Starting phenix.real_space_refine on Sun Jul 21 18:02:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xmi_6733/07_2024/5xmi_6733.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 P 15 5.49 5 S 54 5.16 5 C 9362 2.51 5 N 2539 2.21 5 O 2999 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14969 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "B" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "C" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "D" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "E" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "F" Number of atoms: 2469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2469 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 16, 'TRANS': 302} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.93, per 1000 atoms: 0.53 Number of scatterers: 14969 At special positions: 0 Unit cell: (159.398, 164.624, 82.312, 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) S 54 16.00 P 15 15.00 O 2999 8.00 N 2539 7.00 C 9362 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.74 Conformation dependent library (CDL) restraints added in 2.7 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3552 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 12 sheets defined 48.2% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 138 through 149 removed outlier: 4.279A pdb=" N LYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 159 removed outlier: 4.048A pdb=" N PHE A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 159' Processing helix chain 'A' and resid 178 through 189 removed outlier: 3.745A pdb=" N GLU A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.433A pdb=" N SER A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LYS A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.590A pdb=" N ASN A 224 " --> pdb=" O MET A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.622A pdb=" N GLU A 245 " --> pdb=" O GLY A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 335 through 357 removed outlier: 3.662A pdb=" N MET A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Proline residue: A 350 - end of helix Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 419 through 432 removed outlier: 4.102A pdb=" N LEU A 423 " --> pdb=" O GLU A 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.824A pdb=" N LYS B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 155 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 211 through 224 removed outlier: 3.918A pdb=" N GLU B 223 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN B 224 " --> pdb=" O MET B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 242 through 247 removed outlier: 3.999A pdb=" N GLU B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 removed outlier: 3.992A pdb=" N ILE B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 290 removed outlier: 3.688A pdb=" N ARG B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.764A pdb=" N GLU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 removed outlier: 3.762A pdb=" N TYR B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 357 Proline residue: B 350 - end of helix removed outlier: 3.574A pdb=" N SER B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 Processing helix chain 'B' and resid 418 through 431 removed outlier: 3.559A pdb=" N LEU B 422 " --> pdb=" O ASN B 418 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LYS B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLN B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.757A pdb=" N LYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 removed outlier: 4.163A pdb=" N VAL C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 190 removed outlier: 3.900A pdb=" N THR C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 223 removed outlier: 3.810A pdb=" N LYS C 212 " --> pdb=" O GLY C 208 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 223 " --> pdb=" O ALA C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 4.592A pdb=" N ALA C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 260 removed outlier: 3.713A pdb=" N MET C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 290 Processing helix chain 'C' and resid 300 through 311 Processing helix chain 'C' and resid 321 through 331 removed outlier: 4.248A pdb=" N ARG C 325 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 Proline residue: C 350 - end of helix Processing helix chain 'C' and resid 403 through 413 Processing helix chain 'C' and resid 421 through 432 removed outlier: 3.721A pdb=" N GLN C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.679A pdb=" N LYS D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 155 removed outlier: 4.150A pdb=" N VAL D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 159 Processing helix chain 'D' and resid 178 through 190 removed outlier: 3.825A pdb=" N GLU D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.882A pdb=" N VAL D 214 " --> pdb=" O SER D 210 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN D 224 " --> pdb=" O MET D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 244 through 247 removed outlier: 3.717A pdb=" N GLU D 247 " --> pdb=" O GLY D 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 244 through 247' Processing helix chain 'D' and resid 248 through 260 removed outlier: 3.540A pdb=" N MET D 260 " --> pdb=" O LEU D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 265 removed outlier: 4.000A pdb=" N ASN D 265 " --> pdb=" O ASN D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 288 Processing helix chain 'D' and resid 300 through 313 removed outlier: 4.318A pdb=" N GLU D 309 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 331 removed outlier: 3.779A pdb=" N TYR D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 356 Proline residue: D 350 - end of helix Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.624A pdb=" N ILE D 391 " --> pdb=" O TRP D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 413 removed outlier: 3.646A pdb=" N LEU D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 432 removed outlier: 4.176A pdb=" N LEU D 422 " --> pdb=" O ASN D 418 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 430 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASP D 431 " --> pdb=" O GLN D 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 155 removed outlier: 3.578A pdb=" N LYS E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU E 151 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Proline residue: E 152 - end of helix Processing helix chain 'E' and resid 156 through 160 removed outlier: 3.735A pdb=" N LYS E 160 " --> pdb=" O HIS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 removed outlier: 4.407A pdb=" N ASN E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 224 Processing helix chain 'E' and resid 233 through 237 removed outlier: 3.650A pdb=" N ALA E 236 " --> pdb=" O GLN E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 259 removed outlier: 3.962A pdb=" N LEU E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 290 Processing helix chain 'E' and resid 300 through 311 removed outlier: 4.052A pdb=" N ASN E 311 " --> pdb=" O MET E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 331 removed outlier: 3.789A pdb=" N TYR E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 356 Proline residue: E 350 - end of helix removed outlier: 3.557A pdb=" N SER E 356 " --> pdb=" O ARG E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 402 through 413 removed outlier: 3.827A pdb=" N PHE E 406 " --> pdb=" O THR E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 430 removed outlier: 3.743A pdb=" N LEU E 422 " --> pdb=" O ASN E 418 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS E 424 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 178 through 191 removed outlier: 4.398A pdb=" N ASN F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 224 removed outlier: 3.939A pdb=" N VAL F 214 " --> pdb=" O SER F 210 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 removed outlier: 3.787A pdb=" N LEU F 237 " --> pdb=" O VAL F 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 247 through 265 removed outlier: 4.323A pdb=" N ARG F 251 " --> pdb=" O GLU F 247 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 289 removed outlier: 3.634A pdb=" N ARG F 287 " --> pdb=" O ASP F 283 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 313 removed outlier: 3.537A pdb=" N GLY F 313 " --> pdb=" O GLU F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 331 removed outlier: 3.630A pdb=" N MET F 330 " --> pdb=" O THR F 326 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 Proline residue: F 350 - end of helix Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 