYS cc_start: 0.8527 (tttt) cc_final: 0.8250 (tppt) REVERT: O 223 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8764 (ttp-170) REVERT: O 232 GLN cc_start: 0.8393 (mm-40) cc_final: 0.8024 (mt0) REVERT: P 16 LYS cc_start: 0.8666 (ptmt) cc_final: 0.8166 (mmtm) REVERT: P 154 TRP cc_start: 0.7939 (m100) cc_final: 0.7383 (m-90) REVERT: P 175 ARG cc_start: 0.7850 (mmt-90) cc_final: 0.7506 (mtp85) REVERT: P 181 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6978 (mp0) REVERT: P 204 GLU cc_start: 0.8639 (mp0) cc_final: 0.8087 (mp0) REVERT: Q 8 ARG cc_start: 0.8087 (mtp180) cc_final: 0.7764 (mtm180) REVERT: Q 41 ASP cc_start: 0.7292 (m-30) cc_final: 0.6941 (t0) REVERT: Q 71 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7237 (mmt) REVERT: Q 76 GLU cc_start: 0.8581 (pm20) cc_final: 0.8371 (mm-30) REVERT: Q 161 ASP cc_start: 0.8500 (p0) cc_final: 0.7603 (t70) REVERT: Q 175 GLN cc_start: 0.8111 (mm-40) cc_final: 0.7819 (mm-40) REVERT: R 11 SER cc_start: 0.8648 (m) cc_final: 0.8174 (p) REVERT: R 17 PHE cc_start: 0.8675 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: R 24 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: R 27 LYS cc_start: 0.8365 (mmmm) cc_final: 0.8105 (mmmm) REVERT: R 38 SER cc_start: 0.8423 (m) cc_final: 0.8216 (t) REVERT: R 59 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6383 (mp) REVERT: R 177 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6928 (mmmt) REVERT: R 180 MET cc_start: 0.7947 (mtt) cc_final: 0.7731 (mtt) REVERT: R 202 ARG cc_start: 0.5845 (OUTLIER) cc_final: 0.4878 (ptp-170) REVERT: R 203 ASN cc_start: 0.7678 (OUTLIER) cc_final: 0.7446 (p0) REVERT: R 206 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7835 (pp) REVERT: R 212 LYS cc_start: 0.8569 (mptp) cc_final: 0.7847 (tppt) REVERT: R 213 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6894 (mp0) REVERT: R 215 ARG cc_start: 0.8419 (ttp-170) cc_final: 0.7764 (ttm110) REVERT: R 216 TYR cc_start: 0.8885 (m-80) cc_final: 0.8541 (m-80) REVERT: S 164 MET cc_start: 0.8071 (ptp) cc_final: 0.7346 (ppp) REVERT: S 178 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7875 (ptp) REVERT: S 186 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8297 (mpt-90) REVERT: S 321 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.8068 (mmm-85) REVERT: T 221 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6636 (tt) REVERT: T 230 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: T 391 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6625 (tp30) REVERT: U 34 SER cc_start: 0.8215 (OUTLIER) cc_final: 0.8013 (p) REVERT: U 51 GLU cc_start: 0.8283 (pt0) cc_final: 0.7944 (pt0) REVERT: U 188 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6266 (mp0) REVERT: U 221 ASP cc_start: 0.8365 (t0) cc_final: 0.8111 (t0) REVERT: V 140 MET cc_start: 0.8623 (mtp) cc_final: 0.8379 (mtt) REVERT: W 51 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7203 (pt0) REVERT: W 87 MET cc_start: 0.7840 (ttm) cc_final: 0.7602 (ttm) REVERT: W 89 SER cc_start: 0.8887 (p) cc_final: 0.8557 (m) REVERT: W 186 SER cc_start: 0.9175 (t) cc_final: 0.8825 (p) REVERT: W 209 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8559 (tppt) REVERT: W 222 ASN cc_start: 0.8549 (m-40) cc_final: 0.8182 (m-40) REVERT: W 226 TYR cc_start: 0.7259 (t80) cc_final: 0.6912 (t80) REVERT: X 12 MET cc_start: 0.8891 (tmm) cc_final: 0.8317 (ttp) REVERT: X 33 LYS cc_start: 0.8579 (ptpt) cc_final: 0.8302 (ptpp) REVERT: X 85 LYS cc_start: 0.8795 (mptt) cc_final: 0.8399 (mtpp) REVERT: X 106 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8275 (mt-10) REVERT: X 111 SER cc_start: 0.8993 (p) cc_final: 0.8724 (t) REVERT: X 194 LYS cc_start: 0.8287 (pttm) cc_final: 0.8085 (pttm) REVERT: Y 30 THR cc_start: 0.8667 (t) cc_final: 0.8201 (p) REVERT: Y 56 ASN cc_start: 0.8533 (m-40) cc_final: 0.8203 (m110) REVERT: Y 69 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7464 (mtm-85) REVERT: Y 168 LEU cc_start: 0.8464 (mm) cc_final: 0.8200 (mt) REVERT: Y 181 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8224 (mmt180) REVERT: Z 137 ASN cc_start: 0.6314 (t0) cc_final: 0.6096 (m-40) REVERT: Z 139 TYR cc_start: 0.7106 (m-80) cc_final: 0.6840 (m-80) REVERT: Z 155 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: Z 160 MET cc_start: 0.8653 (ttp) cc_final: 0.8153 (ttp) REVERT: Z 161 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8283 (mm-30) REVERT: Z 190 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7642 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7048 (mp) REVERT: Z 235 TYR cc_start: 0.8697 (m-80) cc_final: 0.7937 (m-80) REVERT: a 142 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7355 (tptp) REVERT: a 193 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8478 (tt) REVERT: a 284 MET cc_start: 0.8002 (mtt) cc_final: 0.7644 (mtt) REVERT: a 314 TYR cc_start: 0.8435 (m-80) cc_final: 0.8055 (m-80) REVERT: a 331 GLN cc_start: 0.7949 (pt0) cc_final: 0.7453 (tt0) REVERT: b 12 TYR cc_start: 0.8830 (p90) cc_final: 0.8624 (p90) REVERT: b 64 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7731 (mt-10) REVERT: b 65 ASP cc_start: 0.8517 (m-30) cc_final: 0.8011 (m-30) REVERT: b 155 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7535 (m-30) REVERT: b 195 ARG cc_start: 0.8804 (mmm-85) cc_final: 0.8512 (ttm110) outliers start: 290 outliers final: 169 residues processed: 1239 average time/residue: 0.5296 time to fit residues: 1067.1263 Evaluate side-chains 1182 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 976 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 60 CYS Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 47 ASP Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 31 LYS Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain N residue 214 GLU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 80 CYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 117 CYS Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 157 GLU Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 247 GLN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 118 GLU Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 243 ILE Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 144 ASN Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain W residue 209 LYS Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 181 ARG Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 247 SER Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 313 ILE Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 155 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 495 optimal weight: 1.9990 chunk 337 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 443 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 508 optimal weight: 2.9990 chunk 411 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 304 optimal weight: 0.7980 chunk 534 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS B 117 GLN B 121 GLN B 187 HIS C 3 HIS C 239 HIS E 113 ASN G 64 ASN K 56 ASN K 72 GLN L 128 GLN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 180 ASN M 204 ASN N 185 GLN O 72 ASN P 61 GLN P 140 ASN P 205 ASN Q 103 HIS S 262 HIS ** S 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 328 HIS T 194 ASN T 225 GLN ** V 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 HIS ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50054 Z= 0.272 Angle : 0.557 9.782 67714 Z= 0.293 Chirality : 0.043 0.257 7544 Planarity : 0.004 0.051 8784 Dihedral : 7.147 88.535 7139 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.07 % Favored : 97.84 % Rotamer: Outliers : 5.06 % Allowed : 19.53 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 6290 helix: 1.29 (0.11), residues: 2336 sheet: -0.64 (0.13), residues: 1516 loop : -0.66 (0.12), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 185 HIS 0.015 0.001 HIS S 262 PHE 0.018 0.002 PHE K 8 TYR 0.025 0.001 TYR b 175 ARG 0.006 0.000 ARG G 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1264 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 999 time to evaluate : 4.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9206 (t80) cc_final: 0.8906 (t80) REVERT: A 41 CYS cc_start: 0.8193 (p) cc_final: 0.7979 (p) REVERT: A 61 ASP cc_start: 0.7855 (t70) cc_final: 0.7630 (t0) REVERT: A 70 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8592 (p) REVERT: A 75 CYS cc_start: 0.8386 (t) cc_final: 0.8185 (t) REVERT: A 83 ASP cc_start: 0.8763 (m-30) cc_final: 0.8527 (m-30) REVERT: A 101 ARG cc_start: 0.8507 (ttm110) cc_final: 0.8290 (mtp85) REVERT: A 150 LYS cc_start: 0.8820 (tttt) cc_final: 0.8556 (ttpt) REVERT: A 223 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7520 (ttm-80) REVERT: B 118 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 167 ASP cc_start: 0.7218 (m-30) cc_final: 0.6850 (m-30) REVERT: B 175 ARG cc_start: 0.7551 (mmt-90) cc_final: 0.7047 (mmm160) REVERT: B 182 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8375 (tt) REVERT: B 197 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.5921 (t80) REVERT: B 205 ASN cc_start: 0.8304 (t0) cc_final: 0.7444 (t0) REVERT: C 60 SER cc_start: 0.8561 (m) cc_final: 0.8204 (t) REVERT: C 61 MET cc_start: 0.8000 (mmt) cc_final: 0.7703 (mmt) REVERT: C 76 GLU cc_start: 0.8807 (tt0) cc_final: 0.8334 (mm-30) REVERT: C 123 GLU cc_start: 0.7985 (tp30) cc_final: 0.7464 (tp30) REVERT: C 138 VAL cc_start: 0.9190 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 204 LYS cc_start: 0.8699 (tptt) cc_final: 0.8408 (tptp) REVERT: C 211 ILE cc_start: 0.8079 (mp) cc_final: 0.7697 (tp) REVERT: C 234 ASP cc_start: 0.7915 (t0) cc_final: 0.7543 (m-30) REVERT: D 4 ASP cc_start: 0.8293 (p0) cc_final: 0.7366 (m-30) REVERT: D 5 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7188 (ttm-80) REVERT: D 11 SER cc_start: 0.8407 (m) cc_final: 0.8096 (p) REVERT: D 17 PHE cc_start: 0.8429 (m-80) cc_final: 0.7934 (m-80) REVERT: D 28 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.7798 (mptt) REVERT: D 46 GLU cc_start: 0.8392 (pt0) cc_final: 0.7631 (tt0) REVERT: D 47 LYS cc_start: 0.8468 (mttt) cc_final: 0.7943 (mtmm) REVERT: D 61 LYS cc_start: 0.7811 (mptp) cc_final: 0.7275 (mtpp) REVERT: D 121 SER cc_start: 0.8517 (t) cc_final: 0.8264 (p) REVERT: D 147 THR cc_start: 0.9136 (m) cc_final: 0.8890 (m) REVERT: D 148 ASP cc_start: 0.8344 (p0) cc_final: 0.7999 (p0) REVERT: D 152 MET cc_start: 0.8073 (ttp) cc_final: 0.7621 (ttp) REVERT: D 188 PHE cc_start: 0.7921 (t80) cc_final: 0.7565 (t80) REVERT: D 205 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: D 232 GLU cc_start: 0.6929 (tt0) cc_final: 0.6535 (tm-30) REVERT: E 125 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7651 (tt0) REVERT: E 138 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8126 (pp) REVERT: E 164 MET cc_start: 0.7995 (ptp) cc_final: 0.7567 (ptm) REVERT: E 204 ASN cc_start: 