Starting phenix.real_space_refine on Fri Feb 6 12:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efq_47977/02_2026/9efq_47977.map" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.012 sd= 0.032 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: 5 Type Number sf(0) Gaussians Zn 3 6.06 5 S 150 5.16 5 C 15899 2.51 5 N 4283 2.21 5 O 4690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25025 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3271 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 8, 'TRANS': 400} Chain breaks: 1 Chain: "B" Number of atoms: 3062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3062 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 362} Chain breaks: 1 Chain: "C" Number of atoms: 3222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3222 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 13, 'TRANS': 391} Chain: "D" Number of atoms: 3233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3233 Classifications: {'peptide': 404} Link IDs: {'PTRANS': 9, 'TRANS': 394} Chain: "E" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2260 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 8, 'TRANS': 276} Chain breaks: 2 Chain: "F" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2208 Classifications: {'peptide': 276} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 265} Chain breaks: 1 Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1687 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 4, 'TRANS': 208} Chain: "H" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1374 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 599 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "J" Number of atoms: 3413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3413 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 9, 'TRANS': 414} Chain breaks: 1 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 693 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain breaks: 1 Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 24621 SG CYS K 53 74.844 70.558 77.206 1.00 7.86 S ATOM 24644 SG CYS K 56 71.430 68.919 77.762 1.00 8.82 S ATOM 24690 SG CYS K 68 72.393 70.317 74.270 1.00 13.76 S ATOM 24535 SG CYS K 42 79.696 74.940 73.175 1.00 5.73 S ATOM 24554 SG CYS K 45 80.049 71.264 74.218 1.00 10.77 S ATOM 24811 SG CYS K 83 77.804 73.564 76.243 1.00 5.59 S ATOM 24740 SG CYS K 75 79.468 86.372 67.890 1.00 14.94 S ATOM 24907 SG CYS K 94 81.401 84.868 70.945 1.00 4.91 S Time building chain proxies: 5.50, per 1000 atoms: 0.22 Number of scatterers: 25025 At special positions: 0 Unit cell: (139.728, 162.732, 201.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 3 29.99 S 150 16.00 O 4690 8.00 N 4283 7.00 C 15899 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 82 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 68 " pdb="ZN ZN K 201 " - pdb=" SG CYS K 56 " pdb=" ZN K 202 " pdb="ZN ZN K 202 " - pdb=" ND1 HIS K 80 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 45 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 83 " pdb="ZN ZN K 202 " - pdb=" SG CYS K 42 " pdb=" ZN K 203 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 94 " pdb="ZN ZN K 203 " - pdb=" ND1 HIS K 77 " pdb="ZN ZN K 203 " - pdb=" SG CYS K 75 " Number of angles added : 6 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5984 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 10 sheets defined 66.3% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.862A pdb=" N HIS A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 81 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 127 through 156 removed outlier: 4.288A pdb=" N VAL A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 214 through 228 removed outlier: 3.863A pdb=" N VAL A 218 " --> pdb=" O ASN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 244 through 260 Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 285 through 301 removed outlier: 3.609A pdb=" N ALA A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 314 through 323 removed outlier: 4.213A pdb=" N LEU A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.511A pdb=" N ARG A 327 " --> pdb=" O GLU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 removed outlier: 4.127A pdb=" N ASP A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN A 351 " --> pdb=" O GLU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.578A pdb=" N LEU A 365 " --> pdb=" O HIS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 430 through 462 Processing helix chain 'B' and resid 65 through 82 Processing helix chain 'B' and resid 84 through 103 Processing helix chain 'B' and resid 104 through 116 removed outlier: 4.511A pdb=" N SER B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 140 removed outlier: 3.589A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 163 through 180 removed outlier: 3.831A pdb=" N HIS B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER B 178 " --> pdb=" O GLN B 174 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N CYS B 179 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 208 Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 232 through 249 Processing helix chain 'B' and resid 250 through 268 removed outlier: 3.556A pdb=" N THR B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 removed outlier: 4.167A pdb=" N THR B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.869A pdb=" N SER B 296 " --> pdb=" O PRO B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.263A pdb=" N ASN B 304 " --> pdb=" O PRO B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 322 through 333 Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.810A pdb=" N HIS B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 371 through 379 Processing helix chain 'B' and resid 381 through 395 Processing helix chain 'B' and resid 418 through 440 removed outlier: 3.520A pdb=" N SER B 440 " --> pdb=" O GLN B 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 20 through 30 removed outlier: 3.605A pdb=" N LEU C 24 " --> pdb=" O GLN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.265A pdb=" N LEU C 42 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 65 removed outlier: 3.515A pdb=" N VAL C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 96 through 112 removed outlier: 4.146A pdb=" N PHE C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.891A pdb=" N GLN C 126 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 152 removed outlier: 4.055A pdb=" N ALA C 143 " --> pdb=" O THR C 139 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 162 Processing helix chain 'C' and resid 177 through 195 removed outlier: 3.733A pdb=" N PHE C 181 " --> pdb=" O ASP C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 210 Processing helix chain 'C' and resid 217 through 235 Processing helix chain 'C' and resid 248 through 257 removed outlier: 4.022A pdb=" N PHE C 252 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE C 253 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) Proline residue: C 255 - end of helix No H-bonds generated for 'chain 'C' and resid 248 through 257' Processing helix chain 'C' and resid 257 through 268 removed outlier: 3.781A pdb=" N HIS C 261 " --> pdb=" O SER C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 282 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 293 through 311 