402 through 413 removed outlier: 4.247A pdb=" N PHE F 406 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS F 411 " --> pdb=" O LEU F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 432 removed outlier: 4.053A pdb=" N LEU F 422 " --> pdb=" O ASN F 418 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 126 removed outlier: 6.385A pdb=" N THR A 193 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE A 230 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE A 195 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP A 232 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL A 197 " --> pdb=" O ASP A 232 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER A 227 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N LEU A 273 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ILE A 229 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA A 275 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE A 231 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG A 292 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.541A pdb=" N HIS A 359 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 193 through 198 removed outlier: 7.011A pdb=" N THR B 193 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N PHE B 230 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE B 195 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP B 232 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 197 " --> pdb=" O ASP B 232 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 231 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA B 275 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ILE B 169 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N THR B 276 " --> pdb=" O ILE B 169 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 171 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE B 294 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU B 170 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 374 removed outlier: 3.637A pdb=" N LYS B 361 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 197 removed outlier: 3.529A pdb=" N PHE C 195 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE C 229 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ALA C 275 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE C 231 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 276 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AA7, first strand: chain 'D' and resid 227 through 232 removed outlier: 6.947A pdb=" N SER D 227 " --> pdb=" O LEU D 271 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU D 273 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE D 229 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ALA D 275 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE D 231 " --> pdb=" O ALA D 275 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 274 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR D 172 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AA9, first strand: chain 'E' and resid 193 through 196 removed outlier: 3.504A pdb=" N LEU E 271 " --> pdb=" O SER E 227 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY E 274 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 373 through 374 removed outlier: 3.505A pdb=" N ILE E 384 " --> pdb=" O PHE E 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 193 through 194 removed outlier: 6.460A pdb=" N THR F 193 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N PHE F 230 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N LEU F 273 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE F 229 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA F 275 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE F 231 " --> pdb=" O ALA F 275 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR F 172 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 361 through 362 removed outlier: 3.505A pdb=" N THR F 374 " --> pdb=" O LYS F 361 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1608 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: 3.59 Time building geometry restraints manager: 6.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2623 1.31 - 1.43: 3587 1.43 - 1.56: 8879 1.56 - 1.69: 46 1.69 - 1.81: 96 Bond restraints: 15231 Sorted by residual: bond pdb=" C4 ATP E 501 " pdb=" C5 ATP E 501 " ideal model delta sigma weight residual 1.388 1.474 -0.086 1.00e-02 1.00e+04 7.46e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.28e+01 bond pdb=" C4 ATP F 501 " pdb=" C5 ATP F 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.28e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.24e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.473 -0.085 1.00e-02 1.00e+04 7.21e+01 ... (remaining 15226 not shown) Histogram of bond angle deviations from ideal: 100.48 - 107.66: 603 107.66 - 114.85: 8903 114.85 - 122.03: 7030 122.03 - 129.22: 4010 129.22 - 136.40: 84 Bond angle restraints: 20630 Sorted by residual: angle pdb=" PB ATP E 501 " pdb=" O3B ATP E 501 " pdb=" PG ATP E 501 " ideal model delta sigma weight residual 139.87 121.56 18.31 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 121.89 17.98 1.00e+00 1.00e+00 3.23e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 121.92 17.95 1.00e+00 1.00e+00 3.22e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 122.13 17.74 1.00e+00 1.00e+00 3.15e+02 angle pdb=" PB ATP F 501 " pdb=" O3B ATP F 501 " pdb=" PG ATP F 501 " ideal model delta sigma weight residual 139.87 122.30 17.57 1.00e+00 1.00e+00 3.09e+02 ... (remaining 20625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 8606 17.76 - 35.52: 665 35.52 - 53.27: 134 53.27 - 71.03: 28 71.03 - 88.79: 7 Dihedral angle restraints: 9440 sinusoidal: 3950 harmonic: 5490 Sorted by residual: dihedral pdb=" CA LYS C 225 " pdb=" C LYS C 225 " pdb=" N PRO C 226 " pdb=" CA PRO C 226 " ideal model delta harmonic sigma weight residual -180.00 -140.79 -39.21 0 5.00e+00 4.00e-02 6.15e+01 dihedral pdb=" CA THR A 315 " pdb=" C THR A 315 " pdb=" N PRO A 316 " pdb=" CA PRO A 316 " ideal model delta harmonic sigma weight residual -180.00 -141.83 -38.17 0 5.00e+00 4.00e-02 5.83e+01 dihedral pdb=" CA LYS B 225 " pdb=" C LYS B 225 " pdb=" N PRO B 226 " pdb=" CA PRO B 226 " ideal model delta harmonic sigma weight residual 180.00 -142.15 -37.85 0 5.00e+00 4.00e-02 5.73e+01 ... (remaining 9437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1752 0.077 - 0.153: 456 0.153 - 0.230: 113 0.230 - 0.307: 18 0.307 - 0.384: 3 Chirality restraints: 2342 Sorted by residual: chirality pdb=" CA PHE A 290 " pdb=" N PHE A 290 " pdb=" C PHE A 290 " pdb=" CB PHE A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA GLN A 281 " pdb=" N GLN A 281 " pdb=" C GLN A 281 " pdb=" CB GLN A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ARG A 289 " pdb=" N ARG A 289 " pdb=" C ARG A 289 " pdb=" CB ARG A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2339 not shown) Planarity restraints: 2657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 225 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.00e+01 pdb=" N PRO B 226 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO B 226 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 226 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 151 " 0.065 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO F 152 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO F 152 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO F 152 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 315 " 0.053 5.00e-02 4.00e+02 7.96e-02 1.01e+01 pdb=" N PRO A 316 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 316 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 316 " 0.045 5.00e-02 4.00e+02 ... (remaining 2654 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 4359 2.85 - 3.37: 14579 3.37 - 3.88: 23288 3.88 - 4.39: 27019 4.39 - 4.90: 43735 Nonbonded interactions: 112980 Sorted by model distance: nonbonded pdb=" O ALA C 303 " pdb=" OG1 THR C 306 " model vdw 2.342 2.440 nonbonded pdb=" O ALA E 303 " pdb=" OG1 THR E 306 " model vdw 2.376 2.440 nonbonded pdb=" O ALA D 303 " pdb=" OG1 THR D 306 " model vdw 2.391 2.440 nonbonded pdb=" O GLN A 425 " pdb=" OG1 THR A 429 " model vdw 2.409 2.440 nonbonded pdb=" OD2 ASP A 201 " pdb=" OG SER F 284 " model vdw 2.432 2.440 ... (remaining 112975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 119 through 437) selection = (chain 'C' and resid 119 through 437) selection = (chain 'D' and resid 119 through 437) selection = (chain 'E' and resid 119 through 437) selection = (chain 'F' and resid 119 through 437) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 38.700 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 