0.8815 (t0) cc_final: 0.8299 (t0) REVERT: E 287 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: E 314 ASN cc_start: 0.7928 (t0) cc_final: 0.7334 (t0) REVERT: E 329 MET cc_start: 0.8206 (mmt) cc_final: 0.7899 (mmt) REVERT: F 170 TYR cc_start: 0.9058 (m-80) cc_final: 0.8781 (m-80) REVERT: F 173 ASP cc_start: 0.8525 (t0) cc_final: 0.7864 (m-30) REVERT: F 276 MET cc_start: 0.7466 (mtt) cc_final: 0.7200 (mtm) REVERT: F 350 ASP cc_start: 0.8158 (m-30) cc_final: 0.7818 (m-30) REVERT: F 387 THR cc_start: 0.8471 (p) cc_final: 0.8266 (p) REVERT: G 129 TYR cc_start: 0.9006 (m-80) cc_final: 0.8739 (m-80) REVERT: G 208 LEU cc_start: 0.8175 (mt) cc_final: 0.7668 (mp) REVERT: G 231 MET cc_start: 0.6348 (mtt) cc_final: 0.5747 (ttm) REVERT: H 74 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8963 (t) REVERT: H 137 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8923 (t80) REVERT: H 139 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8090 (mptt) REVERT: H 140 MET cc_start: 0.8301 (mtp) cc_final: 0.7974 (mtp) REVERT: H 254 LYS cc_start: 0.8516 (mttp) cc_final: 0.8169 (mtpt) REVERT: I 59 ARG cc_start: 0.7586 (mtm-85) cc_final: 0.7108 (mtm110) REVERT: I 61 ARG cc_start: 0.8210 (ttm110) cc_final: 0.7982 (ttm170) REVERT: I 209 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8316 (tppt) REVERT: I 225 MET cc_start: 0.5802 (mmm) cc_final: 0.5251 (mtt) REVERT: J 4 MET cc_start: 0.8289 (mmm) cc_final: 0.7980 (mmm) REVERT: J 12 MET cc_start: 0.8688 (tmm) cc_final: 0.8203 (ttp) REVERT: J 127 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8256 (mp) REVERT: J 203 ARG cc_start: 0.8372 (mtt-85) cc_final: 0.8049 (mmm160) REVERT: K 1 MET cc_start: 0.6930 (mmm) cc_final: 0.6261 (mmm) REVERT: K 70 MET cc_start: 0.7647 (mmp) cc_final: 0.7445 (mmt) REVERT: K 80 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7795 (mp0) REVERT: K 97 ARG cc_start: 0.8579 (ptm-80) cc_final: 0.8228 (ttp-110) REVERT: K 131 TYR cc_start: 0.8642 (p90) cc_final: 0.8292 (p90) REVERT: K 159 ARG cc_start: 0.8441 (mtm110) cc_final: 0.7981 (ttm110) REVERT: K 165 GLN cc_start: 0.8154 (tp40) cc_final: 0.7385 (tp-100) REVERT: K 169 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6730 (mt-10) REVERT: L 160 MET cc_start: 0.9146 (ttm) cc_final: 0.8834 (ttt) REVERT: L 196 MET cc_start: 0.8585 (ptm) cc_final: 0.8291 (ptm) REVERT: L 281 LYS cc_start: 0.8786 (tppt) cc_final: 0.8264 (mptt) REVERT: M 198 LYS cc_start: 0.8517 (tttp) cc_final: 0.8016 (mtpt) REVERT: M 338 LYS cc_start: 0.6335 (mmpt) cc_final: 0.5598 (mtpt) REVERT: N 64 GLU cc_start: 0.8234 (tt0) cc_final: 0.8003 (tt0) REVERT: N 68 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7968 (mp0) REVERT: N 153 ASN cc_start: 0.8827 (m-40) cc_final: 0.8391 (m110) REVERT: N 155 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7509 (t0) REVERT: N 205 HIS cc_start: 0.8233 (t70) cc_final: 0.7433 (m90) REVERT: O 23 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7368 (tt0) REVERT: O 101 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7905 (mtp-110) REVERT: O 122 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8959 (mtp85) REVERT: O 182 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7649 (mt-10) REVERT: O 223 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8694 (ttp-170) REVERT: O 232 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7979 (mt0) REVERT: P 16 LYS cc_start: 0.8658 (ptmt) cc_final: 0.8130 (mmtm) REVERT: P 84 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.7946 (mm) REVERT: P 154 TRP cc_start: 0.7974 (m100) cc_final: 0.7416 (m-90) REVERT: P 175 ARG cc_start: 0.7987 (mmt-90) cc_final: 0.7746 (mmm160) REVERT: P 181 GLU cc_start: 0.7599 (mt-10) cc_final: 0.6835 (mp0) REVERT: P 204 GLU cc_start: 0.8628 (mp0) cc_final: 0.8094 (mp0) REVERT: Q 8 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7744 (mtm180) REVERT: Q 41 ASP cc_start: 0.7300 (m-30) cc_final: 0.6930 (t0) REVERT: Q 71 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.7298 (mmt) REVERT: Q 76 GLU cc_start: 0.8537 (pm20) cc_final: 0.8329 (mm-30) REVERT: Q 161 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.7758 (t70) REVERT: Q 175 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7876 (mm-40) REVERT: R 11 SER cc_start: 0.8595 (m) cc_final: 0.8124 (p) REVERT: R 17 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: R 24 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: R 27 LYS cc_start: 0.8340 (mmmm) cc_final: 0.8087 (mmmm) REVERT: R 177 LYS cc_start: 0.7534 (mtpm) cc_final: 0.6916 (mmmt) REVERT: R 180 MET cc_start: 0.7937 (mtt) cc_final: 0.7729 (mtt) REVERT: R 206 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8074 (pp) REVERT: R 211 TYR cc_start: 0.8026 (t80) cc_final: 0.7642 (t80) REVERT: R 212 LYS cc_start: 0.8567 (mptp) cc_final: 0.7814 (tppt) REVERT: R 213 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6913 (mp0) REVERT: R 215 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7760 (ttm110) REVERT: S 164 MET cc_start: 0.8084 (ptp) cc_final: 0.7398 (ppp) REVERT: S 178 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (ptp) REVERT: S 186 ARG cc_start: 0.8603 (mmt90) cc_final: 0.8356 (mpt-90) REVERT: S 321 ARG cc_start: 0.8345 (mtp-110) cc_final: 0.8077 (mmm-85) REVERT: T 230 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (tt0) REVERT: U 51 GLU cc_start: 0.8286 (pt0) cc_final: 0.7959 (pt0) REVERT: U 221 ASP cc_start: 0.8405 (t0) cc_final: 0.8158 (t0) REVERT: V 140 MET cc_start: 0.8631 (mtp) cc_final: 0.8372 (mtp) REVERT: V 212 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8213 (ttp80) REVERT: W 51 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7058 (pt0) REVERT: W 87 MET cc_start: 0.7845 (ttm) cc_final: 0.7597 (ttm) REVERT: W 186 SER cc_start: 0.9212 (t) cc_final: 0.8818 (p) REVERT: W 209 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8566 (tppt) REVERT: W 222 ASN cc_start: 0.8550 (m-40) cc_final: 0.8169 (m-40) REVERT: W 226 TYR cc_start: 0.7325 (t80) cc_final: 0.6915 (t80) REVERT: X 12 MET cc_start: 0.8882 (tmm) cc_final: 0.8354 (tmm) REVERT: X 33 LYS cc_start: 0.8609 (ptpt) cc_final: 0.8348 (ptpp) REVERT: X 85 LYS cc_start: 0.8790 (mptt) cc_final: 0.8395 (mtpp) REVERT: X 106 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8323 (mt-10) REVERT: X 111 SER cc_start: 0.8974 (p) cc_final: 0.8718 (t) REVERT: X 134 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7487 (mm-30) REVERT: X 194 LYS cc_start: 0.8343 (pttm) cc_final: 0.7948 (pttm) REVERT: Y 30 THR cc_start: 0.8584 (t) cc_final: 0.8172 (p) REVERT: Y 56 ASN cc_start: 0.8545 (m-40) cc_final: 0.8212 (m110) REVERT: Y 70 MET cc_start: 0.7782 (OUTLIER) cc_final: 0.7328 (mpp) REVERT: Y 168 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8200 (mt) REVERT: Z 139 TYR cc_start: 0.7145 (m-80) cc_final: 0.6915 (m-80) REVERT: Z 155 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: Z 160 MET cc_start: 0.8691 (ttp) cc_final: 0.8391 (ttp) REVERT: Z 161 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8453 (mm-30) REVERT: Z 190 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7614 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6938 (mp) REVERT: Z 235 TYR cc_start: 0.8670 (m-80) cc_final: 0.7874 (m-80) REVERT: a 142 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7405 (tptp) REVERT: a 193 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8591 (tt) REVERT: a 251 ASP cc_start: 0.8452 (p0) cc_final: 0.8127 (p0) REVERT: a 301 LEU cc_start: 0.9051 (mt) cc_final: 0.8809 (mt) REVERT: a 331 GLN cc_start: 0.7928 (pt0) cc_final: 0.7458 (tt0) REVERT: b 64 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7745 (mt-10) REVERT: b 65 ASP cc_start: 0.8536 (m-30) cc_final: 0.8053 (m-30) REVERT: b 122 ASP cc_start: 0.8667 (t0) cc_final: 0.8339 (t0) REVERT: b 123 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8472 (p0) REVERT: b 151 GLU cc_start: 0.8520 (tt0) cc_final: 0.8229 (mm-30) REVERT: b 155 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7599 (m-30) REVERT: b 195 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8482 (ttm110) outliers start: 265 outliers final: 168 residues processed: 1188 average time/residue: 0.5371 time to fit residues: 1044.1337 Evaluate side-chains 1128 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 922 time to evaluate : 4.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 96 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 197 PHE Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain I residue 53 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 117 ASP Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 191 ASN Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain N residue 155 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 58 MET Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 132 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 80 CYS Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 161 ASP Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 223 LYS Chi-restraints excluded: chain Q residue 247 GLN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 243 ILE Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 203 LYS Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 374 ASN Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 209 LYS Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 41 LYS Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 240 THR Chi-restraints excluded: chain Z residue 247 SER Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 193 LEU Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 226 ARG Chi-restraints excluded: chain a residue 247 CYS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 313 ILE Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 155 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 200 optimal weight: 0.8980 chunk 536 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 349 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 596 optimal weight: 1.9990 chunk 494 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 312 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS C 3 HIS C 53 HIS C 178 HIS E 113 ASN F 206 ASN K 22 ASN K 72 GLN L 291 GLN M 130 GLN M 224 HIS N 185 GLN O 72 ASN P 61 GLN P 205 ASN S 262 HIS S 309 GLN T 194 ASN V 86 ASN W 91 HIS W 166 GLN ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 50054 Z= 0.190 Angle : 0.528 8.751 67714 Z= 0.278 Chirality : 0.042 0.258 7544 Planarity : 0.004 0.053 8784 Dihedral : 6.669 87.716 7109 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.78 % Favored : 98.16 % Rotamer: Outliers : 4.31 % Allowed : 21.04 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.10), residues: 6290 helix: 1.54 (0.11), residues: 2330 sheet: -0.50 (0.13), residues: 1508 loop : -0.54 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 185 HIS 0.015 0.001 HIS S 262 PHE 0.025 0.001 PHE Z 225 TYR 0.033 0.001 TYR b 12 ARG 0.008 0.000 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1248 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1022 time to evaluate : 4.