removed outlier: 3.531A pdb=" N TYR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C 311 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 326 Processing helix chain 'C' and resid 330 through 344 Processing helix chain 'C' and resid 369 through 400 Processing helix chain 'C' and resid 401 through 406 removed outlier: 4.345A pdb=" N GLN C 405 " --> pdb=" O PRO C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.074A pdb=" N GLN D 7 " --> pdb=" O ALA D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 removed outlier: 4.349A pdb=" N TYR D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS D 32 " --> pdb=" O GLN D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 54 removed outlier: 3.512A pdb=" N ASN D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 93 removed outlier: 4.026A pdb=" N GLU D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 116 Processing helix chain 'D' and resid 119 through 129 Processing helix chain 'D' and resid 140 through 158 Processing helix chain 'D' and resid 160 through 176 removed outlier: 3.607A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 171 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 173 " --> pdb=" O ASN D 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 198 Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 218 through 236 Processing helix chain 'D' and resid 239 through 252 Processing helix chain 'D' and resid 260 through 269 Processing helix chain 'D' and resid 274 through 277 removed outlier: 3.548A pdb=" N GLN D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 274 through 277' Processing helix chain 'D' and resid 278 through 284 removed outlier: 3.519A pdb=" N ALA D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.530A pdb=" N ALA D 291 " --> pdb=" O HIS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 315 removed outlier: 5.047A pdb=" N ILE D 305 " --> pdb=" O ASP D 301 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 314 " --> pdb=" O LEU D 310 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 315 " --> pdb=" O SER D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 327 Processing helix chain 'D' and resid 333 through 343 Processing helix chain 'D' and resid 366 through 392 Processing helix chain 'D' and resid 392 through 405 Processing helix chain 'E' and resid 32 through 43 removed outlier: 4.006A pdb=" N GLN E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 47 Processing helix chain 'E' and resid 59 through 72 Processing helix chain 'E' and resid 111 through 128 removed outlier: 3.836A pdb=" N GLU E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 162 Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 231 through 241 Processing helix chain 'E' and resid 245 through 251 Processing helix chain 'E' and resid 258 through 281 removed outlier: 3.783A pdb=" N GLU E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 329 Processing helix chain 'F' and resid 46 through 63 Processing helix chain 'F' and resid 101 through 113 Processing helix chain 'F' and resid 132 through 143 removed outlier: 3.539A pdb=" N GLN F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 206 Processing helix chain 'F' and resid 215 through 247 removed outlier: 3.605A pdb=" N ALA F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET F 230 " --> pdb=" O SER F 226 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA F 247 " --> pdb=" O LYS F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 Processing helix chain 'F' and resid 272 through 313 removed outlier: 3.682A pdb=" N TYR F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 20 removed outlier: 3.744A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU G 18 " --> pdb=" O GLN G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 60 through 72 removed outlier: 3.567A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 4.120A pdb=" N ALA G 80 " --> pdb=" O PRO G 76 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 76 through 81' Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.561A pdb=" N ARG G 107 " --> pdb=" O SER G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 124 through 138 Processing helix chain 'G' and resid 166 through 221 removed outlier: 3.652A pdb=" N ILE G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 3.682A pdb=" N GLU H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 47 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 61 through 68 removed outlier: 3.623A pdb=" N ASN H 68 " --> pdb=" O ILE H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 83 removed outlier: 4.025A pdb=" N GLY H 72 " --> pdb=" O ASN H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 94 removed outlier: 4.073A pdb=" N TYR H 90 " --> pdb=" O PHE H 86 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 102 through 123 removed outlier: 3.950A pdb=" N GLU H 107 " --> pdb=" O GLN H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 138 Processing helix chain 'H' and resid 141 through 149 removed outlier: 4.088A pdb=" N VAL H 145 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE H 148 " --> pdb=" O ALA H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 209 Processing helix chain 'I' and resid 22 through 34 removed outlier: 3.769A pdb=" N ILE I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 328 Processing helix chain 'J' and resid 334 through 357 Processing helix chain 'J' and resid 361 through 377 removed outlier: 4.062A pdb=" N MET J 365 " --> pdb=" O ASP J 361 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN J 377 " --> pdb=" O THR J 373 " (cutoff:3.500A) Processing helix chain 'J' and resid 386 through 400 Processing helix chain 'J' and resid 407 through 423 removed outlier: 4.538A pdb=" N THR J 420 " --> pdb=" O THR J 416 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL J 421 " --> pdb=" O SER J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 427 through 445 removed outlier: 3.964A pdb=" N PHE J 431 " --> pdb=" O ASP J 427 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 465 Processing helix chain 'J' and resid 470 through 496 removed outlier: 3.840A pdb=" N HIS J 474 " --> pdb=" O THR J 470 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG J 475 " --> pdb=" O SER J 471 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA J 484 " --> pdb=" O MET J 480 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP J 485 " --> pdb=" O SER J 481 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 548 Processing helix chain 'J' and resid 579 through 588 removed outlier: 3.954A pdb=" N VAL J 584 " --> pdb=" O TYR J 580 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU J 585 " --> pdb=" O GLN J 581 " (cutoff:3.500A) Processing helix chain 'J' and resid 595 through 604 Processing helix chain 'J' and resid 606 through 621 Processing helix chain 'J' and resid 671 through 692 Processing helix chain 'J' and resid 696 through 708 Processing helix chain 'J' and resid 714 through 728 Processing helix chain 'K' and resid 54 through 59 Processing helix chain 'K' and resid 81 through 89 Processing sheet with id=AA1, first strand: chain 'G' and resid 110 through 112 removed outlier: 6.801A pdb=" N GLN G 142 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR B 367 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL A 417 " --> pdb=" O LEU C 315 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU C 317 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 315 " --> pdb=" O PHE C 360 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR H 126 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE C 351 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE H 128 " --> pdb=" O ILE C 351 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 54 through 58 removed outlier: 6.687A pdb=" N TYR E 54 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE E 92 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS E 56 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASP E 94 " --> pdb=" O LYS E 56 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER E 58 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU E 82 " --> pdb=" O MET E 93 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER E 95 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU E 80 " --> pdb=" O SER E 95 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY E 135 " --> pdb=" O MET E 81 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLY E 83 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ALA E 133 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL E 168 " --> pdb=" O ILE E 134 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP E 136 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ILE E 170 " --> pdb=" O TRP E 136 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N HIS E 138 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N LEU E 183 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL E 226 " --> pdb=" O LEU E 183 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA E 185 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS E 55 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N PHE E 229 " --> pdb=" O CYS E 55 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE E 57 " --> pdb=" O PHE E 229 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 43 removed outlier: 5.229A pdb=" N VAL F 83 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS F 75 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY F 70 " --> pdb=" O TRP F 124 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP F 124 " --> pdb=" O GLY F 70 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU F 72 " --> pdb=" O LEU F 122 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 167 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'I' and resid 6 through 7 removed outlier: 6.516A pdb=" N LYS I 6 " --> pdb=" O LEU I 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 506 through 513 removed outlier: 6.424A pdb=" N SER J 506 " --> pdb=" O TRP K 27 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA K 29 " --> pdb=" O SER J 506 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN J 508 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA K 31 " --> pdb=" O GLN J 508 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR J 510 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP K 33 " --> pdb=" O TYR J 510 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU J 512 " --> pdb=" O TRP K 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP K 35 " --> pdb=" O LEU J 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 506 through 513 removed outlier: 6.424A pdb=" N SER J 506 " --> pdb=" O TRP K 27 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ALA K 29 " --> pdb=" O SER J 506 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLN J 508 " --> pdb=" O ALA K 29 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ALA K 31 " --> pdb=" O GLN J 508 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N TYR J 510 " --> pdb=" O ALA K 31 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP K 33 " --> pdb=" O TYR J 510 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU J 512 " --> pdb=" O TRP K 33 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N TRP K 35 " --> pdb=" O LEU J 512 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU K 23 " --> pdb=" O LYS J 565 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU J 563 " --> pdb=" O LYS K 25 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TRP K 27 " --> pdb=" O THR J 561 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR J 561 " --> pdb=" O TRP K 27 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 593 through 594 Processing sheet with id=AA9, first strand: chain 'J' and resid 693 through 695 Processing sheet with id=AB1, first strand: chain 'K' and resid 79 through 80 1507 hydrogen bonds defined for protein. 4428 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: 3.61 Time building geometry restraints manager: 2.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8198 1.34 - 1.46: 5006 1.46 - 1.58: 12021 1.58 - 1.70: 0 1.70 - 1.82: 244 Bond restraints: 25469 Sorted by residual: bond pdb=" CB PRO C 72 " pdb=" CG PRO C 72 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.95e+00 bond pdb=" CA TYR G 78 " pdb=" CB TYR G 78 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.30e-02 5.92e+03 1.12e+00 bond pdb=" CA ILE B 371 " pdb=" C ILE B 371 " ideal model delta sigma weight residual 1.520 1.529 -0.009 8.80e-03 1.29e+04 1.08e+00 bond pdb=" CA ASP E 86 " pdb=" CB ASP E 86 " ideal model delta sigma weight residual 1.532 1.516 0.016 1.58e-02 4.01e+03 1.01e+00 bond pdb=" CB GLU J 408 " pdb=" CG GLU J 408 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.75e-01 ... (remaining 25464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 33897 1.97 - 3.95: 391 3.95 - 5.92: 66 5.92 - 7.90: 13 7.90 - 9.87: 7 Bond angle restraints: 34374 Sorted by residual: angle pdb=" C GLN A 234 " pdb=" CA GLN A 234 " pdb=" CB GLN A 234 " ideal model delta sigma weight residual 116.63 110.12 6.51 1.16e+00 7.43e-01 3.15e+01 angle pdb=" CA TYR G 78 " pdb=" CB TYR G 78 " pdb=" CG TYR G 78 " ideal model delta sigma weight residual 113.90 120.65 -6.75 1.80e+00 3.09e-01 1.41e+01 angle pdb=" C GLU E 27 " pdb=" N ILE E 28 " pdb=" CA ILE E 28 " ideal model delta sigma weight residual 121.97 128.67 -6.70 1.80e+00 3.09e-01 1.39e+01 angle pdb=" CA GLN A 234 " pdb=" C GLN A 234 " pdb=" N ARG A 235 " ideal model delta sigma weight residual 119.63 116.70 2.93 8.10e-01 1.52e+00 1.31e+01 angle pdb=" N ARG C 251 " pdb=" CA ARG C 251 " pdb=" C ARG C 251 " ideal model delta sigma weight residual 114.31 109.65 4.66 1.29e+00 6.01e-01 1.31e+01 ... (remaining 34369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 13028 17.96 - 35.93: 1901 35.93 - 53.89: 496 53.89 - 71.85: 102 71.85 - 89.82: 43 Dihedral angle restraints: 15570 sinusoidal: 6358 harmonic: 9212 Sorted by residual: dihedral pdb=" CA ILE D 330 " pdb=" C ILE D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta harmonic sigma weight residual 180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ASP D 301 " pdb=" C ASP D 301 " pdb=" N ARG D 302 " pdb=" CA ARG D 302 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA ARG B 105 " pdb=" C ARG B 105 " pdb=" N ASN B 106 " pdb=" CA ASN B 106 " ideal model delta harmonic sigma weight residual -180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 15567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3090 0.046 - 0.092: 659 0.092 - 0.139: 129 0.139 - 0.185: 4 0.185 - 0.231: 3 Chirality restraints: 3885 Sorted by residual: chirality pdb=" CB VAL C 51 " pdb=" CA VAL C 51 " pdb=" CG1 VAL C 51 " pdb=" CG2 VAL C 51 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO C 72 " pdb=" N PRO C 72 " pdb=" C PRO C 72 " pdb=" CB PRO C 72 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE E 28 " pdb=" CA ILE E 28 " pdb=" CG1 ILE E 28 " pdb=" CG2 ILE E 28 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 3882 not shown) Planarity restraints: 4387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.067 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO C 72 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 78 " -0.015 2.00e-02 2.50e+03 2.18e-02 9.47e+00 pdb=" CG TYR G 78 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR G 78 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR G 78 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR G 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR G 78 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR G 78 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 78 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP F 132 " -0.039 5.00e-02 4.00e+02 5.90e-02 5.56e+00 pdb=" N PRO F 133 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 133 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 133 " -0.033 5.00e-02 4.00e+02 ... (remaining 4384 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 8 2.57 - 3.15: 19955 3.15 - 3.73: 39802 3.73 - 4.32: 52860 4.32 - 4.90: 88775 Nonbonded interactions: 201400 Sorted by model distance: nonbonded pdb=" OD2 ASP K 97 " pdb="ZN ZN K 203 " model vdw 1.985 2.230 nonbonded pdb=" OD1 ASP K 97 " pdb="ZN ZN K 203 " model vdw 1.996 2.230 nonbonded pdb=" CG ASP K 97 " pdb="ZN ZN K 203 " model vdw 2.109 2.460 nonbonded pdb=" O GLN J 313 " pdb=" OD1 ASN J 317 " model vdw 2.481 3.040 nonbonded pdb=" O ASN J 641 " pdb=" OD1 ASN J 641 " model vdw 2.491 3.040 ... (remaining 201395 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.910 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: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25481 Z= 0.136 Angle : 0.569 9.875 34380 Z= 0.311 Chirality : 0.039 0.231 3885 Planarity : 0.004 0.102 4387 Dihedral : 18.473 89.817 9586 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.48 % Favored : 95.26 % Rotamer: Outliers : 1.28 % Allowed : 25.21 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.15), residues: 3081 helix: 1.58 (0.12), residues: 1961 sheet: -0.14 (0.45), residues: 126 loop : -1.88 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 305 TYR 0.053 0.001 TYR G 78 PHE 0.027 0.001 PHE J 339 TRP 0.008 0.001 TRP H 153 HIS 0.007 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00255 (25469) covalent geometry : angle 0.56925 (34374) hydrogen bonds : bond 0.11738 ( 1507) hydrogen bonds : angle 5.09226 ( 4428) metal coordination : bond 0.00368 ( 11) metal coordination : angle 1.11707 ( 6) Misc. bond : bond 0.09607 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 256 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 453 MET cc_start: 0.7939 (tmm) cc_final: 0.7654 (ttp) REVERT: F 157 MET cc_start: 0.5606 (mpp) cc_final: 0.5335 (mpt) REVERT: F 222 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7928 (mp) REVERT: G 122 MET cc_start: 0.8386 (mtp) cc_final: 0.8149 (mtp) REVERT: G 193 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7776 (mp) REVERT: G 216 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6541 (tp) outliers start: 35 outliers final: 19 residues processed: 285 average time/residue: 0.5972 time to fit residues: 198.2843 Evaluate side-chains 250 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 228 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 512 LEU Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain K residue 68 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 72 HIS E 182 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.154380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105114 restraints weight = 44021.272| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.68 r_work: 0.3320 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.0736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25481 Z= 0.116 Angle : 0.519 7.822 34380 Z= 0.269 Chirality : 0.039 0.214 3885 Planarity : 0.004 0.101 4387 Dihedral : 4.895 78.462 3395 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.74 % Favored : 95.00 % Rotamer: Outliers : 2.84 % Allowed : 24.92 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.16), residues: 3081 helix: 1.82 (0.12), residues: 1978 sheet: -0.08 (0.47), residues: 122 loop : -1.90 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 305 TYR 0.014 0.001 TYR C 185 PHE 0.021 0.001 PHE D 69 TRP 0.015 0.001 TRP B 148 HIS 0.005 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00257 (25469) covalent geometry : angle 0.51901 (34374) hydrogen bonds : bond 0.03487 ( 1507) hydrogen bonds : angle 4.01166 ( 4428) metal coordination : bond 0.00256 ( 11) metal coordination : angle 1.08583 ( 6) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: C 137 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: C 214 MET cc_start: 0.7188 (ptt) cc_final: 0.6957 (ptm) REVERT: D 64 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7710 (mm-40) REVERT: D 242 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8416 (ttt-90) REVERT: E 106 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.7361 (ttm-80) REVERT: F 206 MET cc_start: 0.3585 (ppp) cc_final: 0.3004 (pp-130) REVERT: F 222 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8062 (mp) REVERT: G 130 ASP cc_start: 0.8718 (m-30) cc_final: 0.8368 (m-30) REVERT: G 214 THR cc_start: 0.8361 (t) cc_final: 0.8161 (t) REVERT: G 216 ILE cc_start: 0.6007 (OUTLIER) cc_final: 0.5604 (tp) REVERT: H 49 ASP cc_start: 0.8194 (t0) cc_final: 0.7932 (t0) REVERT: H 70 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.4923 (tm-30) REVERT: H 85 ASP cc_start: 0.7962 (t0) cc_final: 0.7600 (t0) REVERT: J 724 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8506 (m) outliers start: 78 outliers final: 23 residues processed: 307 average time/residue: 0.5885 time to fit residues: 210.0589 Evaluate side-chains 262 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain E residue 106 ARG Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain J residue 418 PHE Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 181 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 chunk 156 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 264 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 HIS B 264 ASN B 334 HIS C 116 GLN C 402 GLN D 14 ASN D 54 ASN D 72 HIS ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 GLN J 459 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.147613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096781 restraints weight = 44137.137| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.41 r_work: 0.3241 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 25481 Z= 0.175 Angle : 0.554 7.138 34380 Z= 0.286 Chirality : 0.041 0.211 3885 Planarity : 0.004 0.102 4387 Dihedral : 4.735 74.207 3381 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.00 % Favored : 94.74 % Rotamer: Outliers : 3.72 % Allowed : 24.12 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.15), residues: 3081 helix: 1.74 (0.12), residues: 1979 sheet: -0.18 (0.42), residues: 139 loop : -1.90 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 21 TYR 0.020 0.001 TYR C 244 PHE 0.020 0.002 PHE D 