15231 Z= 0.608 Angle : 1.291 18.308 20630 Z= 0.924 Chirality : 0.075 0.384 2342 Planarity : 0.007 0.112 2657 Dihedral : 13.746 88.791 5888 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 2.47 % Allowed : 8.94 % Favored : 88.59 % Rotamer: Outliers : 1.10 % Allowed : 4.23 % Favored : 94.67 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.17), residues: 1902 helix: -1.48 (0.16), residues: 762 sheet: -2.38 (0.33), residues: 169 loop : -2.41 (0.18), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 280 HIS 0.011 0.001 HIS A 359 PHE 0.019 0.001 PHE B 290 TYR 0.016 0.002 TYR A 181 ARG 0.008 0.001 ARG A 304 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 614 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6552 (t80) cc_final: 0.6292 (t80) REVERT: A 188 THR cc_start: 0.6964 (m) cc_final: 0.6699 (p) REVERT: A 217 LEU cc_start: 0.5027 (tp) cc_final: 0.4576 (tp) REVERT: A 225 LYS cc_start: 0.5695 (mtmm) cc_final: 0.5481 (pttp) REVERT: A 235 ASP cc_start: 0.5092 (p0) cc_final: 0.4811 (p0) REVERT: A 252 ILE cc_start: 0.5876 (mt) cc_final: 0.5441 (mm) REVERT: A 308 PHE cc_start: 0.8028 (m-80) cc_final: 0.7483 (m-80) REVERT: A 322 GLU cc_start: 0.8628 (tt0) cc_final: 0.8418 (mp0) REVERT: A 323 ASP cc_start: 0.8637 (m-30) cc_final: 0.8415 (t0) REVERT: A 339 ILE cc_start: 0.7514 (mt) cc_final: 0.7188 (mt) REVERT: A 371 ARG cc_start: 0.6004 (ptm-80) cc_final: 0.4568 (mtp180) REVERT: A 386 MET cc_start: 0.5273 (ptp) cc_final: 0.4170 (ppp) REVERT: B 139 GLU cc_start: 0.8604 (mp0) cc_final: 0.8351 (mt-10) REVERT: B 147 GLU cc_start: 0.8298 (tt0) cc_final: 0.7790 (pp20) REVERT: B 160 LYS cc_start: 0.6955 (mtpp) cc_final: 0.6475 (mmtp) REVERT: B 189 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7356 (pm20) REVERT: B 202 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6342 (pt) REVERT: B 211 GLU cc_start: 0.7810 (mp0) cc_final: 0.7503 (mm-30) REVERT: B 252 ILE cc_start: 0.8310 (mt) cc_final: 0.8108 (mp) REVERT: B 272 VAL cc_start: 0.8973 (t) cc_final: 0.8761 (m) REVERT: B 278 ILE cc_start: 0.8640 (mt) cc_final: 0.7931 (mm) REVERT: B 283 ASP cc_start: 0.7242 (t70) cc_final: 0.7031 (t0) REVERT: B 301 LEU cc_start: 0.7564 (tp) cc_final: 0.7318 (pt) REVERT: B 334 TYR cc_start: 0.6282 (m-10) cc_final: 0.5429 (m-10) REVERT: B 397 LYS cc_start: 0.6434 (tptm) cc_final: 0.6081 (ptmt) REVERT: B 427 GLN cc_start: 0.7956 (tt0) cc_final: 0.7529 (tm-30) REVERT: B 435 GLU cc_start: 0.5370 (mm-30) cc_final: 0.5009 (pm20) REVERT: C 126 GLU cc_start: 0.7836 (pt0) cc_final: 0.7553 (tp30) REVERT: C 133 GLU cc_start: 0.7897 (mp0) cc_final: 0.6291 (tp30) REVERT: C 146 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7777 (mmtt) REVERT: C 184 LYS cc_start: 0.6794 (mttm) cc_final: 0.6522 (tttt) REVERT: C 212 LYS cc_start: 0.7089 (tttp) cc_final: 0.6812 (tttp) REVERT: C 292 ARG cc_start: 0.8289 (tpp-160) cc_final: 0.7751 (mmm-85) REVERT: C 296 ILE cc_start: 0.8450 (mm) cc_final: 0.7560 (tp) REVERT: C 326 THR cc_start: 0.7178 (m) cc_final: 0.6760 (p) REVERT: C 332 GLU cc_start: 0.6922 (tt0) cc_final: 0.6657 (tm-30) REVERT: C 410 ILE cc_start: 0.6022 (mt) cc_final: 0.5260 (pt) REVERT: C 434 GLN cc_start: 0.5818 (mm-40) cc_final: 0.5394 (tp40) REVERT: D 126 GLU cc_start: 0.7201 (pt0) cc_final: 0.6058 (pm20) REVERT: D 133 GLU cc_start: 0.6568 (pm20) cc_final: 0.5789 (pm20) REVERT: D 160 LYS cc_start: 0.7408 (mtpt) cc_final: 0.6480 (mmmt) REVERT: D 166 THR cc_start: 0.5717 (m) cc_final: 0.5355 (m) REVERT: D 195 PHE cc_start: 0.5237 (m-80) cc_final: 0.4560 (m-80) REVERT: D 245 GLU cc_start: 0.7058 (tp30) cc_final: 0.6604 (tp30) REVERT: D 249 SER cc_start: 0.8868 (t) cc_final: 0.8297 (t) REVERT: D 290 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.5763 (t80) REVERT: D 301 LEU cc_start: 0.8638 (tp) cc_final: 0.8412 (pp) REVERT: D 411 LYS cc_start: 0.7056 (mttt) cc_final: 0.6543 (pttt) REVERT: D 432 PHE cc_start: 0.6949 (m-80) cc_final: 0.6641 (m-80) REVERT: E 129 ASN cc_start: 0.6493 (t0) cc_final: 0.5500 (p0) REVERT: E 164 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7613 (ptpp) REVERT: E 181 TYR cc_start: 0.8131 (t80) cc_final: 0.7643 (t80) REVERT: E 191 ASN cc_start: 0.7916 (t0) cc_final: 0.7692 (t0) REVERT: E 235 ASP cc_start: 0.7059 (p0) cc_final: 0.6404 (p0) REVERT: E 252 ILE cc_start: 0.7204 (mt) cc_final: 0.6652 (mm) REVERT: E 309 GLU cc_start: 0.8280 (pt0) cc_final: 0.7692 (tm-30) REVERT: E 359 HIS cc_start: 0.7714 (m90) cc_final: 0.7381 (m-70) REVERT: E 386 MET cc_start: 0.6200 (ptp) cc_final: 0.5981 (ptm) REVERT: E 389 THR cc_start: 0.7523 (p) cc_final: 0.7296 (p) REVERT: E 404 LYS cc_start: 0.6917 (mtmt) cc_final: 0.6044 (tmmt) REVERT: F 142 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8148 (pptt) REVERT: F 146 LYS cc_start: 0.8535 (mttt) cc_final: 0.8296 (mttt) REVERT: F 172 TYR cc_start: 0.6935 (p90) cc_final: 0.6560 (p90) REVERT: F 184 LYS cc_start: 0.8487 (mttm) cc_final: 0.8275 (mmmt) REVERT: F 194 PHE cc_start: 0.7668 (t80) cc_final: 0.7347 (t80) REVERT: F 195 PHE cc_start: 0.7215 (m-80) cc_final: 0.6458 (m-80) REVERT: F 206 TRP cc_start: 0.6502 (m100) cc_final: 0.5969 (t-100) REVERT: F 207 MET cc_start: 0.1962 (mtm) cc_final: 0.1729 (mtt) REVERT: F 230 PHE cc_start: 0.7954 (t80) cc_final: 0.7741 (t80) REVERT: F 235 ASP cc_start: 0.7744 (p0) cc_final: 0.7167 (p0) REVERT: F 240 THR cc_start: 0.4055 (OUTLIER) cc_final: 0.3661 (t) REVERT: F 265 ASN cc_start: 0.7623 (m-40) cc_final: 0.7222 (t0) REVERT: F 323 ASP cc_start: 0.7173 (m-30) cc_final: 0.6723 (t0) REVERT: F 327 LEU cc_start: 0.7266 (mt) cc_final: 0.6601 (mt) REVERT: F 344 LYS cc_start: 0.7208 (mtpp) cc_final: 0.6563 (tptt) REVERT: F 345 ASP cc_start: 0.8277 (t70) cc_final: 0.7983 (t70) REVERT: F 388 TRP cc_start: 0.6874 (p-90) cc_final: 0.6460 (p-90) REVERT: F 397 LYS cc_start: 0.7280 (tptm) cc_final: 0.6679 (ttpt) outliers start: 18 outliers final: 4 residues processed: 623 average time/residue: 0.2949 time to fit residues: 256.0929 Evaluate side-chains 345 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 338 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain D residue 290 PHE Chi-restraints excluded: chain F residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 224 ASN A 268 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN B 261 ASN C 268 GLN C 425 GLN D 216 GLN D 233 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 GLN E 261 ASN ** F 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 355 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15231 Z= 0.250 Angle : 0.744 10.968 20630 Z= 0.379 Chirality : 0.044 0.261 2342 Planarity : 0.006 0.117 2657 Dihedral : 11.092 89.020 2214 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.10 % Favored : 92.22 % Rotamer: Outliers : 5.15 % Allowed : 13.85 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.25 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.19), residues: 1902 helix: -0.12 (0.18), residues: 799 sheet: -1.39 (0.35), residues: 198 loop : -1.80 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 132 HIS 0.018 0.002 HIS A 157 PHE 0.023 0.002 PHE C 432 TYR 0.018 0.002 TYR C 334 ARG 0.009 0.001 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 339 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8081 (m-80) cc_final: 0.6658 (p90) REVERT: A 181 TYR cc_start: 0.6896 (t80) cc_final: 0.6680 (t80) REVERT: A 308 PHE cc_start: 0.7829 (m-80) cc_final: 0.7540 (m-80) REVERT: A 323 ASP cc_start: 0.8709 (m-30) cc_final: 0.8497 (t0) REVERT: A 325 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8258 (ptp90) REVERT: A 360 PHE cc_start: 0.6493 (m-80) cc_final: 0.6282 (m-10) REVERT: A 386 MET cc_start: 0.4881 (ptp) cc_final: 0.4105 (ppp) REVERT: A 430 ARG cc_start: 0.5261 (mtm180) cc_final: 0.3739 (tpm170) REVERT: B 160 LYS cc_start: 0.6839 (mtpp) cc_final: 0.6491 (mmtt) REVERT: B 202 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5652 (pt) REVERT: B 292 ARG cc_start: 0.5689 (ttm-80) cc_final: 0.4999 (ttt90) REVERT: B 397 LYS cc_start: 0.6379 (tptm) cc_final: 0.5829 (ptmm) REVERT: B 435 GLU cc_start: 0.5670 (mm-30) cc_final: 0.4634 (pm20) REVERT: C 133 GLU cc_start: 0.7923 (mp0) cc_final: 0.7351 (pm20) REVERT: C 145 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8680 (tp) REVERT: C 146 LYS cc_start: 0.8696 (mtpt) cc_final: 0.8150 (mmtt) REVERT: C 211 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7481 (mm-30) REVERT: C 220 MET cc_start: 0.8529 (mtp) cc_final: 0.8299 (ptp) REVERT: C 223 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6057 (pp20) REVERT: C 240 THR cc_start: 0.3635 (OUTLIER) cc_final: 0.3350 (p) REVERT: C 243 GLU cc_start: 0.4505 (mt-10) cc_final: 0.4065 (tm-30) REVERT: C 255 GLU cc_start: 