Starting phenix.real_space_refine on Sat Aug 23 22:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.map" model { file = "/net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tek_41189/08_2025/8tek_41189.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 9612 2.51 5 N 2714 2.21 5 O 2884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15250 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1745 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain breaks: 1 Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1758 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain breaks: 1 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1663 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 1 Chain: "E" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1794 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain: "M" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1373 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 2, 'TRANS': 161} Chain breaks: 1 Chain: "N" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1550 Classifications: {'peptide': 187} Link IDs: {'TRANS': 186} Chain breaks: 1 Chain: "O" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1516 Classifications: {'peptide': 178} Link IDs: {'TRANS': 177} Chain breaks: 1 Chain: "P" Number of atoms: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1150 Classifications: {'peptide': 138} Link IDs: {'TRANS': 137} Chain breaks: 1 Chain: "T" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1145 Classifications: {'peptide': 137} Link IDs: {'TRANS': 136} Chain breaks: 1 Chain: "g" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1556 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Time building chain proxies: 2.90, per 1000 atoms: 0.19 Number of scatterers: 15250 At special positions: 0 Unit cell: (272.63, 105.49, 319.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 2884 8.00 N 2714 7.00 C 9612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 504.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3564 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 3 sheets defined 77.9% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 259 through 288 Processing helix chain 'A' and resid 293 through 364 removed outlier: 4.267A pdb=" N PHE A 299 " --> pdb=" O TYR A 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN A 339 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ALA A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 352 " --> pdb=" O GLU A 348 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 665 removed outlier: 3.824A pdb=" N LYS A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 716 removed outlier: 3.860A pdb=" N PHE A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 680 " --> pdb=" O TRP A 676 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 689 " --> pdb=" O PHE A 685 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A 704 " --> pdb=" O TRP A 700 " (cutoff:3.500A) Proline residue: A 705 - end of helix removed outlier: 3.539A pdb=" N PHE A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 716 " --> pdb=" O TRP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 720 removed outlier: 3.740A pdb=" N LYS A 720 " --> pdb=" O GLN A 717 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 717 through 720' Processing helix chain 'A' and resid 729 through 734 removed outlier: 3.551A pdb=" N ILE A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 729 through 734' Processing helix chain 'B' and resid 254 through 273 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 287 through 361 removed outlier: 3.720A pdb=" N PHE B 293 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASN B 294 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER B 298 " --> pdb=" O ASN B 294 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ALA B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 314 " --> pdb=" O ASN B 310 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 446 removed outlier: 3.713A pdb=" N ASN B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER B 438 " --> pdb=" O GLN B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.873A pdb=" N ASN B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 474 No H-bonds generated for 'chain 'B' and resid 472 through 474' Processing helix chain 'B' and resid 475 through 480 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.511A pdb=" N GLU D 272 " --> pdb=" O GLN D 268 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 304 removed outlier: 3.741A pdb=" N GLU D 287 " --> pdb=" O LYS D 283 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU D 288 " --> pdb=" O GLY D 284 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 4.314A pdb=" N ALA D 294 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE D 297 " --> pdb=" O GLN D 293 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 301 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU D 302 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS D 304 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 347 removed outlier: 4.079A pdb=" N ILE D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N GLU D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU D 318 " --> pdb=" O LYS D 314 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN D 321 " --> pdb=" O GLU D 317 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP D 324 " --> pdb=" O LYS D 320 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN D 325 " --> pdb=" O GLN D 321 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS D 340 " --> pdb=" O GLU D 336 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU D 347 " --> pdb=" O GLN D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 358 removed outlier: 3.504A pdb=" N PHE D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'D' and resid 374 through 394 removed outlier: 5.161A pdb=" N VAL D 380 