69 TRP 0.017 0.001 TRP B 148 HIS 0.006 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00421 (25469) covalent geometry : angle 0.55329 (34374) hydrogen bonds : bond 0.03627 ( 1507) hydrogen bonds : angle 3.94750 ( 4428) metal coordination : bond 0.00576 ( 11) metal coordination : angle 1.68922 ( 6) Misc. bond : bond 0.00079 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 238 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 MET cc_start: 0.6036 (mpm) cc_final: 0.5578 (mpp) REVERT: C 137 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8852 (tm-30) REVERT: C 214 MET cc_start: 0.7535 (ptt) cc_final: 0.7324 (ptm) REVERT: D 271 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8248 (mtt90) REVERT: F 152 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8373 (tp) REVERT: F 222 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8164 (mp) REVERT: G 130 ASP cc_start: 0.8861 (m-30) cc_final: 0.8538 (m-30) REVERT: G 193 LEU cc_start: 0.8713 (tt) cc_final: 0.7897 (mp) REVERT: G 209 VAL cc_start: 0.7462 (t) cc_final: 0.7044 (p) REVERT: G 214 THR cc_start: 0.8447 (OUTLIER) cc_final: 0.8226 (t) REVERT: G 216 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5704 (tp) REVERT: H 49 ASP cc_start: 0.8390 (t0) cc_final: 0.8039 (t0) REVERT: H 70 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.4991 (tm-30) REVERT: H 85 ASP cc_start: 0.8028 (t0) cc_final: 0.7431 (t0) REVERT: J 724 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8585 (m) REVERT: K 53 CYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7849 (p) outliers start: 102 outliers final: 41 residues processed: 313 average time/residue: 0.5548 time to fit residues: 204.3259 Evaluate side-chains 284 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 70 GLU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain J residue 418 PHE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 276 optimal weight: 4.9990 chunk 268 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 283 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 72 HIS D 403 GLN E 138 HIS F 141 GLN H 97 GLN J 320 HIS J 445 HIS J 488 ASN J 625 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.143658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091737 restraints weight = 43821.697| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.39 r_work: 0.3155 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 25481 Z= 0.319 Angle : 0.691 11.838 34380 Z= 0.356 Chirality : 0.046 0.214 3885 Planarity : 0.005 0.100 4387 Dihedral : 5.205 71.745 3377 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.32 % Favored : 94.45 % Rotamer: Outliers : 4.95 % Allowed : 23.79 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.15), residues: 3081 helix: 1.20 (0.12), residues: 1975 sheet: -0.39 (0.43), residues: 133 loop : -1.97 (0.19), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 91 TYR 0.031 0.002 TYR F 105 PHE 0.038 0.002 PHE B 69 TRP 0.020 0.002 TRP B 148 HIS 0.012 0.002 HIS E 140 Details of bonding type rmsd covalent geometry : bond 0.00777 (25469) covalent geometry : angle 0.69038 (34374) hydrogen bonds : bond 0.04440 ( 1507) hydrogen bonds : angle 4.23517 ( 4428) metal coordination : bond 0.01047 ( 11) metal coordination : angle 2.91113 ( 6) Misc. bond : bond 0.00182 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 240 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: -0.2151 (OUTLIER) cc_final: -0.2643 (tp) REVERT: A 262 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7753 (mtmt) REVERT: A 311 ILE cc_start: 0.7258 (mp) cc_final: 0.7030 (mp) REVERT: A 386 MET cc_start: 0.8998 (mtp) cc_final: 0.8735 (mmm) REVERT: B 403 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8390 (t0) REVERT: D 271 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8496 (ttm170) REVERT: E 138 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7874 (t-90) REVERT: F 188 TYR cc_start: 0.7899 (p90) cc_final: 0.7216 (p90) REVERT: F 222 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8295 (mp) REVERT: G 23 SER cc_start: 0.8178 (t) cc_final: 0.7933 (m) REVERT: G 163 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: G 214 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8237 (t) REVERT: G 216 ILE cc_start: 0.6179 (OUTLIER) cc_final: 0.5791 (tp) REVERT: H 85 ASP cc_start: 0.8011 (t0) cc_final: 0.7360 (t0) REVERT: H 106 MET cc_start: 0.5133 (tpt) cc_final: 0.4915 (tpt) REVERT: I 6 LYS cc_start: 0.8299 (mttp) cc_final: 0.8084 (mptt) REVERT: J 724 VAL cc_start: 0.8906 (OUTLIER) cc_final: 0.8600 (m) outliers start: 136 outliers final: 59 residues processed: 337 average time/residue: 0.5996 time to fit residues: 236.3434 Evaluate side-chains 292 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 356 MET Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 303 LYS Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 348 MET Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 138 HIS Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 257 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 146 ILE Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 311 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 163 LEU Chi-restraints excluded: chain J residue 418 PHE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 511 VAL Chi-restraints excluded: chain J residue 537 VAL Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 688 MET Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain J residue 724 VAL Chi-restraints excluded: chain K residue 23 GLU Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 77 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 202 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 205 optimal weight: 0.6980 chunk 253 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 225 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 124 GLN B 223 HIS B 297 GLN D 72 HIS ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS H 97 GLN H 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.152350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101301 restraints weight = 43120.098| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.70 r_work: 0.3194 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25481 Z= 0.126 Angle : 0.550 15.273 34380 Z= 0.283 Chirality : 0.040 0.352 3885 Planarity : 0.004 0.100 4387 Dihedral : 4.800 70.579 3377 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.67 % Favored : 95.13 % Rotamer: Outliers : 3.50 % Allowed : 25.90 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 3081 helix: 1.58 (0.12), residues: 1981 sheet: -0.31 (0.46), residues: 123 loop : -1.90 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 91 TYR 0.027 0.001 TYR F 105 PHE 0.021 0.001 PHE F 168 TRP 0.022 0.001 TRP B 148 HIS 0.017 0.001 HIS E 138 Details of bonding type rmsd covalent geometry : bond 0.00288 (25469) covalent geometry : angle 0.54921 (34374) hydrogen bonds : bond 0.03445 ( 1507) hydrogen bonds : angle 3.96288 ( 4428) metal coordination : bond 0.00487 ( 11) metal coordination : angle 2.01551 ( 6) Misc. bond : bond 0.00023 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 236 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.5538 (mmm) cc_final: 0.4039 (ptm) REVERT: A 98 LEU cc_start: -0.1950 (OUTLIER) cc_final: -0.2483 (tp) REVERT: A 307 GLN cc_start: 0.8041 (tp40) cc_final: 0.7599 (pp30) REVERT: B 403 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8052 (t0) REVERT: B 435 ASN cc_start: 0.7433 (m-40) cc_final: 0.7198 (m-40) REVERT: C 68 MET cc_start: 0.5746 (mpm) cc_final: 0.5032 (mpp) REVERT: C 214 MET cc_start: 0.7595 (ptt) cc_final: 0.7315 (ptm) REVERT: F 79 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7609 (mmm-85) REVERT: F 152 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8155 (tp) REVERT: F 188 TYR cc_start: 0.7839 (p90) cc_final: 0.7199 (p90) REVERT: F 222 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8175 (mp) REVERT: G 23 SER cc_start: 0.8065 (t) cc_final: 0.7836 (m) REVERT: G 130 ASP cc_start: 0.8815 (m-30) cc_final: 0.8522 (m-30) REVERT: G 163 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7175 (ptp90) REVERT: G 214 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8235 (t) REVERT: G 216 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5736 (tp) REVERT: H 58 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7739 (mtmm) REVERT: H 85 ASP cc_start: 0.7989 (t0) cc_final: 0.7304 (t0) REVERT: I 6 LYS cc_start: 0.8087 (mttp) cc_final: 0.7836 (mptt) REVERT: I 32 GLU cc_start: 0.2375 (OUTLIER) cc_final: 0.1843 (pp20) REVERT: K 53 CYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7636 (p) outliers start: 96 outliers final: 42 residues processed: 307 average time/residue: 0.5969 time to fit residues: 214.9186 Evaluate side-chains 277 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 226 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 18 optimal weight: 0.2980 chunk 151 optimal weight: 0.0370 chunk 191 optimal weight: 0.9980 chunk 300 optimal weight: 0.5980 chunk 256 optimal weight: 7.9990 chunk 305 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 207 optimal weight: 0.6980 chunk 129 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 223 HIS C 402 GLN D 72 HIS E 138 HIS J 320 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.153516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.102077 restraints weight = 43402.629| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.63 r_work: 0.3238 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25481 Z= 0.114 Angle : 0.542 14.592 34380 Z= 0.276 Chirality : 0.039 0.235 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.619 69.534 3377 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.03 % Favored : 94.71 % Rotamer: Outliers : 3.50 % Allowed : 25.90 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 3081 helix: 1.73 (0.12), residues: 1989 sheet: -0.49 (0.43), residues: 141 loop : -1.91 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 427 TYR 0.025 0.001 TYR F 105 PHE 0.020 0.001 PHE F 168 TRP 0.028 0.001 TRP B 148 HIS 0.005 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00260 (25469) covalent geometry : angle 0.54172 (34374) hydrogen bonds : bond 0.03238 ( 1507) hydrogen bonds : angle 3.83925 ( 4428) metal coordination : bond 0.00323 ( 11) metal coordination : angle 1.62476 ( 6) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 234 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: -0.2168 (OUTLIER) cc_final: -0.2673 (tp) REVERT: A 307 GLN cc_start: 0.8141 (tp40) cc_final: 0.7626 (pp30) REVERT: B 273 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8136 (ttp-170) REVERT: B 403 ASP cc_start: 0.8622 (OUTLIER) cc_final: 0.8359 (t0) REVERT: B 435 ASN cc_start: 0.7550 (m-40) cc_final: 0.7348 (m-40) REVERT: C 68 MET cc_start: 0.6057 (mpm) cc_final: 0.5379 (mpp) REVERT: C 137 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: C 214 MET cc_start: 0.7755 (ptt) cc_final: 0.7473 (ptm) REVERT: C 357 MET cc_start: 0.8689 (tpp) cc_final: 0.8061 (mmt) REVERT: F 79 ARG cc_start: 0.7868 (mmm-85) cc_final: 0.7566 (mmm-85) REVERT: F 188 TYR cc_start: 0.7819 (p90) cc_final: 0.7131 (p90) REVERT: F 222 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8249 (mp) REVERT: G 130 ASP cc_start: 0.8940 (m-30) cc_final: 0.8650 (m-30) REVERT: G 163 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7278 (ptp90) REVERT: G 214 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8188 (t) REVERT: G 216 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5673 (tp) REVERT: H 85 ASP cc_start: 0.7982 (t0) cc_final: 0.7322 (t0) REVERT: I 38 PRO cc_start: 0.8526 (Cg_exo) cc_final: 0.8293 (Cg_endo) REVERT: J 406 MET cc_start: 0.7547 (mmm) cc_final: 0.7068 (tpt) outliers start: 96 outliers final: 46 residues processed: 310 average time/residue: 0.5980 time to fit residues: 216.6885 Evaluate side-chains 277 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 337 TYR Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 253 optimal weight: 0.5980 chunk 227 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 302 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 283 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 109 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 299 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 129 GLN B 223 HIS D 72 HIS E 138 HIS H 97 GLN H 151 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.152230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.101592 restraints weight = 43648.754| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.55 r_work: 0.3257 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 25481 Z= 0.110 Angle : 0.530 11.724 34380 Z= 0.271 Chirality : 0.039 0.241 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.494 68.305 3377 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.87 % Favored : 94.84 % Rotamer: Outliers : 2.99 % Allowed : 26.89 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.16), residues: 3081 helix: 1.85 (0.12), residues: 1992 sheet: -0.47 (0.43), residues: 141 loop : -1.85 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 427 TYR 0.020 0.001 TYR F 105 PHE 0.019 0.001 PHE F 168 TRP 0.032 0.001 TRP B 148 HIS 0.006 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00245 (25469) covalent geometry : angle 0.53000 (34374) hydrogen bonds : bond 0.03091 ( 1507) hydrogen bonds : angle 3.76796 ( 4428) metal coordination : bond 0.00295 ( 11) metal coordination : angle 1.34015 ( 6) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 241 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.5761 (mmm) cc_final: 0.4298 (ptm) REVERT: A 98 LEU cc_start: -0.2142 (OUTLIER) cc_final: -0.2647 (tp) REVERT: A 307 GLN cc_start: 0.8219 (tp40) cc_final: 0.7614 (pp30) REVERT: B 75 MET cc_start: -0.2600 (OUTLIER) cc_final: -0.2942 (mpp) REVERT: B 435 ASN cc_start: 0.7524 (m-40) cc_final: 0.7312 (m-40) REVERT: C 68 MET cc_start: 0.6065 (mpm) cc_final: 0.5422 (mpp) REVERT: C 133 MET cc_start: 0.8413 (mmp) cc_final: 0.8095 (mmp) REVERT: C 137 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: C 214 MET cc_start: 0.7622 (ptt) cc_final: 0.7318 (ptm) REVERT: C 357 MET cc_start: 0.8708 (tpp) cc_final: 0.8109 (mmt) REVERT: D 309 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8920 (tt) REVERT: F 222 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8248 (mp) REVERT: G 79 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.6432 (pp) REVERT: G 130 ASP cc_start: 0.8933 (m-30) cc_final: 0.8646 (m-30) REVERT: G 214 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8172 (t) REVERT: G 216 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5597 (tp) REVERT: H 85 ASP cc_start: 0.8034 (t0) cc_final: 