0.8145 (tt0) cc_final: 0.7391 (mt-10) REVERT: C 271 LEU cc_start: 0.7846 (tp) cc_final: 0.7044 (mm) REVERT: C 292 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7903 (mmt-90) REVERT: C 332 GLU cc_start: 0.7055 (tt0) cc_final: 0.6717 (tm-30) REVERT: C 410 ILE cc_start: 0.6296 (mt) cc_final: 0.5917 (pt) REVERT: C 425 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5994 (tp-100) REVERT: C 426 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7215 (mt-10) REVERT: C 435 GLU cc_start: 0.6168 (tp30) cc_final: 0.5128 (tt0) REVERT: D 126 GLU cc_start: 0.6990 (pt0) cc_final: 0.6034 (pm20) REVERT: D 131 LYS cc_start: 0.8275 (tptm) cc_final: 0.7498 (tptm) REVERT: D 160 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6440 (mmmt) REVERT: D 195 PHE cc_start: 0.5197 (m-80) cc_final: 0.4474 (m-80) REVERT: D 198 SER cc_start: 0.8440 (t) cc_final: 0.8118 (p) REVERT: D 232 ASP cc_start: 0.8070 (t0) cc_final: 0.7456 (m-30) REVERT: D 245 GLU cc_start: 0.6913 (tp30) cc_final: 0.6641 (tp30) REVERT: D 289 ARG cc_start: 0.5513 (tpp-160) cc_final: 0.5043 (mmp-170) REVERT: D 398 GLU cc_start: 0.7691 (pt0) cc_final: 0.7123 (tt0) REVERT: D 411 LYS cc_start: 0.7195 (mttt) cc_final: 0.6697 (pttt) REVERT: D 432 PHE cc_start: 0.7388 (m-80) cc_final: 0.6971 (m-80) REVERT: E 129 ASN cc_start: 0.6040 (t0) cc_final: 0.5245 (p0) REVERT: E 164 LYS cc_start: 0.7778 (mmmt) cc_final: 0.7201 (ptpp) REVERT: E 181 TYR cc_start: 0.8385 (t80) cc_final: 0.8003 (t80) REVERT: E 191 ASN cc_start: 0.8126 (t0) cc_final: 0.7874 (t0) REVERT: E 207 MET cc_start: 0.4084 (OUTLIER) cc_final: 0.3691 (mtp) REVERT: E 404 LYS cc_start: 0.7133 (mtmt) cc_final: 0.6460 (tmmt) REVERT: F 143 GLU cc_start: 0.7643 (tp30) cc_final: 0.7435 (tp30) REVERT: F 146 LYS cc_start: 0.8438 (mttt) cc_final: 0.8210 (tttt) REVERT: F 169 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8524 (tp) REVERT: F 170 LEU cc_start: 0.8541 (tp) cc_final: 0.8262 (mt) REVERT: F 184 LYS cc_start: 0.8693 (mttm) cc_final: 0.8289 (mmmt) REVERT: F 195 PHE cc_start: 0.6611 (m-80) cc_final: 0.6295 (m-80) REVERT: F 206 TRP cc_start: 0.6433 (m100) cc_final: 0.5899 (t-100) REVERT: F 207 MET cc_start: 0.2135 (mtm) cc_final: 0.1809 (mtt) REVERT: F 218 PHE cc_start: 0.7349 (m-80) cc_final: 0.6943 (m-10) REVERT: F 235 ASP cc_start: 0.7753 (p0) cc_final: 0.7131 (p0) REVERT: F 255 GLU cc_start: 0.8825 (tp30) cc_final: 0.8478 (tp30) REVERT: F 307 MET cc_start: 0.8788 (tpp) cc_final: 0.8502 (tpp) REVERT: F 323 ASP cc_start: 0.6615 (m-30) cc_final: 0.6256 (t0) REVERT: F 344 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6372 (tptt) REVERT: F 345 ASP cc_start: 0.8237 (t70) cc_final: 0.7861 (t70) REVERT: F 396 LEU cc_start: 0.6596 (tp) cc_final: 0.6388 (mt) REVERT: F 397 LYS cc_start: 0.6948 (tptm) cc_final: 0.6333 (ttpt) outliers start: 84 outliers final: 43 residues processed: 393 average time/residue: 0.2846 time to fit residues: 159.5066 Evaluate side-chains 314 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 263 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 311 ASN Chi-restraints excluded: chain A residue 325 ARG Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 425 GLN Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 207 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN C 265 ASN C 425 GLN ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 ASN D 425 GLN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 GLN E 437 ASN F 157 HIS ** F 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 15231 Z= 0.510 Angle : 0.944 13.096 20630 Z= 0.490 Chirality : 0.051 0.287 2342 Planarity : 0.008 0.146 2657 Dihedral : 12.366 89.796 2210 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.88 % Favored : 89.43 % Rotamer: Outliers : 6.43 % Allowed : 16.67 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 1902 helix: -0.79 (0.17), residues: 792 sheet: -1.51 (0.37), residues: 188 loop : -2.02 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP F 132 HIS 0.008 0.003 HIS A 359 PHE 0.041 0.004 PHE C 194 TYR 0.026 0.004 TYR A 172 ARG 0.016 0.002 ARG B 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 286 time to evaluate : 1.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 PHE cc_start: 0.8078 (m-80) cc_final: 0.6649 (p90) REVERT: A 181 TYR cc_start: 0.6872 (t80) cc_final: 0.6535 (t80) REVERT: A 273 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6128 (tt) REVERT: A 323 ASP cc_start: 0.8933 (m-30) cc_final: 0.8568 (t0) REVERT: A 325 ARG cc_start: 0.8387 (mtm110) cc_final: 0.8006 (ptp-110) REVERT: B 160 LYS cc_start: 0.6835 (mtpp) cc_final: 0.6586 (mmtt) REVERT: B 181 TYR cc_start: 0.8244 (t80) cc_final: 0.7750 (t80) REVERT: B 255 GLU cc_start: 0.7055 (tp30) cc_final: 0.6848 (tp30) REVERT: B 281 GLN cc_start: 0.8517 (mp10) cc_final: 0.8091 (mp10) REVERT: B 290 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.5294 (t80) REVERT: B 334 TYR cc_start: 0.5487 (m-80) cc_final: 0.5016 (m-10) REVERT: B 397 LYS cc_start: 0.6486 (tptm) cc_final: 0.5833 (ptmm) REVERT: C 139 GLU cc_start: 0.8487 (tp30) cc_final: 0.6661 (tp30) REVERT: C 243 GLU cc_start: 0.3258 (mt-10) cc_final: 0.2945 (tp30) REVERT: C 255 GLU cc_start: 0.8198 (tt0) cc_final: 0.7893 (tt0) REVERT: C 278 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7721 (pt) REVERT: C 290 PHE cc_start: 0.6348 (OUTLIER) cc_final: 0.5618 (t80) REVERT: C 292 ARG cc_start: 0.8537 (tpp-160) cc_final: 0.8319 (mmt-90) REVERT: C 332 GLU cc_start: 0.7325 (tt0) cc_final: 0.6697 (tm-30) REVERT: D 126 GLU cc_start: 0.7358 (pt0) cc_final: 0.7015 (tp30) REVERT: D 160 LYS cc_start: 0.6959 (mtpt) cc_final: 0.6307 (mmmt) REVERT: D 195 PHE cc_start: 0.5097 (m-80) cc_final: 0.4382 (m-80) REVERT: D 198 SER cc_start: 0.8712 (t) cc_final: 0.8413 (p) REVERT: D 206 TRP cc_start: 0.6500 (m100) cc_final: 0.6117 (m-10) REVERT: D 232 ASP cc_start: 0.8422 (t0) cc_final: 0.8043 (t0) REVERT: D 241 ARG cc_start: 0.6308 (ptt90) cc_final: 0.5895 (ptp90) REVERT: D 245 GLU cc_start: 0.7248 (tp30) cc_final: 0.6742 (tp30) REVERT: D 249 SER cc_start: 0.8736 (t) cc_final: 0.8149 (t) REVERT: D 288 ARG cc_start: 0.6981 (mpt180) cc_final: 0.5277 (ttp80) REVERT: D 307 MET cc_start: 0.7951 (ttm) cc_final: 0.7284 (tpp) REVERT: D 322 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7219 (mp0) REVERT: D 347 LEU cc_start: 0.8580 (mt) cc_final: 0.8370 (tp) REVERT: D 398 GLU cc_start: 0.8124 (pt0) cc_final: 0.7380 (tt0) REVERT: E 164 LYS cc_start: 0.7350 (mmmt) cc_final: 0.6562 (ptpp) REVERT: E 181 TYR cc_start: 0.8474 (t80) cc_final: 0.7405 (t80) REVERT: E 212 LYS cc_start: 0.7187 (tttm) cc_final: 0.6915 (tmtt) REVERT: E 404 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6479 (tmmt) REVERT: F 163 ARG cc_start: 0.5334 (OUTLIER) cc_final: 0.4995 (ptt180) REVERT: F 207 MET cc_start: 0.2272 (mtm) cc_final: 0.1693 (mtt) REVERT: F 251 ARG cc_start: 0.7300 (ptp-170) cc_final: 0.7067 (ptt180) REVERT: F 287 ARG cc_start: 0.5353 (mtm110) cc_final: 0.4825 (ptt-90) REVERT: F 307 MET cc_start: 0.8692 (tpp) cc_final: 0.8285 (tpp) REVERT: F 323 ASP cc_start: 0.6396 (m-30) cc_final: 0.6087 (t0) REVERT: F 330 MET cc_start: 0.8071 (tpt) cc_final: 0.7798 (tmm) REVERT: F 345 ASP cc_start: 0.8277 (t70) cc_final: 0.7958 (t0) outliers start: 105 outliers final: 66 residues processed: 369 average time/residue: 0.2693 time to fit residues: 143.9791 Evaluate side-chains 303 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 232 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 155 PHE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 283 ASP Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 311 ASN Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 339 ILE Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 87 optimal weight: 30.0000 chunk 18 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 chunk 169 optimal weight: 0.9990 chunk 179 optimal weight: 0.0070 chunk 88 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 216 GLN F 355 GLN F 437 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.6963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15231 Z= 0.232 Angle : 0.702 9.435 20630 Z= 0.359 Chirality : 0.044 0.317 2342 Planarity : 0.006 0.117 2657 Dihedral : 11.328 89.938 2205 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.63 % Allowed : 7.68 % Favored : 91.69 % Rotamer: Outliers : 4.29 % Allowed : 20.22 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1902 helix: -0.08 (0.18), residues: 802 sheet: -1.27 (0.38), residues: 191 loop : -1.68 (0.21), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 280 HIS 0.006 0.001 HIS E 359 PHE 0.034 0.002 PHE E 290 TYR 0.021 0.002 TYR A 172 ARG 0.006 0.001 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 271 