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9205 (t80) cc_final: 0.8933 (t80) REVERT: A 41 CYS cc_start: 0.8175 (p) cc_final: 0.7943 (p) REVERT: A 61 ASP cc_start: 0.7869 (t70) cc_final: 0.7640 (t0) REVERT: A 70 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8525 (p) REVERT: A 83 ASP cc_start: 0.8785 (m-30) cc_final: 0.8490 (m-30) REVERT: A 101 ARG cc_start: 0.8489 (ttm110) cc_final: 0.8286 (mtp85) REVERT: A 150 LYS cc_start: 0.8820 (tttt) cc_final: 0.8589 (ttpt) REVERT: A 223 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7421 (ttm-80) REVERT: A 225 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8487 (m) REVERT: B 167 ASP cc_start: 0.7358 (m-30) cc_final: 0.7035 (m-30) REVERT: B 175 ARG cc_start: 0.7673 (mmt-90) cc_final: 0.7125 (mmm160) REVERT: B 182 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 205 ASN cc_start: 0.8254 (t0) cc_final: 0.7568 (t0) REVERT: B 217 GLU cc_start: 0.8205 (pt0) cc_final: 0.7820 (mt-10) REVERT: C 60 SER cc_start: 0.8523 (m) cc_final: 0.8179 (t) REVERT: C 76 GLU cc_start: 0.8755 (tt0) cc_final: 0.8261 (mm-30) REVERT: C 138 VAL cc_start: 0.9164 (OUTLIER) cc_final: 0.8927 (p) REVERT: D 4 ASP cc_start: 0.8306 (p0) cc_final: 0.7372 (m-30) REVERT: D 11 SER cc_start: 0.8445 (m) cc_final: 0.8199 (p) REVERT: D 17 PHE cc_start: 0.8396 (m-80) cc_final: 0.8024 (m-80) REVERT: D 28 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7762 (mptt) REVERT: D 46 GLU cc_start: 0.8338 (pt0) cc_final: 0.7582 (tt0) REVERT: D 47 LYS cc_start: 0.8370 (mttt) cc_final: 0.7901 (mtmm) REVERT: D 61 LYS cc_start: 0.7846 (mptp) cc_final: 0.7327 (mtpp) REVERT: D 121 SER cc_start: 0.8480 (t) cc_final: 0.8242 (p) REVERT: D 147 THR cc_start: 0.9078 (m) cc_final: 0.8850 (m) REVERT: D 148 ASP cc_start: 0.8344 (p0) cc_final: 0.8033 (p0) REVERT: D 152 MET cc_start: 0.7991 (ttp) cc_final: 0.7575 (ttp) REVERT: D 205 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7853 (tp30) REVERT: D 232 GLU cc_start: 0.6934 (tt0) cc_final: 0.6330 (tm-30) REVERT: E 125 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: E 138 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8171 (pp) REVERT: E 164 MET cc_start: 0.7978 (ptp) cc_final: 0.7532 (ptm) REVERT: E 287 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7578 (ttm-80) REVERT: E 314 ASN cc_start: 0.7936 (t0) cc_final: 0.7268 (t0) REVERT: E 329 MET cc_start: 0.8184 (mmt) cc_final: 0.7853 (mmt) REVERT: F 170 TYR cc_start: 0.9041 (m-80) cc_final: 0.8788 (m-80) REVERT: F 173 ASP cc_start: 0.8505 (t0) cc_final: 0.7791 (m-30) REVERT: F 276 MET cc_start: 0.7459 (mtt) cc_final: 0.7180 (mtm) REVERT: F 387 THR cc_start: 0.8420 (p) cc_final: 0.8208 (p) REVERT: G 129 TYR cc_start: 0.8973 (m-80) cc_final: 0.8752 (m-80) REVERT: G 208 LEU cc_start: 0.8214 (mt) cc_final: 0.7714 (mp) REVERT: G 231 MET cc_start: 0.6418 (mtt) cc_final: 0.5830 (ttm) REVERT: H 74 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8859 (t) REVERT: H 137 PHE cc_start: 0.9333 (OUTLIER) cc_final: 0.8913 (t80) REVERT: H 139 LYS cc_start: 0.8431 (ttmm) cc_final: 0.8096 (mptt) REVERT: H 254 LYS cc_start: 0.8506 (mttp) cc_final: 0.8153 (mtpt) REVERT: I 59 ARG cc_start: 0.7551 (mtm-85) cc_final: 0.7151 (mtm110) REVERT: I 61 ARG cc_start: 0.8177 (ttm110) cc_final: 0.7943 (ttm170) REVERT: I 117 TYR cc_start: 0.9076 (t80) cc_final: 0.8853 (t80) REVERT: I 209 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8253 (tppt) REVERT: J 12 MET cc_start: 0.8674 (tmm) cc_final: 0.7833 (ttp) REVERT: J 78 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7852 (mt-10) REVERT: J 203 ARG cc_start: 0.8335 (mtt-85) cc_final: 0.8027 (mmm160) REVERT: K 1 MET cc_start: 0.6936 (mmm) cc_final: 0.6382 (mmm) REVERT: K 80 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7820 (mp0) REVERT: K 97 ARG cc_start: 0.8565 (ptm-80) cc_final: 0.8137 (ttp-110) REVERT: K 131 TYR cc_start: 0.8681 (p90) cc_final: 0.8310 (p90) REVERT: K 159 ARG cc_start: 0.8447 (mtm110) cc_final: 0.7960 (ttm110) REVERT: K 165 GLN cc_start: 0.8108 (tp40) cc_final: 0.7638 (tp-100) REVERT: L 160 MET cc_start: 0.9144 (ttm) cc_final: 0.8864 (ttt) REVERT: L 196 MET cc_start: 0.8607 (ptm) cc_final: 0.8286 (ptm) REVERT: L 281 LYS cc_start: 0.8746 (tppt) cc_final: 0.8165 (mptt) REVERT: M 185 ASP cc_start: 0.8629 (m-30) cc_final: 0.8189 (m-30) REVERT: M 198 LYS cc_start: 0.8479 (tttp) cc_final: 0.8015 (tttt) REVERT: M 338 LYS cc_start: 0.6158 (mmpt) cc_final: 0.5440 (mtpt) REVERT: N 64 GLU cc_start: 0.8243 (tt0) cc_final: 0.7929 (tt0) REVERT: N 68 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: N 106 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7532 (mmt) REVERT: N 135 THR cc_start: 0.8896 (p) cc_final: 0.8635 (p) REVERT: N 153 ASN cc_start: 0.8762 (m-40) cc_final: 0.8369 (m110) REVERT: N 205 HIS cc_start: 0.8165 (t70) cc_final: 0.7341 (m90) REVERT: O 23 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7417 (tt0) REVERT: O 83 ASP cc_start: 0.8828 (m-30) cc_final: 0.8436 (m-30) REVERT: O 101 ARG cc_start: 0.8307 (ttm110) cc_final: 0.7862 (mtp-110) REVERT: O 122 ARG cc_start: 0.9262 (OUTLIER) cc_final: 0.8979 (mtp85) REVERT: O 182 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7624 (mt-10) REVERT: O 223 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8694 (ttp-170) REVERT: O 232 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7980 (mt0) REVERT: P 16 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8111 (mmtm) REVERT: P 84 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7842 (mm) REVERT: P 154 TRP cc_start: 0.7940 (m100) cc_final: 0.7387 (m-90) REVERT: P 175 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7746 (mmm160) REVERT: P 181 GLU cc_start: 0.7516 (mt-10) cc_final: 0.6771 (mp0) REVERT: P 204 GLU cc_start: 0.8620 (mp0) cc_final: 0.8088 (mp0) REVERT: Q 8 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7732 (mtm180) REVERT: Q 41 ASP cc_start: 0.7098 (m-30) cc_final: 0.6749 (t0) REVERT: Q 71 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7207 (mmt) REVERT: R 11 SER cc_start: 0.8542 (m) cc_final: 0.8110 (p) REVERT: R 17 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: R 24 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7318 (mt-10) REVERT: R 90 GLU cc_start: 0.8296 (tp30) cc_final: 0.7978 (tp30) REVERT: R 93 ARG cc_start: 0.8759 (tmm160) cc_final: 0.8477 (ttt-90) REVERT: R 177 LYS cc_start: 0.7548 (mtpm) cc_final: 0.6951 (mmmt) REVERT: R 202 ARG cc_start: 0.5324 (OUTLIER) cc_final: 0.4212 (ptp-110) REVERT: R 206 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8058 (pp) REVERT: R 212 LYS cc_start: 0.8501 (mptp) cc_final: 0.7997 (tppt) REVERT: R 213 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6908 (pt0) REVERT: R 215 ARG cc_start: 0.8377 (ttp-170) cc_final: 0.7709 (ttm110) REVERT: S 178 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7809 (ptp) REVERT: S 186 ARG cc_start: 0.8593 (mmt90) cc_final: 0.8335 (mpt-90) REVERT: S 207 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8735 (ttm) REVERT: S 268 GLN cc_start: 0.8423 (tp40) cc_final: 0.8166 (tp-100) REVERT: T 230 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: U 51 GLU cc_start: 0.8282 (pt0) cc_final: 0.7956 (pt0) REVERT: V 140 MET cc_start: 0.8587 (mtp) cc_final: 0.8310 (mtp) REVERT: V 212 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: W 38 ARG cc_start: 0.8924 (ptp-170) cc_final: 0.8353 (ttm110) REVERT: W 51 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6998 (pt0) REVERT: W 87 MET cc_start: 0.7769 (ttm) cc_final: 0.7529 (ttm) REVERT: W 120 GLN cc_start: 0.8838 (mp10) cc_final: 0.8634 (mp10) REVERT: W 222 ASN cc_start: 0.8533 (m-40) cc_final: 0.8116 (m-40) REVERT: W 226 TYR cc_start: 0.7391 (t80) cc_final: 0.7114 (t80) REVERT: X 12 MET cc_start: 0.8844 (tmm) cc_final: 0.8342 (tmm) REVERT: X 33 LYS cc_start: 0.8550 (ptpt) cc_final: 0.8303 (ptpp) REVERT: X 85 LYS cc_start: 0.8758 (mptt) cc_final: 0.8380 (mtpp) REVERT: X 106 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8253 (mt-10) REVERT: X 111 SER cc_start: 0.8927 (p) cc_final: 0.8674 (t) REVERT: X 134 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7419 (mm-30) REVERT: Y 30 THR cc_start: 0.8582 (t) cc_final: 0.8192 (p) REVERT: Y 56 ASN cc_start: 0.8519 (m-40) cc_final: 0.8200 (m110) REVERT: Y 70 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.6998 (mpp) REVERT: Y 168 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8072 (mt) REVERT: Z 117 SER cc_start: 0.8863 (p) cc_final: 0.8438 (p) REVERT: Z 155 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: Z 160 MET cc_start: 0.8670 (ttp) cc_final: 0.8406 (ttp) REVERT: Z 161 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8419 (mm-30) REVERT: Z 190 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7445 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6838 (mp) REVERT: Z 235 TYR cc_start: 0.8628 (m-80) cc_final: 0.7756 (m-80) REVERT: a 142 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7382 (tptp) REVERT: a 269 SER cc_start: 0.9012 (m) cc_final: 0.8741 (p) REVERT: a 275 LEU cc_start: 0.8851 (mt) cc_final: 0.8595 (mt) REVERT: a 301 LEU cc_start: 0.8994 (mt) cc_final: 0.8761 (mt) REVERT: a 331 GLN cc_start: 0.7895 (pt0) cc_final: 0.7455 (tt0) REVERT: b 64 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7699 (mt-10) REVERT: b 65 ASP cc_start: 0.8513 (m-30) cc_final: 0.8000 (m-30) REVERT: b 122 ASP cc_start: 0.8664 (t0) cc_final: 0.8292 (t0) REVERT: b 123 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8430 (p0) REVERT: b 195 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8515 (ttm110) outliers start: 226 outliers final: 138 residues processed: 1175 average time/residue: 0.5078 time to fit residues: 972.2024 Evaluate side-chains 1127 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 954 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 291 GLN Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 MET Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 223 LYS Chi-restraints excluded: chain Q residue 247 GLN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 207 MET Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 163 HIS Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 123 ASP Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 155 ASP Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 574 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 435 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 501 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 593 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 361 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 187 HIS B 214 ASN C 3 HIS D 164 HIS E 304 GLN G 64 ASN G 121 HIS H 264 GLN ** J 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN K 76 HIS L 128 GLN M 180 ASN O 72 ASN P 61 GLN P 205 ASN Q 152 GLN R 210 GLN S 262 HIS ** S 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 194 ASN U 121 HIS V 147 ASN W 91 HIS ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 50054 Z= 0.372 Angle : 0.596 10.477 67714 Z= 0.312 Chirality : 0.045 0.328 7544 Planarity : 0.004 0.067 8784 Dihedral : 6.555 85.405 7085 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.34 % Favored : 97.58 % Rotamer: Outliers : 5.10 % Allowed : 20.48 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.10), residues: 6290 helix: 1.39 (0.11), residues: 2336 sheet: -0.53 (0.13), residues: 1478 loop : -0.62 (0.12), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP O 161 HIS 0.014 0.001 HIS S 262 PHE 0.025 0.002 PHE K 8 TYR 0.032 0.002 TYR J 74 ARG 0.014 0.001 ARG I 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1225 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 958 time to evaluate : 4.