0.7401 (t0) REVERT: I 6 LYS cc_start: 0.8211 (mttp) cc_final: 0.7926 (mptt) REVERT: I 32 GLU cc_start: 0.2448 (OUTLIER) cc_final: 0.1904 (pp20) REVERT: I 38 PRO cc_start: 0.8531 (Cg_exo) cc_final: 0.8299 (Cg_endo) REVERT: J 406 MET cc_start: 0.7501 (mmm) cc_final: 0.7092 (tpt) outliers start: 82 outliers final: 48 residues processed: 308 average time/residue: 0.5949 time to fit residues: 214.8611 Evaluate side-chains 287 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 230 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 96 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 280 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 306 optimal weight: 0.8980 chunk 199 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 223 HIS D 72 HIS ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS H 97 GLN H 151 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104565 restraints weight = 43778.420| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.42 r_work: 0.3253 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25481 Z= 0.119 Angle : 0.543 11.606 34380 Z= 0.276 Chirality : 0.040 0.319 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.477 66.958 3377 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.90 % Favored : 94.81 % Rotamer: Outliers : 3.39 % Allowed : 26.41 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 3081 helix: 1.86 (0.12), residues: 1993 sheet: -0.44 (0.43), residues: 141 loop : -1.86 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 305 TYR 0.023 0.001 TYR F 105 PHE 0.020 0.001 PHE D 69 TRP 0.007 0.001 TRP D 395 HIS 0.005 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00279 (25469) covalent geometry : angle 0.54304 (34374) hydrogen bonds : bond 0.03135 ( 1507) hydrogen bonds : angle 3.75645 ( 4428) metal coordination : bond 0.00347 ( 11) metal coordination : angle 1.35462 ( 6) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 243 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: -0.2079 (OUTLIER) cc_final: -0.2581 (tp) REVERT: A 307 GLN cc_start: 0.8222 (tp40) cc_final: 0.7654 (pp30) REVERT: B 75 MET cc_start: -0.2722 (OUTLIER) cc_final: -0.3078 (mpp) REVERT: B 95 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6663 (mt) REVERT: B 125 MET cc_start: 0.4821 (tpt) cc_final: 0.3748 (tpt) REVERT: B 403 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8363 (t0) REVERT: B 435 ASN cc_start: 0.7590 (m-40) cc_final: 0.7358 (m-40) REVERT: C 133 MET cc_start: 0.8406 (mmp) cc_final: 0.8102 (mmp) REVERT: C 137 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: C 357 MET cc_start: 0.8729 (tpp) cc_final: 0.8295 (mmt) REVERT: D 242 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8550 (ttt-90) REVERT: D 309 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (tt) REVERT: F 152 LEU cc_start: 0.8722 (tp) cc_final: 0.8521 (tp) REVERT: F 188 TYR cc_start: 0.7646 (p90) cc_final: 0.7091 (p90) REVERT: F 222 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8271 (mp) REVERT: G 130 ASP cc_start: 0.8938 (m-30) cc_final: 0.8654 (m-30) REVERT: G 163 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7291 (ptp90) REVERT: G 214 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.8188 (t) REVERT: G 216 ILE cc_start: 0.6125 (OUTLIER) cc_final: 0.5680 (tp) REVERT: H 58 LYS cc_start: 0.7958 (mtmm) cc_final: 0.7694 (mtmm) REVERT: H 74 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6555 (tp) REVERT: H 85 ASP cc_start: 0.8052 (t0) cc_final: 0.7412 (t0) REVERT: I 1 MET cc_start: 0.4174 (pp-130) cc_final: 0.3807 (pmm) REVERT: I 6 LYS cc_start: 0.8150 (mttp) cc_final: 0.7844 (mptt) REVERT: I 32 GLU cc_start: 0.2382 (OUTLIER) cc_final: 0.1804 (pp20) REVERT: J 406 MET cc_start: 0.7438 (mmm) cc_final: 0.6779 (tpt) REVERT: K 53 CYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7757 (p) outliers start: 93 outliers final: 55 residues processed: 323 average time/residue: 0.5942 time to fit residues: 225.1973 Evaluate side-chains 300 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 418 PHE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 200 optimal weight: 20.0000 chunk 201 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 288 optimal weight: 9.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 223 HIS D 72 HIS ** D 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS H 97 GLN H 151 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.150357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100240 restraints weight = 44092.569| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.42 r_work: 0.3256 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25481 Z= 0.116 Angle : 0.544 11.558 34380 Z= 0.277 Chirality : 0.040 0.209 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.458 65.511 3377 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.77 % Favored : 94.94 % Rotamer: Outliers : 2.81 % Allowed : 26.99 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.16), residues: 3081 helix: 1.88 (0.12), residues: 1995 sheet: -0.39 (0.43), residues: 141 loop : -1.83 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 344 TYR 0.020 0.001 TYR F 105 PHE 0.031 0.001 PHE D 48 TRP 0.039 0.001 TRP B 148 HIS 0.005 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00270 (25469) covalent geometry : angle 0.54360 (34374) hydrogen bonds : bond 0.03099 ( 1507) hydrogen bonds : angle 3.74432 ( 4428) metal coordination : bond 0.00324 ( 11) metal coordination : angle 1.37489 ( 6) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 244 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 MET cc_start: 0.5649 (mmm) cc_final: 0.4245 (ptm) REVERT: A 98 LEU cc_start: -0.2057 (OUTLIER) cc_final: -0.2565 (tp) REVERT: A 307 GLN cc_start: 0.8185 (tp40) cc_final: 0.7622 (pp30) REVERT: B 75 MET cc_start: -0.2625 (OUTLIER) cc_final: -0.2999 (mpp) REVERT: B 95 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6641 (mt) REVERT: B 125 MET cc_start: 0.4786 (tpt) cc_final: 0.3661 (tpt) REVERT: B 403 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8360 (t0) REVERT: B 435 ASN cc_start: 0.7592 (m-40) cc_final: 0.7362 (m-40) REVERT: C 68 MET cc_start: 0.5752 (mpm) cc_final: 0.5127 (mpp) REVERT: C 133 MET cc_start: 0.8351 (mmp) cc_final: 0.8078 (mmp) REVERT: C 137 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: C 357 MET cc_start: 0.8720 (tpp) cc_final: 0.8295 (mmt) REVERT: D 242 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8503 (ttt-90) REVERT: D 309 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8936 (tt) REVERT: F 152 LEU cc_start: 0.8709 (tp) cc_final: 0.8484 (tp) REVERT: F 188 TYR cc_start: 0.7676 (p90) cc_final: 0.7158 (p90) REVERT: F 222 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8254 (mp) REVERT: G 130 ASP cc_start: 0.8939 (m-30) cc_final: 0.8650 (m-30) REVERT: G 163 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7290 (ptp90) REVERT: G 209 VAL cc_start: 0.7489 (t) cc_final: 0.7076 (p) REVERT: G 214 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8183 (t) REVERT: G 216 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5652 (tp) REVERT: H 58 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7688 (mtmm) REVERT: H 85 ASP cc_start: 0.8031 (t0) cc_final: 0.7391 (t0) REVERT: I 1 MET cc_start: 0.4217 (OUTLIER) cc_final: 0.3911 (pmm) REVERT: I 6 LYS cc_start: 0.8142 (mttp) cc_final: 0.7829 (mptt) REVERT: I 32 GLU