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6758 (t80) cc_final: 0.6421 (t80) REVERT: A 259 GLN cc_start: 0.4753 (mm-40) cc_final: 0.4302 (mt0) REVERT: A 323 ASP cc_start: 0.9001 (m-30) cc_final: 0.8709 (t0) REVERT: B 138 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7255 (mt) REVERT: B 139 GLU cc_start: 0.8679 (mp0) cc_final: 0.7849 (tm-30) REVERT: B 160 LYS cc_start: 0.6792 (mtpp) cc_final: 0.6530 (mmtt) REVERT: B 169 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7878 (mp) REVERT: B 202 LEU cc_start: 0.6293 (mt) cc_final: 0.5214 (pt) REVERT: B 255 GLU cc_start: 0.6931 (tp30) cc_final: 0.6721 (tp30) REVERT: B 260 MET cc_start: 0.6980 (ppp) cc_final: 0.6450 (ppp) REVERT: B 281 GLN cc_start: 0.8371 (mp10) cc_final: 0.7918 (mp10) REVERT: B 290 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5516 (t80) REVERT: B 308 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: B 334 TYR cc_start: 0.6093 (m-80) cc_final: 0.5564 (m-10) REVERT: B 397 LYS cc_start: 0.6575 (tptm) cc_final: 0.5926 (ptmm) REVERT: C 132 TRP cc_start: 0.5782 (m100) cc_final: 0.4335 (m100) REVERT: C 139 GLU cc_start: 0.7964 (tp30) cc_final: 0.6675 (tp30) REVERT: C 143 GLU cc_start: 0.8020 (mm-30) cc_final: 0.6947 (mm-30) REVERT: C 240 THR cc_start: 0.3816 (OUTLIER) cc_final: 0.3555 (p) REVERT: C 243 GLU cc_start: 0.3163 (mt-10) cc_final: 0.2765 (tp30) REVERT: C 290 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5644 (t80) REVERT: C 332 GLU cc_start: 0.7077 (tt0) cc_final: 0.6467 (tm-30) REVERT: C 435 GLU cc_start: 0.6913 (tp30) cc_final: 0.4754 (pp20) REVERT: D 126 GLU cc_start: 0.7394 (pt0) cc_final: 0.7088 (tp30) REVERT: D 131 LYS cc_start: 0.8741 (tptm) cc_final: 0.7907 (mmtt) REVERT: D 154 LYS cc_start: 0.8483 (tttt) cc_final: 0.8172 (mtmm) REVERT: D 160 LYS cc_start: 0.6837 (mtpt) cc_final: 0.6075 (mmmt) REVERT: D 195 PHE cc_start: 0.5266 (m-80) cc_final: 0.4619 (m-80) REVERT: D 198 SER cc_start: 0.8571 (t) cc_final: 0.8149 (p) REVERT: D 232 ASP cc_start: 0.8260 (t0) cc_final: 0.7949 (t0) REVERT: D 245 GLU cc_start: 0.7335 (tp30) cc_final: 0.6890 (tp30) REVERT: D 249 SER cc_start: 0.8579 (t) cc_final: 0.7846 (t) REVERT: D 288 ARG cc_start: 0.7042 (mpt180) cc_final: 0.5204 (tmm160) REVERT: D 307 MET cc_start: 0.7963 (ttm) cc_final: 0.7193 (tpp) REVERT: D 311 ASN cc_start: 0.8359 (m110) cc_final: 0.7775 (m-40) REVERT: D 322 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7168 (mp0) REVERT: D 398 GLU cc_start: 0.8146 (pt0) cc_final: 0.7444 (tt0) REVERT: E 124 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6233 (mp) REVERT: E 164 LYS cc_start: 0.7168 (mmmt) cc_final: 0.6406 (ptpp) REVERT: E 181 TYR cc_start: 0.8271 (t80) cc_final: 0.7326 (t80) REVERT: E 212 LYS cc_start: 0.7408 (tttm) cc_final: 0.6945 (tmtt) REVERT: E 215 LYS cc_start: 0.8798 (tppt) cc_final: 0.8578 (tppt) REVERT: E 260 MET cc_start: 0.6941 (tpt) cc_final: 0.6727 (tpp) REVERT: E 335 SER cc_start: 0.8515 (m) cc_final: 0.8091 (p) REVERT: E 386 MET cc_start: 0.5647 (ppp) cc_final: 0.5444 (ppp) REVERT: E 404 LYS cc_start: 0.7082 (mtmt) cc_final: 0.6475 (tmmt) REVERT: E 423 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8169 (mm) REVERT: F 194 PHE cc_start: 0.7820 (t80) cc_final: 0.7377 (t80) REVERT: F 207 MET cc_start: 0.2369 (mtm) cc_final: 0.1716 (mtt) REVERT: F 230 PHE cc_start: 0.8060 (t80) cc_final: 0.7844 (t80) REVERT: F 251 ARG cc_start: 0.6993 (ptp-170) cc_final: 0.6512 (ptt180) REVERT: F 255 GLU cc_start: 0.8812 (tp30) cc_final: 0.8512 (mt-10) REVERT: F 287 ARG cc_start: 0.5401 (mtm110) cc_final: 0.4886 (ptt-90) REVERT: F 307 MET cc_start: 0.8803 (tpp) cc_final: 0.8385 (tpp) REVERT: F 323 ASP cc_start: 0.6387 (m-30) cc_final: 0.6031 (t0) REVERT: F 327 LEU cc_start: 0.8365 (mt) cc_final: 0.8008 (mt) REVERT: F 330 MET cc_start: 0.8044 (tpt) cc_final: 0.7802 (tmm) outliers start: 70 outliers final: 40 residues processed: 317 average time/residue: 0.2705 time to fit residues: 124.8260 Evaluate side-chains 286 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 238 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 320 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.0060 chunk 102 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.7676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 15231 Z= 0.337 Angle : 0.761 9.253 20630 Z= 0.391 Chirality : 0.045 0.255 2342 Planarity : 0.006 0.117 2657 Dihedral : 11.413 88.102 2205 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.15 % Favored : 89.22 % Rotamer: Outliers : 6.19 % Allowed : 20.71 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.19), residues: 1902 helix: -0.21 (0.18), residues: 808 sheet: -1.15 (0.38), residues: 192 loop : -1.69 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 280 HIS 0.010 0.002 HIS F 157 PHE 0.033 0.003 PHE C 432 TYR 0.020 0.002 TYR A 172 ARG 0.006 0.001 ARG C 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 243 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6741 (t80) cc_final: 0.6440 (t80) REVERT: A 323 ASP cc_start: 0.8754 (m-30) cc_final: 0.8357 (t0) REVERT: A 325 ARG cc_start: 0.8399 (ptp-110) cc_final: 0.8147 (ppt170) REVERT: A 427 GLN cc_start: 0.6154 (mp10) cc_final: 0.5542 (pp30) REVERT: B 255 GLU cc_start: 0.6910 (tp30) cc_final: 0.6556 (tp30) REVERT: B 257 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7641 (tp) REVERT: B 260 MET cc_start: 0.7269 (ppp) cc_final: 0.6674 (ppp) REVERT: B 290 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5541 (t80) REVERT: B 308 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6756 (m-10) REVERT: B 334 TYR cc_start: 0.5841 (m-10) cc_final: 0.5522 (m-10) REVERT: C 139 GLU cc_start: 0.8044 (tp30) cc_final: 0.7308 (tp30) REVERT: C 143 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7713 (mm-30) REVERT: C 243 GLU cc_start: 0.4043 (mt-10) cc_final: 0.3093 (tp30) REVERT: C 290 PHE cc_start: 0.6622 (OUTLIER) cc_final: 0.5895 (t80) REVERT: C 292 ARG cc_start: 0.8443 (tpp-160) cc_final: 0.7990 (tpp80) REVERT: C 332 GLU cc_start: 0.7161 (tt0) cc_final: 0.6503 (tm-30) REVERT: D 131 LYS cc_start: 0.8674 (tptm) cc_final: 0.7913 (mmtm) REVERT: D 143 GLU cc_start: 0.8172 (pt0) cc_final: 0.7894 (pp20) REVERT: D 146 LYS cc_start: 0.8759 (mttt) cc_final: 0.8062 (mmtm) REVERT: D 147 GLU cc_start: 0.8165 (pt0) cc_final: 0.7804 (pt0) REVERT: D 160 LYS cc_start: 0.7297 (mtpt) cc_final: 0.6465 (mmmt) REVERT: D 195 PHE cc_start: 0.5328 (m-80) cc_final: 0.4649 (m-80) REVERT: D 198 SER cc_start: 0.8514 (t) cc_final: 0.8159 (p) REVERT: D 232 ASP cc_start: 0.8273 (t0) cc_final: 0.8003 (t0) REVERT: D 307 MET cc_start: 0.8025 (ttm) cc_final: 0.7061 (tpp) REVERT: D 311 ASN cc_start: 0.8266 (m110) cc_final: 0.7712 (m-40) REVERT: D 322 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7143 (mp0) REVERT: D 398 GLU cc_start: 0.8115 (pt0) cc_final: 0.7349 (tt0) REVERT: D 432 PHE cc_start: 0.7742 (m-80) cc_final: 0.7183 (m-80) REVERT: E 164 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6698 (mmmt) REVERT: E 181 TYR cc_start: 0.8537 (t80) cc_final: 0.7447 (t80) REVERT: E 335 SER cc_start: 0.8577 (m) cc_final: 0.8087 (p) REVERT: E 404 LYS cc_start: 0.7189 (mtmt) cc_final: 0.6552 (tptt) REVERT: E 423 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8108 (mm) REVERT: F 194 PHE cc_start: 0.7808 (t80) cc_final: 0.7337 (t80) REVERT: F 207 MET cc_start: 0.2427 (mtm) cc_final: 0.1923 (mtm) REVERT: F 251 ARG cc_start: 0.6982 (ptp-170) cc_final: 0.6529 (ptp-170) REVERT: F 255 GLU cc_start: 0.8763 (tp30) cc_final: 0.8513 (mt-10) REVERT: F 276 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7868 (m) REVERT: F 307 MET cc_start: 0.8683 (tpp) cc_final: 0.8404 (tpp) REVERT: F 323 ASP cc_start: 0.6220 (m-30) cc_final: 0.5905 (t0) REVERT: F 327 LEU cc_start: 0.8450 (mt) cc_final: 0.8096 (mt) REVERT: F 330 MET cc_start: 0.8121 (tpt) cc_final: 0.7807 (tmm) REVERT: F 334 TYR cc_start: 0.8463 (m-80) cc_final: 0.8176 (m-80) REVERT: F 371 ARG cc_start: 0.7539 (ttt-90) cc_final: 0.7239 (ptt180) outliers start: 101 outliers final: 66 residues processed: 324 average time/residue: 0.2416 time to fit residues: 117.6533 Evaluate side-chains 292 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 220 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 286 ILE Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 402 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 179 optimal weight: 0.0770 chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 overall best weight: 2.