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9237 (t80) cc_final: 0.9023 (t80) REVERT: A 41 CYS cc_start: 0.8208 (p) cc_final: 0.7976 (p) REVERT: A 61 ASP cc_start: 0.7882 (t70) cc_final: 0.7659 (t0) REVERT: A 70 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8639 (p) REVERT: A 83 ASP cc_start: 0.8807 (m-30) cc_final: 0.8551 (m-30) REVERT: A 101 ARG cc_start: 0.8543 (ttm110) cc_final: 0.8328 (mtp85) REVERT: A 150 LYS cc_start: 0.8813 (tttt) cc_final: 0.8574 (ttpt) REVERT: A 223 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7483 (ttm-80) REVERT: B 118 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8019 (mt-10) REVERT: B 167 ASP cc_start: 0.7349 (m-30) cc_final: 0.7084 (m-30) REVERT: B 175 ARG cc_start: 0.7712 (mmt-90) cc_final: 0.7125 (mmm160) REVERT: B 182 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8390 (tt) REVERT: B 205 ASN cc_start: 0.8350 (t0) cc_final: 0.7629 (t0) REVERT: C 60 SER cc_start: 0.8444 (m) cc_final: 0.8061 (t) REVERT: C 76 GLU cc_start: 0.8868 (tt0) cc_final: 0.8423 (mm-30) REVERT: C 123 GLU cc_start: 0.7975 (tp30) cc_final: 0.7428 (tp30) REVERT: C 138 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8992 (p) REVERT: C 234 ASP cc_start: 0.7909 (t0) cc_final: 0.7602 (m-30) REVERT: D 4 ASP cc_start: 0.8325 (p0) cc_final: 0.7481 (m-30) REVERT: D 11 SER cc_start: 0.8590 (m) cc_final: 0.8289 (p) REVERT: D 17 PHE cc_start: 0.8514 (m-80) cc_final: 0.8015 (m-80) REVERT: D 61 LYS cc_start: 0.7791 (mptp) cc_final: 0.7425 (tttm) REVERT: D 147 THR cc_start: 0.9207 (m) cc_final: 0.8970 (m) REVERT: D 148 ASP cc_start: 0.8474 (p0) cc_final: 0.8114 (p0) REVERT: D 152 MET cc_start: 0.8121 (ttp) cc_final: 0.7700 (ttp) REVERT: D 205 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: E 125 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: E 138 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8242 (pp) REVERT: E 164 MET cc_start: 0.8025 (ptp) cc_final: 0.7593 (ptm) REVERT: E 204 ASN cc_start: 0.8855 (t0) cc_final: 0.8378 (t0) REVERT: E 329 MET cc_start: 0.8239 (mmt) cc_final: 0.7898 (mmt) REVERT: F 170 TYR cc_start: 0.9074 (m-80) cc_final: 0.8777 (m-80) REVERT: F 173 ASP cc_start: 0.8562 (t0) cc_final: 0.7842 (m-30) REVERT: F 276 MET cc_start: 0.7493 (mtt) cc_final: 0.7223 (mtm) REVERT: F 326 MET cc_start: 0.8085 (ptm) cc_final: 0.7642 (ttp) REVERT: G 23 GLN cc_start: 0.8462 (mm-40) cc_final: 0.8259 (tp40) REVERT: G 114 ASN cc_start: 0.8637 (m-40) cc_final: 0.8198 (m-40) REVERT: G 208 LEU cc_start: 0.8267 (mt) cc_final: 0.7736 (mp) REVERT: H 74 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8911 (t) REVERT: H 137 PHE cc_start: 0.9320 (OUTLIER) cc_final: 0.8982 (t80) REVERT: H 139 LYS cc_start: 0.8486 (ttmm) cc_final: 0.8118 (mptt) REVERT: H 140 MET cc_start: 0.8426 (mmm) cc_final: 0.7981 (mmt) REVERT: H 254 LYS cc_start: 0.8606 (mttp) cc_final: 0.8118 (mtpt) REVERT: I 59 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7179 (mtm110) REVERT: I 61 ARG cc_start: 0.8262 (ttm110) cc_final: 0.8017 (ttm170) REVERT: I 117 TYR cc_start: 0.9070 (t80) cc_final: 0.8841 (t80) REVERT: I 175 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7686 (ttm) REVERT: I 209 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (tppt) REVERT: I 225 MET cc_start: 0.5943 (mtt) cc_final: 0.5463 (mtt) REVERT: J 12 MET cc_start: 0.8682 (tmm) cc_final: 0.7869 (ttp) REVERT: J 78 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7855 (mt-10) REVERT: K 1 MET cc_start: 0.7009 (mmm) cc_final: 0.6413 (mmm) REVERT: K 80 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7856 (mp0) REVERT: K 97 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.8182 (ttp-110) REVERT: K 131 TYR cc_start: 0.8680 (p90) cc_final: 0.8308 (p90) REVERT: K 159 ARG cc_start: 0.8474 (mtm110) cc_final: 0.8048 (ttm110) REVERT: K 165 GLN cc_start: 0.8132 (tp40) cc_final: 0.7656 (tp-100) REVERT: L 137 ASN cc_start: 0.6714 (OUTLIER) cc_final: 0.6349 (m-40) REVERT: L 160 MET cc_start: 0.9146 (ttm) cc_final: 0.8806 (ttt) REVERT: L 196 MET cc_start: 0.8556 (ptm) cc_final: 0.8233 (ptm) REVERT: L 281 LYS cc_start: 0.8780 (tppt) cc_final: 0.8249 (mptt) REVERT: M 185 ASP cc_start: 0.8614 (m-30) cc_final: 0.8218 (m-30) REVERT: M 338 LYS cc_start: 0.6458 (mmpt) cc_final: 0.5497 (mtpt) REVERT: N 64 GLU cc_start: 0.8205 (tt0) cc_final: 0.7853 (tt0) REVERT: N 66 ASN cc_start: 0.9140 (t0) cc_final: 0.8865 (t0) REVERT: N 68 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: N 106 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7627 (mmt) REVERT: N 153 ASN cc_start: 0.8693 (m-40) cc_final: 0.8262 (m110) REVERT: O 23 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7435 (tt0) REVERT: O 101 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7871 (mtp-110) REVERT: O 122 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.8960 (mtp85) REVERT: O 223 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8682 (ttp-170) REVERT: O 232 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7972 (mt0) REVERT: P 16 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8172 (mmtm) REVERT: P 98 MET cc_start: 0.8629 (tpp) cc_final: 0.8425 (tpp) REVERT: P 154 TRP cc_start: 0.7853 (m100) cc_final: 0.7306 (m-90) REVERT: P 175 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7622 (mtp85) REVERT: P 181 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6807 (mp0) REVERT: P 204 GLU cc_start: 0.8647 (mp0) cc_final: 0.8107 (mp0) REVERT: Q 8 ARG cc_start: 0.8069 (mtp180) cc_final: 0.7727 (mtm180) REVERT: Q 41 ASP cc_start: 0.7104 (m-30) cc_final: 0.6723 (t0) REVERT: Q 71 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7418 (mmt) REVERT: R 11 SER cc_start: 0.8631 (m) cc_final: 0.8210 (p) REVERT: R 17 PHE cc_start: 0.8668 (OUTLIER) cc_final: 0.7938 (m-80) REVERT: R 24 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7378 (mt-10) REVERT: R 103 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.7865 (p0) REVERT: R 177 LYS cc_start: 0.7394 (mtpm) cc_final: 0.6965 (mmmt) REVERT: R 202 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4205 (ptp-110) REVERT: R 206 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8253 (pp) REVERT: R 215 ARG cc_start: 0.8429 (ttp-170) cc_final: 0.7692 (ttm110) REVERT: S 164 MET cc_start: 0.8062 (ptp) cc_final: 0.7131 (ppp) REVERT: S 178 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7721 (ptp) REVERT: S 186 ARG cc_start: 0.8696 (mmt90) cc_final: 0.8431 (mpt-90) REVERT: S 257 ASP cc_start: 0.7914 (t0) cc_final: 0.7601 (t70) REVERT: S 324 ASP cc_start: 0.7461 (p0) cc_final: 0.6275 (t0) REVERT: T 230 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7816 (tt0) REVERT: U 34 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7971 (p) REVERT: U 51 GLU cc_start: 0.8332 (pt0) cc_final: 0.7982 (pt0) REVERT: U 221 ASP cc_start: 0.8363 (t0) cc_final: 0.7914 (t0) REVERT: V 137 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.8783 (t80) REVERT: V 212 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8252 (ttp80) REVERT: W 38 ARG cc_start: 0.9054 (ptp-170) cc_final: 0.8535 (ttm110) REVERT: W 87 MET cc_start: 0.7954 (ttm) cc_final: 0.7724 (ttm) REVERT: W 209 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8570 (tppt) REVERT: W 222 ASN cc_start: 0.8561 (m-40) cc_final: 0.8171 (m-40) REVERT: X 12 MET cc_start: 0.8918 (tmm) cc_final: 0.8398 (tmm) REVERT: X 33 LYS cc_start: 0.8648 (ptpt) cc_final: 0.8387 (ptpp) REVERT: X 85 LYS cc_start: 0.8837 (mptt) cc_final: 0.8424 (mtpp) REVERT: X 106 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8259 (mt-10) REVERT: X 111 SER cc_start: 0.9042 (p) cc_final: 0.8775 (t) REVERT: X 125 ASP cc_start: 0.8681 (OUTLIER) cc_final: 0.8442 (p0) REVERT: X 134 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: Y 1 MET cc_start: 0.7069 (mmm) cc_final: 0.6516 (mmm) REVERT: Y 9 ARG cc_start: 0.8562 (ttp-110) cc_final: 0.7914 (ttp-170) REVERT: Y 30 THR cc_start: 0.8594 (t) cc_final: 0.8165 (p) REVERT: Y 56 ASN cc_start: 0.8587 (m-40) cc_final: 0.8252 (m110) REVERT: Y 70 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.6979 (mpp) REVERT: Y 168 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8083 (mt) REVERT: Y 169 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8075 (tt0) REVERT: Z 117 SER cc_start: 0.8876 (p) cc_final: 0.8438 (p) REVERT: Z 155 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: Z 190 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7519 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7083 (mp) REVERT: Z 235 TYR cc_start: 0.8667 (m-80) cc_final: 0.7707 (m-80) REVERT: a 142 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7385 (tptp) REVERT: a 226 ARG cc_start: 0.8258 (ptm-80) cc_final: 0.8019 (ptm-80) REVERT: a 251 ASP cc_start: 0.8475 (p0) cc_final: 0.8159 (p0) REVERT: a 314 TYR cc_start: 0.8525 (m-80) cc_final: 0.8099 (m-80) REVERT: a 331 GLN cc_start: 0.7883 (pt0) cc_final: 0.7391 (tt0) REVERT: b 64 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7714 (mt-10) REVERT: b 195 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8540 (ttm110) outliers start: 267 outliers final: 185 residues processed: 1147 average time/residue: 0.5029 time to fit residues: 945.9993 Evaluate side-chains 1146 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 924 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 304 GLN Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 328 HIS Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 248 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 14 MET Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 137 ASN Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 253 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 MET Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain N residue 143 