cc_start: 0.2388 (OUTLIER) cc_final: 0.1809 (pp20) REVERT: J 406 MET cc_start: 0.7425 (mmm) cc_final: 0.6770 (tpt) REVERT: J 438 MET cc_start: 0.8576 (mtp) cc_final: 0.8363 (mtm) outliers start: 77 outliers final: 55 residues processed: 309 average time/residue: 0.5737 time to fit residues: 206.9654 Evaluate side-chains 305 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 237 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 418 PHE Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 303 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 195 optimal weight: 0.4980 chunk 124 optimal weight: 0.4980 chunk 293 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 223 HIS D 72 HIS E 138 HIS H 97 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.150203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.100070 restraints weight = 44145.206| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.41 r_work: 0.3252 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25481 Z= 0.121 Angle : 0.560 12.590 34380 Z= 0.283 Chirality : 0.040 0.333 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.454 63.848 3377 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.00 % Favored : 94.71 % Rotamer: Outliers : 2.84 % Allowed : 27.14 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 3081 helix: 1.90 (0.12), residues: 1989 sheet: -0.42 (0.42), residues: 146 loop : -1.82 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 344 TYR 0.022 0.001 TYR F 105 PHE 0.021 0.001 PHE D 69 TRP 0.008 0.001 TRP D 395 HIS 0.005 0.001 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00285 (25469) covalent geometry : angle 0.55953 (34374) hydrogen bonds : bond 0.03117 ( 1507) hydrogen bonds : angle 3.75470 ( 4428) metal coordination : bond 0.00347 ( 11) metal coordination : angle 1.38018 ( 6) Misc. bond : bond 0.00042 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6162 Ramachandran restraints generated. 3081 Oldfield, 0 Emsley, 3081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 241 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: -0.2074 (OUTLIER) cc_final: -0.2579 (tp) REVERT: A 307 GLN cc_start: 0.8178 (tp40) cc_final: 0.7630 (pp30) REVERT: B 75 MET cc_start: -0.2645 (OUTLIER) cc_final: -0.3018 (mpp) REVERT: B 89 MET cc_start: 0.7943 (tpp) cc_final: 0.7400 (ptp) REVERT: B 95 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.6655 (mt) REVERT: B 125 MET cc_start: 0.4832 (tpt) cc_final: 0.3735 (tpt) REVERT: B 403 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 435 ASN cc_start: 0.7603 (m-40) cc_final: 0.7369 (m-40) REVERT: C 68 MET cc_start: 0.5707 (mpm) cc_final: 0.5098 (mpp) REVERT: C 133 MET cc_start: 0.8348 (mmp) cc_final: 0.8113 (mmp) REVERT: C 137 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 357 MET cc_start: 0.8738 (tpp) cc_final: 0.8341 (mmt) REVERT: D 181 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: D 242 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8575 (ttt-90) REVERT: D 309 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8921 (tt) REVERT: F 152 LEU cc_start: 0.8703 (tp) cc_final: 0.8462 (tp) REVERT: F 188 TYR cc_start: 0.7704 (p90) cc_final: 0.7141 (p90) REVERT: F 222 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8262 (mp) REVERT: G 130 ASP cc_start: 0.8937 (m-30) cc_final: 0.8646 (m-30) REVERT: G 163 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7303 (ptp90) REVERT: G 193 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7943 (mp) REVERT: G 209 VAL cc_start: 0.7491 (t) cc_final: 0.7092 (p) REVERT: G 214 THR cc_start: 0.8391 (OUTLIER) cc_final: 0.8173 (t) REVERT: G 216 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5640 (tp) REVERT: H 58 LYS cc_start: 0.7980 (mtmm) cc_final: 0.7707 (mtmm) REVERT: H 74 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6529 (tp) REVERT: H 85 ASP cc_start: 0.8061 (t0) cc_final: 0.7416 (t0) REVERT: H 141 VAL cc_start: 0.7764 (t) cc_final: 0.7552 (t) REVERT: I 1 MET cc_start: 0.4259 (OUTLIER) cc_final: 0.3989 (pmm) REVERT: I 6 LYS cc_start: 0.8134 (mttp) cc_final: 0.7927 (mptt) REVERT: I 32 GLU cc_start: 0.2454 (OUTLIER) cc_final: 0.1871 (pp20) REVERT: J 406 MET cc_start: 0.7442 (mmm) cc_final: 0.6719 (tpt) REVERT: J 438 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8335 (mtm) REVERT: K 53 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7739 (p) outliers start: 78 outliers final: 55 residues processed: 306 average time/residue: 0.5755 time to fit residues: 204.8571 Evaluate side-chains 311 residues out of total 2745 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 238 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 385 GLU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 168 ILE Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 190 CYS Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 242 ARG Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 313 SER Chi-restraints excluded: chain D residue 327 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 279 GLN Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 93 THR Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 160 HIS Chi-restraints excluded: chain F residue 183 PHE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 163 ARG Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 214 THR Chi-restraints excluded: chain G residue 216 ILE Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 123 GLN Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain J residue 438 MET Chi-restraints excluded: chain J residue 499 THR Chi-restraints excluded: chain J residue 578 THR Chi-restraints excluded: chain J residue 714 SER Chi-restraints excluded: chain K residue 26 LYS Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 68 CYS Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 272 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 125 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 285 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 173 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 HIS B 223 HIS D 72 HIS E 138 HIS H 97 GLN I 40 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.150666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100691 restraints weight = 44098.538| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.42 r_work: 0.3264 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 25481 Z= 0.112 Angle : 0.554 10.962 34380 Z= 0.280 Chirality : 0.039 0.208 3885 Planarity : 0.004 0.099 4387 Dihedral : 4.400 61.969 3377 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.84 % Favored : 94.87 % Rotamer: Outliers : 2.84 % Allowed : 27.18 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.16), residues: 3081 helix: 1.94 (0.12), residues: 1990 sheet: -0.35 (0.45), residues: 131 loop : -1.79 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 344 TYR 0.020 0.001 TYR F 105 PHE 0.021 0.001 PHE D 69 TRP 0.045 0.001 TRP B 148 HIS 0.005 0.000 HIS F 225 Details of bonding type rmsd covalent geometry : bond 0.00258 (25469) covalent geometry : angle 0.55423 (34374) hydrogen bonds : bond 0.03024 ( 1507) hydrogen bonds : angle 3.73191 ( 4428) metal coordination : bond 0.00300 ( 11) metal coordination : angle 1.33280 ( 6) Misc. bond : bond 0.00030 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11723.41 seconds wall clock time: 200 minutes 4.60 seconds (12004.60 seconds total)