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 GLN ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15231 Z= 0.230 Angle : 0.680 8.880 20630 Z= 0.349 Chirality : 0.043 0.227 2342 Planarity : 0.006 0.117 2657 Dihedral : 10.796 69.597 2205 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.83 % Favored : 91.59 % Rotamer: Outliers : 5.27 % Allowed : 22.55 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.19), residues: 1902 helix: -0.00 (0.18), residues: 810 sheet: -1.05 (0.38), residues: 192 loop : -1.53 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 280 HIS 0.006 0.001 HIS F 157 PHE 0.029 0.002 PHE E 290 TYR 0.018 0.002 TYR A 172 ARG 0.007 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 263 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6541 (t80) cc_final: 0.6254 (t80) REVERT: A 259 GLN cc_start: 0.4477 (mm110) cc_final: 0.4012 (mt0) REVERT: A 323 ASP cc_start: 0.8702 (m-30) cc_final: 0.8352 (t0) REVERT: A 325 ARG cc_start: 0.8414 (ptp-110) cc_final: 0.8137 (ppt170) REVERT: A 427 GLN cc_start: 0.6004 (mp10) cc_final: 0.5422 (pp30) REVERT: B 169 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7782 (mp) REVERT: B 202 LEU cc_start: 0.6547 (mt) cc_final: 0.5554 (pt) REVERT: B 255 GLU cc_start: 0.6943 (tp30) cc_final: 0.6447 (tp30) REVERT: B 259 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7720 (tp40) REVERT: B 290 PHE cc_start: 0.6567 (OUTLIER) cc_final: 0.5862 (t80) REVERT: B 308 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: C 139 GLU cc_start: 0.7869 (tp30) cc_final: 0.6975 (tp30) REVERT: C 143 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7976 (mm-30) REVERT: C 207 MET cc_start: 0.6493 (tmm) cc_final: 0.6174 (tmm) REVERT: C 240 THR cc_start: 0.3748 (OUTLIER) cc_final: 0.3478 (p) REVERT: C 243 GLU cc_start: 0.4005 (mt-10) cc_final: 0.3001 (tp30) REVERT: C 255 GLU cc_start: 0.8097 (tt0) cc_final: 0.7845 (mt-10) REVERT: C 290 PHE cc_start: 0.6631 (OUTLIER) cc_final: 0.5854 (t80) REVERT: C 292 ARG cc_start: 0.8340 (tpp-160) cc_final: 0.7940 (tpp80) REVERT: C 332 GLU cc_start: 0.7132 (tt0) cc_final: 0.6514 (tm-30) REVERT: C 435 GLU cc_start: 0.7125 (tp30) cc_final: 0.5997 (mt-10) REVERT: D 131 LYS cc_start: 0.8779 (tptm) cc_final: 0.7949 (mmtm) REVERT: D 143 GLU cc_start: 0.8190 (pt0) cc_final: 0.7848 (pp20) REVERT: D 147 GLU cc_start: 0.8205 (pt0) cc_final: 0.7867 (pt0) REVERT: D 160 LYS cc_start: 0.7028 (mtpt) cc_final: 0.6161 (mmmt) REVERT: D 195 PHE cc_start: 0.5021 (m-80) cc_final: 0.4414 (m-80) REVERT: D 198 SER cc_start: 0.8660 (t) cc_final: 0.8277 (p) REVERT: D 211 GLU cc_start: 0.8090 (mp0) cc_final: 0.7599 (mp0) REVERT: D 232 ASP cc_start: 0.8103 (t0) cc_final: 0.7795 (t0) REVERT: D 245 GLU cc_start: 0.7275 (tp30) cc_final: 0.6958 (tp30) REVERT: D 307 MET cc_start: 0.7922 (ttm) cc_final: 0.7126 (tpp) REVERT: D 322 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7136 (mp0) REVERT: D 398 GLU cc_start: 0.8176 (pt0) cc_final: 0.7640 (tp30) REVERT: D 432 PHE cc_start: 0.7730 (m-80) cc_final: 0.7121 (m-80) REVERT: E 164 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6252 (ptpp) REVERT: E 181 TYR cc_start: 0.8275 (t80) cc_final: 0.7246 (t80) REVERT: E 335 SER cc_start: 0.8476 (m) cc_final: 0.8080 (p) REVERT: E 386 MET cc_start: 0.6381 (ppp) cc_final: 0.6111 (ppp) REVERT: E 404 LYS cc_start: 0.7206 (mtmt) cc_final: 0.6588 (tmmt) REVERT: E 423 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8067 (mt) REVERT: F 194 PHE cc_start: 0.7824 (t80) cc_final: 0.7340 (t80) REVERT: F 207 MET cc_start: 0.2246 (mtm) cc_final: 0.1764 (mtm) REVERT: F 251 ARG cc_start: 0.6780 (ptp-170) cc_final: 0.6515 (ptp-170) REVERT: F 307 MET cc_start: 0.8685 (tpp) cc_final: 0.8369 (tpp) REVERT: F 327 LEU cc_start: 0.8328 (mt) cc_final: 0.8109 (mt) REVERT: F 330 MET cc_start: 0.8192 (tpt) cc_final: 0.7846 (tmm) REVERT: F 334 TYR cc_start: 0.8426 (m-80) cc_final: 0.7607 (m-80) REVERT: F 371 ARG cc_start: 0.7540 (ttt-90) cc_final: 0.7244 (ptt180) REVERT: F 396 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6065 (pp) REVERT: F 419 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7640 (mm-30) outliers start: 86 outliers final: 60 residues processed: 323 average time/residue: 0.2403 time to fit residues: 117.0663 Evaluate side-chains 310 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 242 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 362 ASP Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 419 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.8023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15231 Z= 0.231 Angle : 0.675 8.477 20630 Z= 0.347 Chirality : 0.042 0.206 2342 Planarity : 0.006 0.117 2657 Dihedral : 10.572 71.879 2205 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.89 % Favored : 90.54 % Rotamer: Outliers : 5.39 % Allowed : 23.22 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.21 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.20), residues: 1902 helix: 0.11 (0.18), residues: 811 sheet: -1.02 (0.38), residues: 194 loop : -1.48 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 280 HIS 0.006 0.001 HIS E 359 PHE 0.025 0.002 PHE E 290 TYR 0.021 0.002 TYR E 172 ARG 0.004 0.000 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 248 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6431 (t80) cc_final: 0.6157 (t80) REVERT: A 259 GLN cc_start: 0.4696 (mm110) cc_final: 0.4270 (mt0) REVERT: A 323 ASP cc_start: 0.8705 (m-30) cc_final: 0.8352 (t0) REVERT: A 325 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8133 (ppt170) REVERT: A 427 GLN cc_start: 0.6000 (mp10) cc_final: 0.5423 (pp30) REVERT: B 169 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7859 (mp) REVERT: B 202 LEU cc_start: 0.6548 (mt) cc_final: 0.5585 (pt) REVERT: B 255 GLU cc_start: 0.6915 (tp30) cc_final: 0.6426 (tp30) REVERT: B 259 GLN cc_start: 0.7809 (tp-100) cc_final: 0.7574 (tp40) REVERT: B 290 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5474 (t80) REVERT: B 308 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6951 (m-10) REVERT: B 395 GLU cc_start: 0.4606 (OUTLIER) cc_final: 0.4401 (pm20) REVERT: C 139 GLU cc_start: 0.7632 (tp30) cc_final: 0.6487 (tp30) REVERT: C 143 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8046 (mm-30) REVERT: C 240 THR cc_start: 0.4023 (OUTLIER) cc_final: 0.3731 (p) REVERT: C 243 GLU cc_start: 0.4038 (mt-10) cc_final: 0.2995 (tp30) REVERT: C 268 GLN cc_start: 0.5337 (tt0) cc_final: 0.4294 (pm20) REVERT: C 290 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5793 (t80) REVERT: C 292 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.8034 (tpp80) REVERT: C 332 GLU cc_start: 0.7043 (tt0) cc_final: 0.6412 (tm-30) REVERT: D 131 LYS cc_start: 0.8743 (tptm) cc_final: 0.7858 (mmtm) REVERT: D 143 GLU cc_start: 0.8227 (pt0) cc_final: 0.7843 (pp20) REVERT: D 147 GLU cc_start: 0.8251 (pt0) cc_final: 0.7770 (pt0) REVERT: D 160 LYS cc_start: 0.7101 (mtpt) cc_final: 0.6242 (mmmt) REVERT: D 198 SER cc_start: 0.8676 (t) cc_final: 0.8294 (p) REVERT: D 211 GLU cc_start: 0.8104 (mp0) cc_final: 0.7613 (mp0) REVERT: D 232 ASP cc_start: 0.8161 (t0) cc_final: 0.7805 (t0) REVERT: D 253 LYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6918 (mtmm) REVERT: D 288 ARG cc_start: 0.7179 (mmt-90) cc_final: 0.5321 (ttp80) REVERT: D 307 MET cc_start: 0.8022 (ttm) cc_final: 0.7074 (tpp) REVERT: D 311 ASN cc_start: 0.8348 (m110) cc_final: 0.7787 (m110) REVERT: D 322 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7225 (mp0) REVERT: D 398 GLU cc_start: 0.8209 (pt0) cc_final: 0.7621 (tp30) REVERT: D 404 LYS cc_start: 0.8080 (mtmt) cc_final: 0.7775 (tptt) REVERT: D 432 PHE cc_start: 0.7688 (m-80) cc_final: 0.7178 (m-80) REVERT: E 127 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.6007 (tptt) REVERT: E 164 LYS cc_start: 0.7102 (mmmt) cc_final: 0.6857 (mmmt) REVERT: E 181 TYR cc_start: 0.8272 (t80) cc_final: 0.7266 (t80) REVERT: E 260 MET cc_start: 0.6824 (tpp) cc_final: 0.6496 (tpt) REVERT: E 335 SER cc_start: 0.8569 (m) cc_final: 0.8018 (p) REVERT: E 359 HIS cc_start: 0.7162 (m-70) cc_final: 0.6774 (m170) REVERT: E 386 MET cc_start: 0.6180 (ppp) cc_final: 0.5887 (ppp) REVERT: E 404 LYS cc_start: 0.7191 (mtmt) cc_final: 0.6618 (tptt) REVERT: E 417 VAL cc_start: 0.5785 (OUTLIER) cc_final: 0.5321 (t) REVERT: E 423 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8058 (mt) REVERT: F 194 PHE cc_start: 0.7836 (t80) cc_final: 0.7404 (t80) REVERT: F 207 MET cc_start: 0.2279 (mtm) cc_final: 0.1769 (mtm) REVERT: F 251 ARG cc_start: 0.6782 (ptp-170) cc_final: 0.6522 (ptp-170) REVERT: F 330 MET cc_start: 0.8115 (tpt) cc_final: 0.7764 (tmm) REVERT: F 334 TYR cc_start: 0.8309 (m-80) cc_final: 0.8031 (m-80) REVERT: F 349 GLN cc_start: 0.8510 (tp40) cc_final: 0.8294 (tp40) REVERT: F 371 ARG cc_start: 0.7468 (ttt-90) cc_final: 0.7214 (ptt180) REVERT: F 396 LEU cc_start: 0.6355 (OUTLIER) cc_final: 0.6085 (pp) REVERT: F 419 