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 64 THR Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 155 THR Chi-restraints excluded: chain O residue 191 ASP Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 163 THR Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 19 TYR Chi-restraints excluded: chain Q residue 51 VAL Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 119 ILE Chi-restraints excluded: chain Q residue 142 LEU Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 188 SER Chi-restraints excluded: chain Q residue 223 LYS Chi-restraints excluded: chain Q residue 247 GLN Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 240 SER Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain S residue 333 THR Chi-restraints excluded: chain T residue 203 LYS Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 235 VAL Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain T residue 368 ILE Chi-restraints excluded: chain T residue 374 ASN Chi-restraints excluded: chain T residue 384 THR Chi-restraints excluded: chain U residue 34 SER Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 115 ARG Chi-restraints excluded: chain U residue 140 SER Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 144 ASN Chi-restraints excluded: chain V residue 147 ASN Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 230 THR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 209 LYS Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 125 ASP Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 130 ASP Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 247 SER Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 163 HIS Chi-restraints excluded: chain a residue 164 ASP Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 310 GLU Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 78 GLU Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 367 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 354 optimal weight: 0.0980 chunk 178 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 377 optimal weight: 0.6980 chunk 404 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 466 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 187 HIS C 3 HIS G 64 ASN I 194 ASN K 72 GLN L 108 ASN ** L 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 204 ASN O 72 ASN ** O 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN P 205 ASN S 262 HIS ** S 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 194 ASN V 246 ASN ** V 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 91 HIS X 147 HIS ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 50054 Z= 0.172 Angle : 0.531 11.218 67714 Z= 0.279 Chirality : 0.042 0.247 7544 Planarity : 0.004 0.052 8784 Dihedral : 6.248 84.371 7078 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.72 % Favored : 98.24 % Rotamer: Outliers : 3.80 % Allowed : 21.69 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.11), residues: 6290 helix: 1.67 (0.11), residues: 2330 sheet: -0.38 (0.13), residues: 1506 loop : -0.53 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP V 146 HIS 0.015 0.001 HIS S 262 PHE 0.013 0.001 PHE Z 225 TYR 0.028 0.001 TYR b 175 ARG 0.009 0.000 ARG J 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1219 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1020 time to evaluate : 4.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9218 (t80) cc_final: 0.8965 (t80) REVERT: A 41 CYS cc_start: 0.8214 (p) cc_final: 0.7936 (p) REVERT: A 61 ASP cc_start: 0.7869 (t70) cc_final: 0.7662 (t0) REVERT: A 70 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8526 (p) REVERT: A 83 ASP cc_start: 0.8739 (m-30) cc_final: 0.8515 (m-30) REVERT: A 223 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7313 (ttm-80) REVERT: A 225 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8499 (m) REVERT: A 232 GLN cc_start: 0.7739 (mm-40) cc_final: 0.7494 (mp10) REVERT: B 167 ASP cc_start: 0.7343 (m-30) cc_final: 0.7097 (m-30) REVERT: B 175 ARG cc_start: 0.7643 (mmt-90) cc_final: 0.7067 (mmm160) REVERT: B 182 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 205 ASN cc_start: 0.8194 (t0) cc_final: 0.7479 (t0) REVERT: B 217 GLU cc_start: 0.8206 (pt0) cc_final: 0.7824 (mt-10) REVERT: C 60 SER cc_start: 0.8333 (m) cc_final: 0.8023 (t) REVERT: C 76 GLU cc_start: 0.8738 (tt0) cc_final: 0.8285 (mm-30) REVERT: C 234 ASP cc_start: 0.7918 (t0) cc_final: 0.7626 (m-30) REVERT: D 4 ASP cc_start: 0.8319 (p0) cc_final: 0.7520 (m-30) REVERT: D 11 SER cc_start: 0.8586 (m) cc_final: 0.8354 (p) REVERT: D 17 PHE cc_start: 0.8414 (m-10) cc_final: 0.7956 (m-80) REVERT: D 46 GLU cc_start: 0.8306 (pt0) cc_final: 0.7563 (tt0) REVERT: D 61 LYS cc_start: 0.7777 (mptp) cc_final: 0.7428 (tttm) REVERT: D 147 THR cc_start: 0.9105 (m) cc_final: 0.8901 (m) REVERT: D 148 ASP cc_start: 0.8391 (p0) cc_final: 0.8019 (p0) REVERT: D 172 MET cc_start: 0.7783 (mtm) cc_final: 0.7545 (mtp) REVERT: D 205 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7695 (tp30) REVERT: E 125 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: E 138 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8187 (pp) REVERT: E 164 MET cc_start: 0.7934 (ptp) cc_final: 0.7541 (ptm) REVERT: E 166 LYS cc_start: 0.8183 (mmmm) cc_final: 0.7937 (mmmm) REVERT: E 287 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7823 (ttm-80) REVERT: E 329 MET cc_start: 0.8198 (mmt) cc_final: 0.7861 (mmt) REVERT: F 170 TYR cc_start: 0.9034 (m-80) cc_final: 0.8774 (m-80) REVERT: F 173 ASP cc_start: 0.8511 (t0) cc_final: 0.7767 (m-30) REVERT: F 187 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: F 276 MET cc_start: 0.7450 (mtt) cc_final: 0.7179 (mtm) REVERT: G 23 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8157 (tp40) REVERT: G 208 LEU cc_start: 0.8235 (mt) cc_final: 0.7776 (mp) REVERT: H 74 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8756 (t) REVERT: H 137 PHE cc_start: 0.9324 (OUTLIER) cc_final: 0.8961 (t80) REVERT: H 139 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8069 (mptt) REVERT: H 140 MET cc_start: 0.8231 (mmm) cc_final: 0.7811 (mtp) REVERT: H 254 LYS cc_start: 0.8514 (mttp) cc_final: 0.8154 (mtpt) REVERT: I 59 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7068 (mtm110) REVERT: I 61 ARG cc_start: 0.8273 (ttm110) cc_final: 0.8020 (ttm170) REVERT: I 175 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7673 (ttm) REVERT: I 209 LYS cc_start: 0.8494 (tptt) cc_final: 0.8200 (tppt) REVERT: I 225 MET cc_start: 0.5997 (mtt) cc_final: 0.5556 (mtt) REVERT: J 12 MET cc_start: 0.8666 (tmm) cc_final: 0.8193 (ttp) REVERT: J 78 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: J 80 ARG cc_start: 0.9130 (ptt90) cc_final: 0.8832 (ptt90) REVERT: K 1 MET cc_start: 0.6952 (mmm) cc_final: 0.6321 (mmm) REVERT: K 80 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7863 (mp0) REVERT: K 97 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.7927 (ttp80) REVERT: K 98 GLU cc_start: 0.8001 (mp0) cc_final: 0.7555 (mt-10) REVERT: K 131 TYR cc_start: 0.8612 (p90) cc_final: 0.8217 (p90) REVERT: K 159 ARG cc_start: 0.8415 (mtm110) cc_final: 0.8010 (ttm110) REVERT: K 165 GLN cc_start: 0.7985 (tp40) cc_final: 0.7452 (tp-100) REVERT: L 141 LEU cc_start: 0.8911 (mt) cc_final: 0.8683 (mt) REVERT: L 160 MET cc_start: 0.9150 (ttm) cc_final: 0.8919 (ttt) REVERT: L 172 ARG cc_start: 0.8659 (ttm-80) cc_final: 0.7020 (ttt90) REVERT: L 281 LYS cc_start: 0.8724 (tppt) cc_final: 0.8191 (mptt) REVERT: M 185 ASP cc_start: 0.8607 (m-30) cc_final: 0.8288 (m-30) REVERT: M 198 LYS cc_start: 0.8478 (tttp) cc_final: 0.7949 (mtpt) REVERT: M 201 LYS cc_start: 0.8261 (ttmt) cc_final: 0.8057 (ttmt) REVERT: M 338 LYS cc_start: 0.6262 (mmpt) cc_final: 0.5506 (mtpt) REVERT: N 66 ASN cc_start: 0.9179 (t0) cc_final: 0.8922 (t0) REVERT: N 68 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.7745 (mp0) REVERT: N 106 MET cc_start: 0.8325 (OUTLIER) cc_final: 0.7483 (mmt) REVERT: N 153 ASN cc_start: 0.8593 (m-40) cc_final: 0.8172 (m110) REVERT: N 205 HIS cc_start: 0.8344 (t70) cc_final: 0.7447 (m90) REVERT: O 23 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7393 (tt0) REVERT: O 101 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7815 (mtp-110) REVERT: O 122 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.8991 (mtp85) REVERT: O 138 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8965 (pt) REVERT: O 223 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8702 (ttp-170) REVERT: O 232 GLN cc_start: 0.8334 (mm-40) cc_final: 0.7985 (mt0) REVERT: P 16 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8077 (mmtm) REVERT: P 84 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7897 (mm) REVERT: P 154 TRP cc_start: 0.7847 (m100) cc_final: 0.7286 (m-90) REVERT: P 175 ARG cc_start: 0.7864 (mmt-90) cc_final: 0.7535 (mtp85) REVERT: P 180 MET cc_start: 0.7667 (mtt) cc_final: 0.7367 (mtp) REVERT: P 181 GLU cc_start: 0.7505 (mt-10) cc_final: 0.6751 (mp0) REVERT: P 204 GLU cc_start: 0.8627 (mp0) cc_final: 0.8097 (mp0) REVERT: Q 8 ARG cc_start: 0.8052 (mtp180) cc_final: 0.7704 (mtm180) REVERT: Q 41 ASP cc_start: 0.7080 (m-30) cc_final: 0.6750 (t0) REVERT: Q 71 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7129 (mmt) REVERT: Q 161 ASP cc_start: 0.8697 (p0) cc_final: 0.7622 (t70) REVERT: R 11 SER cc_start: 0.8527 (m) cc_final: 0.8102 (p) REVERT: R 17 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7809 (m-80) REVERT: R 24 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7389 (mt-10) REVERT: R 27 LYS cc_start: 0.8328 (mmmm) cc_final: 0.8054 (mmmt) REVERT: R 90 GLU cc_start: 0.8198 (tp30) cc_final: 0.7863 (tp30) REVERT: R 93 ARG cc_start: 0.8734 (tmm160) cc_final: 0.8443 (ttt-90) REVERT: R 138 GLU cc_start: 0.7690 (tp30) cc_final: 0.6829 (tm-30) REVERT: R 177 LYS cc_start: 0.7383 (mtpm) cc_final: 0.7007 (mmmt) REVERT: R 202 ARG cc_start: 0.5251 (OUTLIER) cc_final: 0.4177 (ptp-110) REVERT: R 206 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8114 (pp) REVERT: R 212 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8215 (mmmt) REVERT: R 213 GLU cc_start: 0.7128 (mt-10) cc_final: 0.6836 (pt0) REVERT: R 215 ARG cc_start: 0.8361 (ttp-170) cc_final: 0.7585 (ttm110) REVERT: S 164 MET cc_start: 0.8041 (ptp) cc_final: 0.7172 (ppp) REVERT: S 178 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7823 (ptp) REVERT: S 186 ARG cc_start: 0.8603 (mmt90) cc_final: 0.8369 (mpt-90) REVERT: S 257 ASP cc_start: 0.7838 (t0) cc_final: 0.7488 (t70) REVERT: S 324 ASP cc_start: 0.7416 (p0) cc_final: 0.6212 (t0) REVERT: T 230 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: U 51 GLU cc_start: 0.8317 (pt0) cc_final: 0.7896 (pt0) REVERT: U 221 ASP cc_start: 0.8307 (t0) cc_final: 0.7840 (t0) REVERT: V 212 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8208 (ttp80) REVERT: W 38 ARG cc_start: 0.9044 (ptp-170) cc_final: 0.8497 (ttm110) REVERT: W 51 GLU cc_start: 0.7649 (pt0) cc_final: 0.7445 (pt0) REVERT: W 87 MET cc_start: 0.7848 (ttm) cc_final: 0.7584 (ttm) REVERT: W 222 ASN cc_start: 0.8483 (m-40) cc_final: 0.8067 (m-40) REVERT: X 12 MET cc_start: 0.8845 (tmm) cc_final: 0.8344 (tmm) REVERT: X 33 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8221 (ptpp) REVERT: X 85 LYS cc_start: 0.8803 (mptt) cc_final: 0.8384 (mtpp) REVERT: X 106 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8263 (mt-10) REVERT: X 111 SER cc_start: 0.8948 (p) cc_final: 0.8677 (t) REVERT: X 134 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: X 162 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7895 (mt-10) REVERT: Y 1 MET cc_start: 0.7232 (mmm) cc_final: 0.6681 (mmm) REVERT: Y 9 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.7737 (ttp-170) REVERT: Y 30 THR cc_start: 0.8530 (t) cc_final: 0.8170 (p) REVERT: Y 56 ASN cc_start: 0.8532 (m-40) cc_final: 0.8238 (m110) REVERT: Y 60 TYR cc_start: 0.9318 (t80) cc_final: 0.9018 (t80) REVERT: Y 168 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7998 (mt) REVERT: Y 169 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8057 (tt0) REVERT: Z 117 SER cc_start: 0.8880 (p) cc_final: 0.8393 (p) REVERT: Z 155 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8225 (mt-10) REVERT: Z 160 MET cc_start: 0.8507 (ttp) cc_final: 0.7827 (ttp) REVERT: Z 161 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8357 (mm-30) REVERT: Z 190 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7460 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6701 (mp) REVERT: Z 235 TYR cc_start: 0.8604 (m-80) cc_final: 0.7690 (m-80) REVERT: a 142 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7388 (tptp) REVERT: a 226 ARG cc_start: 0.8119 (ptm-80) cc_final: 0.7879 (ptm-80) REVERT: a 269 SER cc_start: 0.9029 (m) cc_final: 0.8752 (p) REVERT: a 275 LEU cc_start: 0.8867 (mt) cc_final: 0.8618 (mt) REVERT: a 301 LEU cc_start: 0.8981 (mt) cc_final: 0.8768 (mt) REVERT: a 314 TYR cc_start: 0.8477 (m-80) cc_final: 0.8180 (m-80) REVERT: a 331 GLN cc_start: 0.7840 (pt0) cc_final: 0.7469 (tt0) REVERT: b 64 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7716 (mt-10) outliers start: 199 outliers final: 128 residues processed: 1160 average time/residue: 0.5151 time to fit residues: 975.7963 Evaluate side-chains 1116 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 956 time to evaluate : 4.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 73 GLN Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 90 LYS Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 93 SER Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 59 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 135 GLU Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 68 GLU Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 MET Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 18 ILE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 80 CYS Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 241 LEU Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain T residue 208 VAL Chi-restraints excluded: chain T residue 230 GLU Chi-restraints excluded: chain T residue 384 THR Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 125 ASP Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 187 SER Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 163 HIS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 540 optimal weight: 0.9980 chunk 568 optimal weight: 0.0980 chunk 518 optimal weight: 0.9980 chunk 553 optimal weight: 0.7980 chunk 333 optimal weight: 5.9990 chunk 241 optimal weight: 0.6980 chunk 434 optimal weight: 0.6980 chunk 169 optimal weight: 6.9990 chunk 499 optimal weight: 4.9990 chunk 523 optimal weight: 0.9990 chunk 551 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 187 HIS C 3 HIS G 64 ASN H 241 GLN ** J 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN L 291 GLN O 72 ASN ** O 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 61 GLN P 117 GLN P 121 GLN P 205 ASN R 120 GLN S 262 HIS T 194 ASN V 266 GLN W 91 HIS ** Y 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 50054 Z= 0.172 Angle : 0.527 12.741 67714 Z= 0.275 Chirality : 0.042 0.244 7544 Planarity : 0.004 0.051 8784 Dihedral : 6.021 82.400 7069 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.76 % Favored : 98.22 % Rotamer: Outliers : 3.46 % Allowed : 22.05 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.11), residues: 6290 helix: 1.82 (0.11), residues: 2320 sheet: -0.32 (0.13), residues: 1528 loop : -0.45 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 161 HIS 0.015 0.001 HIS S 262 PHE 0.014 0.001 PHE Z 225 TYR 0.029 0.001 TYR J 96 ARG 0.012 0.000 ARG H 247 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1017 time to evaluate : 4.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.9204 (t80) cc_final: 0.8971 (t80) REVERT: A 41 CYS cc_start: 0.8214 (p) cc_final: 0.7928 (p) REVERT: A 61 ASP cc_start: 0.7860 (t70) cc_final: 0.7648 (t0) REVERT: A 70 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8491 (p) REVERT: A 83 ASP cc_start: 0.8768 (m-30) cc_final: 0.8533 (m-30) REVERT: A 223 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7380 (ttm-80) REVERT: A 225 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (m) REVERT: A 232 GLN cc_start: 0.7651 (mm-40) cc_final: 0.7444 (mp10) REVERT: B 77 MET cc_start: 0.8028 (mtt) cc_final: 0.7737 (mtt) REVERT: B 167 ASP cc_start: 0.7346 (m-30) cc_final: 0.7094 (m-30) REVERT: B 175 ARG cc_start: 0.7657 (mmt-90) cc_final: 0.7073 (mmm160) REVERT: B 182 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8362 (tt) REVERT: B 205 ASN cc_start: 0.8092 (t0) cc_final: 0.7603 (t0) REVERT: B 217 GLU cc_start: 0.8198 (pt0) cc_final: 0.7814 (mt-10) REVERT: C 60 SER cc_start: 0.8263 (m) cc_final: 0.7939 (t) REVERT: C 76 GLU cc_start: 0.8773 (tt0) cc_final: 0.8242 (mm-30) REVERT: D 4 ASP cc_start: 0.8277 (p0) cc_final: 0.7506 (m-30) REVERT: D 11 SER cc_start: 0.8596 (m) cc_final: 0.8378 (p) REVERT: D 17 PHE cc_start: 0.8383 (m-10) cc_final: 0.8064 (m-80) REVERT: D 46 GLU cc_start: 0.8278 (pt0) cc_final: 0.7578 (tt0) REVERT: D 61 LYS cc_start: 0.7762 (mptp) cc_final: 0.7407 (tttm) REVERT: D 148 ASP cc_start: 0.8424 (p0) cc_final: 0.8099 (p0) REVERT: D 152 MET cc_start: 0.8088 (ttp) cc_final: 0.7702 (ttp) REVERT: D 205 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 232 GLU cc_start: 0.6940 (tt0) cc_final: 0.6715 (tm-30) REVERT: E 125 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: E 138 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8253 (pp) REVERT: E 164 MET cc_start: 0.7954 (ptp) cc_final: 0.7553 (ptm) REVERT: E 166 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7927 (mmmm) REVERT: E 287 ARG cc_start: 0.7933 (ttm-80) cc_final: 0.7703 (ttm-80) REVERT: E 329 MET cc_start: 0.8155 (mmt) cc_final: 0.7774 (mmt) REVERT: F 170 TYR cc_start: 0.9024 (m-80) cc_final: 0.8730 (m-80) REVERT: F 173 ASP cc_start: 0.8442 (t0) cc_final: 0.7737 (m-30) REVERT: F 187 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: F 276 MET cc_start: 0.7451 (mtt) cc_final: 0.7181 (mtm) REVERT: G 23 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8145 (tp40) REVERT: G 208 LEU cc_start: 0.8194 (mt) cc_final: 0.7736 (mp) REVERT: H 74 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8731 (t) REVERT: H 137 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8952 (t80) REVERT: H 139 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8066 (mptt) REVERT: H 140 MET cc_start: 0.8203 (mmm) cc_final: 0.7854 (mmt) REVERT: H 198 LYS cc_start: 0.8368 (tptp) cc_final: 0.8082 (ttmt) REVERT: H 254 LYS cc_start: 0.8478 (mttp) cc_final: 0.8114 (mtpt) REVERT: H 264 GLN cc_start: 0.9135 (mm110) cc_final: 0.8837 (mm-40) REVERT: I 59 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7056 (mtm110) REVERT: I 61 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8003 (ttm170) REVERT: I 175 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: I 209 LYS cc_start: 0.8418 (tptt) cc_final: 0.8166 (tppt) REVERT: J 4 MET cc_start: 0.8494 (mmm) cc_final: 0.8108 (mmm) REVERT: J 12 MET cc_start: 0.8678 (tmm) cc_final: 0.8217 (ttp) REVERT: J 78 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7849 (mt-10) REVERT: K 1 MET cc_start: 0.6931 (mmm) cc_final: 0.6324 (mmm) REVERT: K 80 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7859 (mp0) REVERT: K 97 ARG cc_start: 0.8538 (ptm-80) cc_final: 0.7987 (ttp80) REVERT: K 98 GLU cc_start: 0.7943 (mp0) cc_final: 0.7570 (mt-10) REVERT: K 131 TYR cc_start: 0.8608 (p90) cc_final: 0.8222 (p90) REVERT: K 159 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8023 (ttm110) REVERT: L 141 LEU cc_start: 0.8910 (mt) cc_final: 0.8669 (mt) REVERT: L 160 MET cc_start: 0.9112 (ttm) cc_final: 0.8901 (ttt) REVERT: L 172 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.7062 (ttt90) REVERT: L 281 LYS cc_start: 0.8706 (tppt) cc_final: 0.8176 (mptt) REVERT: M 185 ASP cc_start: 0.8611 (m-30) cc_final: 0.8235 (m-30) REVERT: M 201 LYS cc_start: 0.8262 (ttmt) cc_final: 0.8031 (ttmt) REVERT: M 338 LYS cc_start: 0.6255 (mmpt) cc_final: 0.5475 (mtpt) REVERT: N 66 ASN cc_start: 0.9171 (t0) cc_final: 0.8923 (t0) REVERT: N 106 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7433 (mmt) REVERT: N 153 ASN cc_start: 0.8676 (m-40) cc_final: 0.8278 (m110) REVERT: N 205 HIS cc_start: 0.8328 (t70) cc_final: 0.7389 (m90) REVERT: O 101 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7865 (mtp-110) REVERT: O 122 ARG cc_start: 0.9250 (OUTLIER) cc_final: 0.8957 (mtp85) REVERT: O 138 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8974 (pt) REVERT: O 223 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8729 (ttp-170) REVERT: O 232 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7987 (mt0) REVERT: P 16 LYS cc_start: 0.8566 (ptmt) cc_final: 0.7999 (mmtm) REVERT: P 22 TYR cc_start: 0.8985 (m-10) cc_final: 0.8764 (m-10) REVERT: P 84 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7889 (mm) REVERT: P 121 GLN cc_start: 0.8809 (tt0) cc_final: 0.8563 (tt0) REVERT: P 154 TRP cc_start: 0.7734 (m100) cc_final: 0.7227 (m-90) REVERT: P 175 ARG cc_start: 0.7878 (mmt-90) cc_final: 0.7544 (mtp85) REVERT: P 181 GLU cc_start: 0.7510 (mt-10) cc_final: 0.6780 (mp0) REVERT: P 204 GLU cc_start: 0.8607 (mp0) cc_final: 0.8059 (mp0) REVERT: Q 8 ARG cc_start: 0.8029 (mtp180) cc_final: 0.7672 (mtm180) REVERT: Q 41 ASP cc_start: 0.7047 (m-30) cc_final: 0.6711 (t0) REVERT: Q 71 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7124 (mmt) REVERT: Q 161 ASP cc_start: 0.8600 (p0) cc_final: 0.7531 (t70) REVERT: Q 195 MET cc_start: 0.8458 (tpp) cc_final: 0.7951 (tpp) REVERT: Q 196 LEU cc_start: 0.8283 (tp) cc_final: 0.7836 (mt) REVERT: R 11 SER cc_start: 0.8536 (m) cc_final: 0.8125 (p) REVERT: R 17 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: R 24 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: R 90 GLU cc_start: 0.8195 (tp30) cc_final: 0.7844 (tp30) REVERT: R 93 ARG cc_start: 0.8722 (tmm160) cc_final: 0.8439 (ttt-90) REVERT: R 177 LYS cc_start: 0.7404 (mtpm) cc_final: 0.6994 (mmmt) REVERT: R 202 ARG cc_start: 0.5180 (OUTLIER) cc_final: 0.4215 (ptp-110) REVERT: R 206 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8114 (pp) REVERT: R 212 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8174 (mmmt) REVERT: R 213 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6696 (mp0) REVERT: R 215 ARG cc_start: 0.8340 (ttp-170) cc_final: 0.7580 (ttm110) REVERT: S 178 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7801 (ptp) REVERT: S 186 ARG cc_start: 0.8553 (mmt90) cc_final: 0.8349 (mpt-90) REVERT: S 257 ASP cc_start: 0.7816 (t0) cc_final: 0.7457 (t70) REVERT: S 278 GLN cc_start: 0.8037 (mt0) cc_final: 0.7619 (mm-40) REVERT: S 324 ASP cc_start: 0.7434 (p0) cc_final: 0.6194 (t0) REVERT: U 51 GLU cc_start: 0.8320 (pt0) cc_final: 0.7895 (pt0) REVERT: U 210 GLU cc_start: 0.7889 (pt0) cc_final: 0.7366 (pt0) REVERT: U 221 ASP cc_start: 0.8309 (t0) cc_final: 0.7845 (t0) REVERT: V 140 MET cc_start: 0.8496 (mmm) cc_final: 0.8203 (mtp) REVERT: V 212 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8197 (ttp80) REVERT: W 38 ARG cc_start: 0.9030 (ptp-170) cc_final: 0.8493 (ttm110) REVERT: W 51 GLU cc_start: 0.7766 (pt0) cc_final: 0.7557 (pt0) REVERT: W 61 ARG cc_start: 0.7499 (tpp80) cc_final: 0.7280 (tpt-90) REVERT: W 222 ASN cc_start: 0.8461 (m-40) cc_final: 0.8082 (m-40) REVERT: X 12 MET cc_start: 0.8828 (tmm) cc_final: 0.8331 (tmm) REVERT: X 33 LYS cc_start: 0.8458 (ptpt) cc_final: 0.8210 (ptpp) REVERT: X 85 LYS cc_start: 0.8774 (mptt) cc_final: 0.8381 (mtpp) REVERT: X 106 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8223 (mt-10) REVERT: X 111 SER cc_start: 0.8933 (p) cc_final: 0.8686 (t) REVERT: X 134 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7403 (mm-30) REVERT: X 162 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7941 (mt-10) REVERT: Y 1 MET cc_start: 0.6889 (mmm) cc_final: 0.6367 (mmm) REVERT: Y 9 ARG cc_start: 0.8518 (ttp-110) cc_final: 0.7765 (ttp-170) REVERT: Y 30 THR cc_start: 0.8565 (t) cc_final: 0.8147 (p) REVERT: Y 60 TYR cc_start: 0.9342 (t80) cc_final: 0.9115 (t80) REVERT: Y 168 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8014 (mt) REVERT: Y 169 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8063 (tt0) REVERT: Z 117 SER cc_start: 0.8889 (p) cc_final: 0.8448 (p) REVERT: Z 155 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: Z 160 MET cc_start: 0.8491 (ttp) cc_final: 0.7814 (ttp) REVERT: Z 161 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8259 (mm-30) REVERT: Z 190 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7510 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6455 (mp) REVERT: a 142 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7384 (tptp) REVERT: a 226 ARG cc_start: 0.8063 (ptm-80) cc_final: 0.7824 (ptm-80) REVERT: a 269 SER cc_start: 0.9031 (m) cc_final: 0.8752 (p) REVERT: a 275 LEU cc_start: 0.8837 (mt) cc_final: 0.8591 (mt) REVERT: a 301 LEU cc_start: 0.8976 (mt) cc_final: 0.8769 (mt) REVERT: a 331 GLN cc_start: 0.8014 (pt0) cc_final: 0.7473 (tt0) outliers start: 181 outliers final: 126 residues processed: 1144 average time/residue: 0.5069 time to fit residues: 952.1487 Evaluate side-chains 1125 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 969 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 241 GLN Chi-restraints excluded: chain I residue 78 SER Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 MET Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 80 CYS Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain T residue 208 VAL Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain T residue 374 ASN Chi-restraints excluded: chain T residue 384 THR Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 58 MET Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 129 LEU Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 125 ASP Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 163 HIS Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 363 optimal weight: 0.8980 chunk 585 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 277 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 613 optimal weight: 3.9990 chunk 564 optimal weight: 3.9990 chunk 488 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 377 optimal weight: 0.9990 chunk 299 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS C 3 HIS C 247 GLN E 262 HIS G 64 ASN H 241 GLN J 147 HIS K 72 GLN L 291 GLN M 180 ASN M 204 ASN O 72 ASN P 61 GLN P 117 GLN P 121 GLN P 205 ASN S 123 GLN S 262 HIS S 286 HIS T 194 ASN T 206 ASN W 91 HIS Y 72 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 50054 Z= 0.285 Angle : 0.571 15.027 67714 Z= 0.296 Chirality : 0.044 0.309 7544 Planarity : 0.004 0.057 8784 Dihedral : 5.901 79.993 7053 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.03 % Favored : 97.95 % Rotamer: Outliers : 3.26 % Allowed : 22.58 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.11), residues: 6290 helix: 1.68 (0.11), residues: 2328 sheet: -0.35 (0.13), residues: 1488 loop : -0.48 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 161 HIS 0.015 0.001 HIS S 262 PHE 0.016 0.002 PHE L 105 TYR 0.042 0.002 TYR J 96 ARG 0.012 0.001 ARG Y 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12580 Ramachandran restraints generated. 6290 Oldfield, 0 Emsley, 6290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 981 time to evaluate : 4.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 CYS cc_start: 0.8231 (p) cc_final: 0.7941 (p) REVERT: A 56 ARG cc_start: 0.7755 (ptm160) cc_final: 0.7531 (ptm160) REVERT: A 61 ASP cc_start: 0.7876 (t70) cc_final: 0.7667 (t0) REVERT: A 70 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8581 (p) REVERT: A 223 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7391 (ttm-80) REVERT: A 225 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8595 (m) REVERT: A 232 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7464 (mp10) REVERT: B 118 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7957 (mt-10) REVERT: B 167 ASP cc_start: 0.7348 (m-30) cc_final: 0.7124 (m-30) REVERT: B 175 ARG cc_start: 0.7692 (mmt-90) cc_final: 0.7072 (mmm160) REVERT: B 182 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (tt) REVERT: B 205 ASN cc_start: 0.8161 (t0) cc_final: 0.7512 (t0) REVERT: B 217 GLU cc_start: 0.8220 (pt0) cc_final: 0.7821 (mt-10) REVERT: C 60 SER cc_start: 0.8289 (m) cc_final: 0.7978 (t) REVERT: C 76 GLU cc_start: 0.8843 (tt0) cc_final: 0.8262 (mm-30) REVERT: C 234 ASP cc_start: 0.7923 (t0) cc_final: 0.7636 (m-30) REVERT: D 4 ASP cc_start: 0.8199 (p0) cc_final: 0.7486 (m-30) REVERT: D 11 SER cc_start: 0.8670 (m) cc_final: 0.8418 (p) REVERT: D 17 PHE cc_start: 0.8442 (m-10) cc_final: 0.8026 (m-80) REVERT: D 46 GLU cc_start: 0.8304 (pt0) cc_final: 0.7591 (tt0) REVERT: D 61 LYS cc_start: 0.7775 (mptp) cc_final: 0.7418 (tttm) REVERT: D 148 ASP cc_start: 0.8484 (p0) cc_final: 0.8141 (p0) REVERT: D 152 MET cc_start: 0.8106 (ttp) cc_final: 0.7819 (ttm) REVERT: D 171 TYR cc_start: 0.8249 (t80) cc_final: 0.8017 (t80) REVERT: D 205 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: E 125 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: E 138 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8260 (pp) REVERT: E 164 MET cc_start: 0.7986 (ptp) cc_final: 0.7582 (ptm) REVERT: E 204 ASN cc_start: 0.8794 (t0) cc_final: 0.8340 (t0) REVERT: E 295 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7520 (mt-10) REVERT: E 329 MET cc_start: 0.8239 (mmt) cc_final: 0.7844 (mmt) REVERT: F 170 TYR cc_start: 0.9033 (m-80) cc_final: 0.8706 (m-80) REVERT: F 173 ASP cc_start: 0.8484 (t0) cc_final: 0.7787 (m-30) REVERT: F 187 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7434 (mt-10) REVERT: F 276 MET cc_start: 0.7458 (mtt) cc_final: 0.7182 (mtm) REVERT: G 114 ASN cc_start: 0.8569 (m-40) cc_final: 0.8219 (m-40) REVERT: G 208 LEU cc_start: 0.8174 (mt) cc_final: 0.7718 (mp) REVERT: H 74 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8878 (t) REVERT: H 137 PHE cc_start: 0.9317 (OUTLIER) cc_final: 0.8959 (t80) REVERT: H 139 LYS cc_start: 0.8461 (ttmm) cc_final: 0.8079 (mptt) REVERT: H 140 MET cc_start: 0.8212 (mmm) cc_final: 0.7839 (mmt) REVERT: H 198 LYS cc_start: 0.8388 (tptp) cc_final: 0.8094 (ttmt) REVERT: H 254 LYS cc_start: 0.8550 (mttp) cc_final: 0.8179 (mtpt) REVERT: I 59 ARG cc_start: 0.7560 (mtm-85) cc_final: 0.7083 (mtm110) REVERT: I 61 ARG cc_start: 0.8277 (ttm110) cc_final: 0.8030 (ttm170) REVERT: I 175 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7738 (ttm) REVERT: I 209 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8109 (tptp) REVERT: J 12 MET cc_start: 0.8672 (tmm) cc_final: 0.8198 (ttp) REVERT: J 78 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7827 (mt-10) REVERT: K 80 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7882 (mp0) REVERT: K 97 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8004 (ttp80) REVERT: K 98 GLU cc_start: 0.8013 (mp0) cc_final: 0.7578 (mt-10) REVERT: K 131 TYR cc_start: 0.8634 (p90) cc_final: 0.8263 (p90) REVERT: K 159 ARG cc_start: 0.8438 (mtm110) cc_final: 0.8014 (ttm110) REVERT: K 165 GLN cc_start: 0.7960 (tp40) cc_final: 0.7403 (tp-100) REVERT: L 160 MET cc_start: 0.9119 (ttm) cc_final: 0.8831 (ttt) REVERT: L 172 ARG cc_start: 0.8660 (ttm-80) cc_final: 0.7019 (ttt90) REVERT: L 281 LYS cc_start: 0.8734 (tppt) cc_final: 0.8183 (mptt) REVERT: M 185 ASP cc_start: 0.8638 (m-30) cc_final: 0.8184 (m-30) REVERT: M 338 LYS cc_start: 0.6485 (mmpt) cc_final: 0.6172 (mmmt) REVERT: N 66 ASN cc_start: 0.9185 (t0) cc_final: 0.8908 (t0) REVERT: N 106 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7488 (mmt) REVERT: N 153 ASN cc_start: 0.8720 (m-40) cc_final: 0.8299 (m110) REVERT: N 205 HIS cc_start: 0.8384 (t70) cc_final: 0.7468 (m90) REVERT: O 23 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7380 (tt0) REVERT: O 101 ARG cc_start: 0.8291 (ttm110) cc_final: 0.7782 (mtp-110) REVERT: O 122 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8942 (mtp85) REVERT: O 138 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.9003 (pt) REVERT: O 182 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7553 (mt-10) REVERT: O 223 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8665 (ttp-170) REVERT: O 232 GLN cc_start: 0.8303 (mm-40) cc_final: 0.7964 (mt0) REVERT: P 16 LYS cc_start: 0.8651 (ptmt) cc_final: 0.8094 (mmtm) REVERT: P 84 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7966 (mm) REVERT: P 154 TRP cc_start: 0.7830 (m100) cc_final: 0.7282 (m-90) REVERT: P 175 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7557 (mtp85) REVERT: P 181 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6804 (mp0) REVERT: P 204 GLU cc_start: 0.8660 (mp0) cc_final: 0.8070 (mp0) REVERT: Q 8 ARG cc_start: 0.8037 (mtp180) cc_final: 0.7683 (mtm180) REVERT: Q 41 ASP cc_start: 0.7135 (m-30) cc_final: 0.6675 (t0) REVERT: Q 71 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7251 (mmt) REVERT: Q 161 ASP cc_start: 0.8643 (p0) cc_final: 0.7637 (t70) REVERT: Q 196 LEU cc_start: 0.8262 (tp) cc_final: 0.7847 (mt) REVERT: R 11 SER cc_start: 0.8568 (m) cc_final: 0.8193 (p) REVERT: R 17 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: R 24 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7361 (mt-10) REVERT: R 90 GLU cc_start: 0.8161 (tp30) cc_final: 0.7830 (tp30) REVERT: R 93 ARG cc_start: 0.8751 (tmm160) cc_final: 0.8460 (ttt-90) REVERT: R 177 LYS cc_start: 0.7418 (mtpm) cc_final: 0.7005 (mmmt) REVERT: R 202 ARG cc_start: 0.5164 (OUTLIER) cc_final: 0.4132 (ptp-110) REVERT: R 206 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8133 (pp) REVERT: R 212 LYS cc_start: 0.8646 (mmmt) cc_final: 0.8207 (mmmt) REVERT: R 213 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6770 (mp0) REVERT: R 215 ARG cc_start: 0.8333 (ttp-170) cc_final: 0.7602 (ttm110) REVERT: S 178 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7672 (ptp) REVERT: S 186 ARG cc_start: 0.8667 (mmt90) cc_final: 0.8453 (mpt-90) REVERT: S 257 ASP cc_start: 0.7834 (t0) cc_final: 0.7440 (t70) REVERT: S 324 ASP cc_start: 0.7483 (p0) cc_final: 0.6253 (t0) REVERT: T 184 PHE cc_start: 0.8930 (m-80) cc_final: 0.8730 (m-80) REVERT: U 51 GLU cc_start: 0.8328 (pt0) cc_final: 0.7980 (pt0) REVERT: U 221 ASP cc_start: 0.8459 (t0) cc_final: 0.7962 (t0) REVERT: V 212 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8232 (ttp80) REVERT: W 51 GLU cc_start: 0.7748 (pt0) cc_final: 0.7451 (pt0) REVERT: W 61 ARG cc_start: 0.7496 (tpp80) cc_final: 0.7223 (tpt-90) REVERT: W 222 ASN cc_start: 0.8474 (m-40) cc_final: 0.8108 (m-40) REVERT: X 12 MET cc_start: 0.8867 (tmm) cc_final: 0.8363 (tmm) REVERT: X 33 LYS cc_start: 0.8563 (ptpt) cc_final: 0.8325 (ptpp) REVERT: X 85 LYS cc_start: 0.8834 (mptt) cc_final: 0.8410 (mtpp) REVERT: X 106 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8248 (mt-10) REVERT: X 111 SER cc_start: 0.8987 (p) cc_final: 0.8739 (t) REVERT: X 134 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7421 (mm-30) REVERT: X 162 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7983 (mt-10) REVERT: Y 1 MET cc_start: 0.6884 (mmm) cc_final: 0.6371 (mmm) REVERT: Y 9 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.7786 (ttp-170) REVERT: Y 30 THR cc_start: 0.8578 (t) cc_final: 0.8162 (p) REVERT: Y 70 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6809 (mpp) REVERT: Y 168 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8094 (mt) REVERT: Y 169 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8107 (tt0) REVERT: Y 180 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7156 (tmt-80) REVERT: Z 117 SER cc_start: 0.8892 (p) cc_final: 0.8437 (p) REVERT: Z 155 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8176 (mt-10) REVERT: Z 160 MET cc_start: 0.8531 (ttp) cc_final: 0.7943 (ttp) REVERT: Z 161 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8205 (mm-30) REVERT: Z 190 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7603 (ptt-90) REVERT: Z 194 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6776 (mp) REVERT: a 142 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7410 (tptp) REVERT: a 275 LEU cc_start: 0.8877 (mt) cc_final: 0.8639 (mt) REVERT: a 301 LEU cc_start: 0.9002 (mt) cc_final: 0.8759 (mt) REVERT: a 331 GLN cc_start: 0.8054 (pt0) cc_final: 0.7478 (tt0) REVERT: b 18 MET cc_start: 0.9167 (ttm) cc_final: 0.8949 (ttp) outliers start: 171 outliers final: 129 residues processed: 1104 average time/residue: 0.5042 time to fit residues: 910.3800 Evaluate side-chains 1118 residues out of total 5238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 957 time to evaluate : 4.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain C residue 19 TYR Chi-restraints excluded: chain C residue 20 GLN Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain D residue 18 GLN Chi-restraints excluded: chain D residue 59 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 185 CYS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 GLU Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 125 GLU Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 178 MET Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 187 GLU Chi-restraints excluded: chain F residue 199 THR Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 404 ARG Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 42 CYS Chi-restraints excluded: chain G residue 46 VAL Chi-restraints excluded: chain G residue 115 ARG Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 137 PHE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 206 CYS Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 175 MET Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 78 GLU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 127 ILE Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 147 HIS Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 47 CYS Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 114 VAL Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain L residue 120 SER Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 129 THR Chi-restraints excluded: chain L residue 232 ILE Chi-restraints excluded: chain L residue 291 GLN Chi-restraints excluded: chain M residue 167 LYS Chi-restraints excluded: chain M residue 247 CYS Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain N residue 16 VAL Chi-restraints excluded: chain N residue 45 SER Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 106 MET Chi-restraints excluded: chain N residue 113 ASP Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 53 ILE Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 122 ARG Chi-restraints excluded: chain O residue 138 ILE Chi-restraints excluded: chain O residue 206 LEU Chi-restraints excluded: chain O residue 223 ARG Chi-restraints excluded: chain P residue 42 VAL Chi-restraints excluded: chain P residue 75 SER Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain Q residue 66 THR Chi-restraints excluded: chain Q residue 67 SER Chi-restraints excluded: chain Q residue 71 MET Chi-restraints excluded: chain Q residue 80 CYS Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain Q residue 163 SER Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 17 PHE Chi-restraints excluded: chain R residue 24 GLU Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 202 ARG Chi-restraints excluded: chain R residue 206 LEU Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 142 THR Chi-restraints excluded: chain S residue 178 MET Chi-restraints excluded: chain S residue 182 VAL Chi-restraints excluded: chain S residue 279 SER Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain S residue 323 ASP Chi-restraints excluded: chain T residue 208 VAL Chi-restraints excluded: chain T residue 288 SER Chi-restraints excluded: chain T residue 290 LYS Chi-restraints excluded: chain T residue 374 ASN Chi-restraints excluded: chain T residue 384 THR Chi-restraints excluded: chain U residue 42 CYS Chi-restraints excluded: chain U residue 58 MET Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 175 GLU Chi-restraints excluded: chain U residue 216 VAL Chi-restraints excluded: chain V residue 74 THR Chi-restraints excluded: chain V residue 100 SER Chi-restraints excluded: chain V residue 137 PHE Chi-restraints excluded: chain V residue 212 ARG Chi-restraints excluded: chain V residue 218 TYR Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 241 GLN Chi-restraints excluded: chain W residue 129 LEU Chi-restraints excluded: chain W residue 148 THR Chi-restraints excluded: chain W residue 215 THR Chi-restraints excluded: chain X residue 54 THR Chi-restraints excluded: chain X residue 91 ILE Chi-restraints excluded: chain X residue 134 GLU Chi-restraints excluded: chain X residue 166 ILE Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 47 CYS Chi-restraints excluded: chain Y residue 70 MET Chi-restraints excluded: chain Y residue 162 LEU Chi-restraints excluded: chain Y residue 168 LEU Chi-restraints excluded: chain Y residue 195 THR Chi-restraints excluded: chain Z residue 144 LEU Chi-restraints excluded: chain Z residue 155 GLU Chi-restraints excluded: chain Z residue 190 ARG Chi-restraints excluded: chain Z residue 194 LEU Chi-restraints excluded: chain Z residue 232 ILE Chi-restraints excluded: chain Z residue 274 THR Chi-restraints excluded: chain a residue 142 LYS Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 163 HIS Chi-restraints excluded: chain a residue 210 SER Chi-restraints excluded: chain a residue 249 SER Chi-restraints excluded: chain a residue 326 LYS Chi-restraints excluded: chain b residue 82 SER Chi-restraints excluded: chain b residue 198 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 616 random chunks: chunk 388 optimal weight: 8.9990 chunk 520 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 450 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 489 optimal weight: 0.1980 chunk 204 optimal weight: 9.9990 chunk 502 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS C 3 HIS D 223 GLN E 262 HIS ** G 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 ASN H 241 GLN ** J 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN ** M 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 72 ASN P 61 GLN P 117 GLN P 121 GLN P 143 HIS P 205 ASN S 262 HIS ** S 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 194 ASN W 91 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.127760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.109228 restraints weight = 64419.131| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.55 r_work: 0.3015 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.171 50054 Z= 0.297 Angle : 0.689 59.190 67714 Z= 0.396 Chirality : 0.046 1.081 7544 Planarity : 0.005 0.247 8784 Dihedral : 5.901 79.963 7053 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 3.40 % Allowed : 22.53 % Favored : 74.07 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.11), residues: 6290 helix: 1.67 (0.11), residues: 2328 sheet: -0.35 (0.13), residues: 1488 loop : -0.48 (0.12), residues: 2474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 161 HIS 0.457 0.003 HIS J 147 PHE 0.015 0.001 PHE L 105 TYR 0.039 0.002 TYR J 96 ARG 0.011 0.000 ARG J 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15471.00 seconds wall clock time: 266 minutes 26.84 seconds (15986.84 seconds total)