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7400 (mm-30) outliers start: 88 outliers final: 65 residues processed: 313 average time/residue: 0.2405 time to fit residues: 112.8089 Evaluate side-chains 312 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 235 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 SER Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 260 MET Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 LYS Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 354 ILE Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 308 PHE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 419 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 16 optimal weight: 9.9990 chunk 140 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.8080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15231 Z= 0.191 Angle : 0.656 8.227 20630 Z= 0.335 Chirality : 0.042 0.202 2342 Planarity : 0.006 0.118 2657 Dihedral : 10.149 83.572 2205 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.31 % Favored : 92.11 % Rotamer: Outliers : 4.90 % Allowed : 23.90 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.17 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.20), residues: 1902 helix: 0.29 (0.19), residues: 811 sheet: -0.92 (0.38), residues: 194 loop : -1.37 (0.22), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 280 HIS 0.006 0.001 HIS E 359 PHE 0.026 0.002 PHE E 290 TYR 0.013 0.001 TYR F 181 ARG 0.019 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 260 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6303 (t80) cc_final: 0.6051 (t80) REVERT: A 259 GLN cc_start: 0.4678 (mm110) cc_final: 0.4251 (mt0) REVERT: A 323 ASP cc_start: 0.8693 (m-30) cc_final: 0.8338 (t0) REVERT: A 325 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8120 (ppt170) REVERT: A 427 GLN cc_start: 0.5996 (mp10) cc_final: 0.5429 (pp30) REVERT: B 169 ILE cc_start: 0.8174 (OUTLIER) cc_final: 0.7808 (mp) REVERT: B 202 LEU cc_start: 0.6450 (mt) cc_final: 0.5476 (pt) REVERT: B 250 ARG cc_start: 0.7231 (ttm-80) cc_final: 0.6373 (tpt90) REVERT: B 255 GLU cc_start: 0.6752 (tp30) cc_final: 0.6345 (tp30) REVERT: B 259 GLN cc_start: 0.7719 (tp-100) cc_final: 0.6816 (tp-100) REVERT: B 290 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5416 (t80) REVERT: B 308 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7112 (m-10) REVERT: B 395 GLU cc_start: 0.4677 (OUTLIER) cc_final: 0.4461 (pm20) REVERT: C 139 GLU cc_start: 0.7629 (tp30) cc_final: 0.6496 (tp30) REVERT: C 143 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8108 (mm-30) REVERT: C 240 THR cc_start: 0.3864 (OUTLIER) cc_final: 0.3549 (p) REVERT: C 243 GLU cc_start: 0.3763 (mt-10) cc_final: 0.2737 (tp30) REVERT: C 268 GLN cc_start: 0.5360 (tt0) cc_final: 0.4255 (pm20) REVERT: C 290 PHE cc_start: 0.6458 (OUTLIER) cc_final: 0.5930 (t80) REVERT: C 292 ARG cc_start: 0.8460 (tpp-160) cc_final: 0.7999 (tpp80) REVERT: C 332 GLU cc_start: 0.6972 (tt0) cc_final: 0.6399 (tm-30) REVERT: C 418 ASN cc_start: 0.7734 (t0) cc_final: 0.7477 (t0) REVERT: D 131 LYS cc_start: 0.8677 (tptm) cc_final: 0.7751 (mmtm) REVERT: D 143 GLU cc_start: 0.8204 (pt0) cc_final: 0.7850 (pp20) REVERT: D 147 GLU cc_start: 0.8273 (pt0) cc_final: 0.7912 (pt0) REVERT: D 160 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6267 (mmmt) REVERT: D 211 GLU cc_start: 0.8145 (mp0) cc_final: 0.7665 (mp0) REVERT: D 307 MET cc_start: 0.8005 (ttm) cc_final: 0.7128 (tpp) REVERT: D 322 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7203 (mp0) REVERT: D 348 MET cc_start: 0.7986 (mmt) cc_final: 0.7750 (mmt) REVERT: D 398 GLU cc_start: 0.8331 (pt0) cc_final: 0.7729 (tp30) REVERT: D 404 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7735 (tptt) REVERT: D 414 ARG cc_start: 0.7750 (tpt-90) cc_final: 0.7345 (tpp80) REVERT: D 432 PHE cc_start: 0.7689 (m-80) cc_final: 0.7130 (m-80) REVERT: E 164 LYS cc_start: 0.7275 (mmmt) cc_final: 0.7014 (mmmt) REVERT: E 181 TYR cc_start: 0.8270 (t80) cc_final: 0.7401 (t80) REVERT: E 260 MET cc_start: 0.6591 (tpp) cc_final: 0.6322 (tpt) REVERT: E 335 SER cc_start: 0.8544 (m) cc_final: 0.8090 (p) REVERT: E 359 HIS cc_start: 0.6990 (m-70) cc_final: 0.6632 (m170) REVERT: E 386 MET cc_start: 0.6409 (ppp) cc_final: 0.6117 (ppp) REVERT: E 404 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6615 (tptt) REVERT: E 423 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7951 (mm) REVERT: F 194 PHE cc_start: 0.7825 (t80) cc_final: 0.7328 (t80) REVERT: F 207 MET cc_start: 0.2238 (mtm) cc_final: 0.1739 (mtm) REVERT: F 251 ARG cc_start: 0.6746 (ptp-170) cc_final: 0.6512 (ptp-170) REVERT: F 255 GLU cc_start: 0.8815 (tp30) cc_final: 0.8539 (tt0) REVERT: F 290 PHE cc_start: 0.5859 (OUTLIER) cc_final: 0.5405 (t80) REVERT: F 323 ASP cc_start: 0.6440 (m-30) cc_final: 0.6147 (t70) REVERT: F 330 MET cc_start: 0.8117 (tpt) cc_final: 0.7855 (tmm) REVERT: F 334 TYR cc_start: 0.8348 (m-80) cc_final: 0.8116 (m-80) REVERT: F 349 GLN cc_start: 0.8469 (tp40) cc_final: 0.8233 (tp40) REVERT: F 371 ARG cc_start: 0.7460 (ttt-90) cc_final: 0.7209 (ptt180) REVERT: F 396 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5956 (pp) REVERT: F 419 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7393 (mm-30) outliers start: 80 outliers final: 54 residues processed: 317 average time/residue: 0.2459 time to fit residues: 117.5258 Evaluate side-chains 307 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 243 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 308 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 396 LEU Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 437 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 6.9990 chunk 171 optimal weight: 0.7980 chunk 156 optimal weight: 0.3980 chunk 167 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 150 optimal weight: 20.0000 chunk 158 optimal weight: 10.0000 chunk 166 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 355 GLN F 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.8176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15231 Z= 0.194 Angle : 0.666 8.418 20630 Z= 0.340 Chirality : 0.042 0.194 2342 Planarity : 0.006 0.118 2657 Dihedral : 9.942 87.650 2205 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.15 % Favored : 91.27 % Rotamer: Outliers : 4.60 % Allowed : 24.51 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1902 helix: 0.31 (0.19), residues: 815 sheet: -0.83 (0.38), residues: 194 loop : -1.33 (0.22), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 280 HIS 0.005 0.001 HIS E 359 PHE 0.023 0.002 PHE C 155 TYR 0.022 0.001 TYR E 172 ARG 0.016 0.001 ARG B 289 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 253 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6205 (t80) cc_final: 0.5969 (t80) REVERT: A 259 GLN cc_start: 0.4858 (mm110) cc_final: 0.4450 (mt0) REVERT: A 323 ASP cc_start: 0.8683 (m-30) cc_final: 0.8331 (t0) REVERT: A 325 ARG cc_start: 0.8432 (ptp-110) cc_final: 0.8141 (ppt170) REVERT: A 427 GLN cc_start: 0.6012 (mp10) cc_final: 0.5430 (pp30) REVERT: B 202 LEU cc_start: 0.6274 (mt) cc_final: 0.5375 (pt) REVERT: B 250 ARG cc_start: 0.7213 (ttm-80) cc_final: 0.6353 (tpt90) REVERT: B 255 GLU cc_start: 0.6770 (tp30) cc_final: 0.6525 (tp30) REVERT: B 259 GLN cc_start: 0.7678 (tp-100) cc_final: 0.6753 (tp-100) REVERT: B 290 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5576 (t80) REVERT: B 308 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: B 395 GLU cc_start: 0.4623 (OUTLIER) cc_final: 0.4410 (pm20) REVERT: C 139 GLU cc_start: 0.7656 (tp30) cc_final: 0.6481 (tp30) REVERT: C 143 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 240 THR cc_start: 0.4006 (OUTLIER) cc_final: 0.3699 (p) REVERT: C 243 GLU cc_start: 0.4180 (mt-10) cc_final: 0.3059 (tp30) REVERT: C 268 GLN cc_start: 0.5681 (tt0) cc_final: 0.4614 (pm20) REVERT: C 290 PHE cc_start: 0.6495 (OUTLIER) cc_final: 0.5902 (t80) REVERT: C 292 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.7801 (tpp80) REVERT: C 332 GLU cc_start: 0.6994 (tt0) cc_final: 0.6431 (tm-30) REVERT: C 418 ASN cc_start: 0.7733 (t0) cc_final: 0.7469 (t0) REVERT: D 131 LYS cc_start: 0.8659 (tptm) cc_final: 0.7738 (mmtm) REVERT: D 160 LYS cc_start: 0.7106 (mtpt) cc_final: 0.6210 (mmmt) REVERT: D 211 GLU cc_start: 0.8221 (mp0) cc_final: 0.7726 (mp0) REVERT: D 232 ASP cc_start: 0.7966 (t0) cc_final: 0.7578 (m-30) REVERT: D 288 ARG cc_start: 0.7798 (mpt180) cc_final: 0.6091 (tmt-80) REVERT: D 310 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8473 (pt) REVERT: D 322 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7210 (mp0) REVERT: D 348 MET cc_start: 0.7933 (mmt) cc_final: 0.7685 (mmt) REVERT: D 398 GLU cc_start: 0.8344 (pt0) cc_final: 0.7723 (tp30) REVERT: D 404 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7697 (tptt) REVERT: D 432 PHE cc_start: 0.7634 (m-80) cc_final: 0.7095 (m-80) REVERT: E 164 LYS cc_start: 0.7278 (mmmt) cc_final: 0.7015 (mmmt) REVERT: E 181 TYR cc_start: 0.8209 (t80) cc_final: 0.7420 (t80) REVERT: E 260 MET cc_start: 0.6564 (tpp) cc_final: 0.6258 (tpt) REVERT: E 335 SER cc_start: 0.8487 (m) cc_final: 0.7900 (p) REVERT: E 386 MET cc_start: 0.6649 (ppp) cc_final: 0.6371 (ppp) REVERT: E 404 LYS cc_start: 0.7155 (mtmt) cc_final: 0.6489 (tmmt) REVERT: E 423 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7868 (mm) REVERT: F 194 PHE cc_start: 0.7856 (t80) cc_final: 0.7384 (t80) REVERT: F 207 MET cc_start: 0.2108 (mtm) cc_final: 0.1631 (mtm) REVERT: F 255 GLU cc_start: 0.8819 (tp30) cc_final: 0.8537 (tt0) REVERT: F 290 PHE cc_start: 0.5716 (OUTLIER) cc_final: 0.5298 (t80) REVERT: F 323 ASP cc_start: 0.6556 (m-30) cc_final: 0.6261 (t70) REVERT: F 330 MET cc_start: 0.8085 (tpt) cc_final: 0.7830 (tmm) REVERT: F 334 TYR cc_start: 0.8404 (m-80) cc_final: 0.8158 (m-80) REVERT: F 349 GLN cc_start: 0.8470 (tp40) cc_final: 0.8216 (tp40) REVERT: F 371 ARG cc_start: 0.7458 (ttt-90) cc_final: 0.7210 (ptt180) REVERT: F 419 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7393 (mm-30) outliers start: 75 outliers final: 58 residues processed: 306 average time/residue: 0.2415 time to fit residues: 111.5923 Evaluate side-chains 308 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 241 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 258 VAL Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 437 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 HIS ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.8380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15231 Z= 0.232 Angle : 0.693 9.869 20630 Z= 0.356 Chirality : 0.042 0.215 2342 Planarity : 0.006 0.118 2657 Dihedral : 10.004 82.155 2204 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.68 % Favored : 90.85 % Rotamer: Outliers : 4.41 % Allowed : 25.06 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1902 helix: 0.30 (0.19), residues: 814 sheet: -0.78 (0.38), residues: 194 loop : -1.34 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 280 HIS 0.019 0.002 HIS A 157 PHE 0.036 0.002 PHE F 218 TYR 0.016 0.001 TYR B 334 ARG 0.013 0.001 ARG B 289 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 241 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 TYR cc_start: 0.6319 (t80) cc_final: 0.6081 (t80) REVERT: A 259 GLN cc_start: 0.4947 (mm110) cc_final: 0.4516 (mt0) REVERT: A 323 ASP cc_start: 0.8673 (m-30) cc_final: 0.8306 (t0) REVERT: A 325 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8120 (ppt170) REVERT: A 427 GLN cc_start: 0.6015 (mp10) cc_final: 0.5424 (pp30) REVERT: B 202 LEU cc_start: 0.6400 (mt) cc_final: 0.5451 (pt) REVERT: B 250 ARG cc_start: 0.7205 (ttm-80) cc_final: 0.6362 (tpt90) REVERT: B 255 GLU cc_start: 0.6780 (tp30) cc_final: 0.6394 (tp30) REVERT: B 259 GLN cc_start: 0.7722 (tp-100) cc_final: 0.6736 (tp-100) REVERT: B 290 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5659 (t80) REVERT: B 308 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: B 395 GLU cc_start: 0.4108 (OUTLIER) cc_final: 0.3880 (pm20) REVERT: C 139 GLU cc_start: 0.7861 (tp30) cc_final: 0.6983 (tp30) REVERT: C 143 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8109 (mm-30) REVERT: C 240 THR cc_start: 0.3645 (OUTLIER) cc_final: 0.3319 (p) REVERT: C 243 GLU cc_start: 0.3967 (mt-10) cc_final: 0.2864 (tp30) REVERT: C 268 GLN cc_start: 0.5711 (tt0) cc_final: 0.4668 (pm20) REVERT: C 290 PHE cc_start: 0.6503 (OUTLIER) cc_final: 0.5805 (t80) REVERT: C 292 ARG cc_start: 0.8434 (tpp-160) cc_final: 0.8020 (tpp80) REVERT: C 332 GLU cc_start: 0.7043 (tt0) cc_final: 0.6457 (tm-30) REVERT: C 418 ASN cc_start: 0.7581 (t0) cc_final: 0.7275 (t0) REVERT: D 131 LYS cc_start: 0.8680 (tptm) cc_final: 0.7798 (mmtm) REVERT: D 147 GLU cc_start: 0.8159 (pt0) cc_final: 0.7955 (pt0) REVERT: D 160 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6230 (mmmt) REVERT: D 211 GLU cc_start: 0.8228 (mp0) cc_final: 0.7727 (mp0) REVERT: D 232 ASP cc_start: 0.8023 (t0) cc_final: 0.7573 (m-30) REVERT: D 307 MET cc_start: 0.7947 (ttm) cc_final: 0.7105 (tpp) REVERT: D 311 ASN cc_start: 0.8357 (m110) cc_final: 0.7851 (m110) REVERT: D 322 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7223 (mp0) REVERT: D 348 MET cc_start: 0.7911 (mmt) cc_final: 0.7665 (mmt) REVERT: D 398 GLU cc_start: 0.8363 (pt0) cc_final: 0.7720 (tp30) REVERT: D 404 LYS cc_start: 0.8204 (mtmt) cc_final: 0.7777 (tptt) REVERT: E 164 LYS cc_start: 0.7268 (mmmt) cc_final: 0.7009 (mmmt) REVERT: E 181 TYR cc_start: 0.8323 (t80) cc_final: 0.7501 (t80) REVERT: E 335 SER cc_start: 0.8557 (m) cc_final: 0.8055 (p) REVERT: E 386 MET cc_start: 0.6448 (ppp) cc_final: 0.6126 (ppp) REVERT: E 404 LYS cc_start: 0.7159 (mtmt) cc_final: 0.6497 (tmmt) REVERT: E 423 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7880 (mm) REVERT: F 146 LYS cc_start: 0.8518 (mttt) cc_final: 0.8192 (tppt) REVERT: F 194 PHE cc_start: 0.7933 (t80) cc_final: 0.7403 (t80) REVERT: F 207 MET cc_start: 0.2008 (mtm) cc_final: 0.1660 (mtm) REVERT: F 255 GLU cc_start: 0.8839 (tp30) cc_final: 0.8618 (mm-30) REVERT: F 290 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5402 (t80) REVERT: F 323 ASP cc_start: 0.6573 (m-30) cc_final: 0.6277 (t70) REVERT: F 330 MET cc_start: 0.8093 (tpt) cc_final: 0.7833 (tmm) REVERT: F 334 TYR cc_start: 0.8383 (m-80) cc_final: 0.8093 (m-80) REVERT: F 349 GLN cc_start: 0.8487 (tp40) cc_final: 0.8245 (tp40) REVERT: F 371 ARG cc_start: 0.7501 (ttt-90) cc_final: 0.7231 (ptt180) REVERT: F 419 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7406 (mm-30) outliers start: 72 outliers final: 58 residues processed: 293 average time/residue: 0.2453 time to fit residues: 108.9364 Evaluate side-chains 299 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 207 MET Chi-restraints excluded: chain B residue 290 PHE Chi-restraints excluded: chain B residue 308 PHE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 395 GLU Chi-restraints excluded: chain B residue 405 ASP Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 194 PHE Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 286 ILE Chi-restraints excluded: chain C residue 290 PHE Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 390 ASP Chi-restraints excluded: chain C residue 434 GLN Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 277 ASN Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 431 ASP Chi-restraints excluded: chain E residue 127 LYS Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 220 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 277 ASN Chi-restraints excluded: chain E residue 290 PHE Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 343 VAL Chi-restraints excluded: chain E residue 423 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 234 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 PHE Chi-restraints excluded: chain F residue 294 ILE Chi-restraints excluded: chain F residue 320 THR Chi-restraints excluded: chain F residue 348 MET Chi-restraints excluded: chain F residue 374 THR Chi-restraints excluded: chain F residue 402 THR Chi-restraints excluded: chain F residue 405 ASP Chi-restraints excluded: chain F residue 419 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 8.9990 chunk 157 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.0770 chunk 21 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 overall best weight: 1.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.147664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.126291 restraints weight = 38201.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.125554 restraints weight = 46557.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.126551 restraints weight = 36174.222| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.8516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15231 Z= 0.224 Angle : 0.691 9.467 20630 Z= 0.354 Chirality : 0.043 0.199 2342 Planarity : 0.006 0.119 2657 Dihedral : 9.948 78.606 2204 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.68 % Favored : 90.85 % Rotamer: Outliers : 4.47 % Allowed : 25.12 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1902 helix: 0.27 (0.19), residues: 818 sheet: -0.68 (0.37), residues: 204 loop : -1.35 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 280 HIS 0.004 0.001 HIS E 359 PHE 0.037 0.002 PHE D 432 TYR 0.022 0.002 TYR E 172 ARG 0.014 0.001 ARG B 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3112.13 seconds wall clock time: 56 minutes 23.34 seconds (3383.34 seconds total)