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG D 384 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 385 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 Processing helix chain 'D' and resid 424 through 453 removed outlier: 3.974A pdb=" N GLN D 432 " --> pdb=" O GLU D 428 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN D 435 " --> pdb=" O ALA D 431 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS D 445 " --> pdb=" O SER D 441 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA D 446 " --> pdb=" O HIS D 442 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU D 448 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY D 449 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 260 Processing helix chain 'E' and resid 263 through 290 removed outlier: 3.573A pdb=" N ALA E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN E 270 " --> pdb=" O VAL E 266 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Proline residue: E 279 - end of helix Processing helix chain 'E' and resid 296 through 316 removed outlier: 3.763A pdb=" N LEU E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 345 removed outlier: 3.569A pdb=" N LEU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 389 removed outlier: 4.199A pdb=" N GLN E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU E 352 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN E 360 " --> pdb=" O ASN E 356 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 363 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU E 374 " --> pdb=" O ILE E 370 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR E 375 " --> pdb=" O LEU E 371 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU E 379 " --> pdb=" O TYR E 375 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU E 381 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 389 " --> pdb=" O ILE E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 436 removed outlier: 3.624A pdb=" N LYS E 415 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG E 433 " --> pdb=" O ASN E 429 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 236 removed outlier: 4.100A pdb=" N TYR M 180 " --> pdb=" O ASN M 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU M 181 " --> pdb=" O GLU M 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU M 182 " --> pdb=" O LYS M 178 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU M 188 " --> pdb=" O GLN M 184 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG M 189 " --> pdb=" O ALA M 185 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS M 191 " --> pdb=" O ILE M 187 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU M 194 " --> pdb=" O GLU M 190 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU M 203 " --> pdb=" O GLU M 199 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU M 210 " --> pdb=" O GLN M 206 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HIS M 211 " --> pdb=" O GLN M 207 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE M 219 " --> pdb=" O GLN M 215 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN M 220 " --> pdb=" O ILE M 216 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG M 221 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE M 224 " --> pdb=" O GLN M 220 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS M 229 " --> pdb=" O LYS M 225 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS M 232 " --> pdb=" O ARG M 228 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET M 236 " --> pdb=" O LYS M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 239 No H-bonds generated for 'chain 'M' and resid 237 through 239' Processing helix chain 'M' and resid 240 through 245 removed outlier: 4.521A pdb=" N ARG M 244 " --> pdb=" O GLU M 240 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 255 removed outlier: 3.696A pdb=" N PHE M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 270 removed outlier: 4.015A pdb=" N LYS M 270 " --> pdb=" O SER M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 294 removed outlier: 3.779A pdb=" N HIS M 292 " --> pdb=" O LEU M 288 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY M 294 " --> pdb=" O ALA M 290 " (cutoff:3.500A) Processing helix chain 'M' and resid 321 through 326 removed outlier: 4.446A pdb=" N GLY M 326 " --> pdb=" O TYR M 323 " (cutoff:3.500A) Processing helix chain 'M' and resid 327 through 343 removed outlier: 4.221A pdb=" N ASP M 333 " --> pdb=" O LYS M 329 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE M 335 " --> pdb=" O ALA M 331 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU M 340 " --> pdb=" O ASN M 336 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN M 341 " --> pdb=" O GLY M 337 " (cutoff:3.500A) Processing helix chain 'M' and resid 344 through 346 No H-bonds generated for 'chain 'M' and resid 344 through 346' Processing helix chain 'N' and resid 566 through 709 removed outlier: 3.850A pdb=" N GLU N 593 " --> pdb=" O SER N 589 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU N 594 " --> pdb=" O SER N 590 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN N 619 " --> pdb=" O GLU N 615 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU N 632 " --> pdb=" O LYS N 628 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER N 633 " --> pdb=" O LYS N 629 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU N 644 " --> pdb=" O LYS N 640 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU N 645 " --> pdb=" O VAL N 641 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN N 646 " --> pdb=" O PHE N 642 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN N 647 " --> pdb=" O ASN N 643 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLN N 656 " --> pdb=" O GLU N 652 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU N 661 " --> pdb=" O GLU N 657 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE N 662 " --> pdb=" O ARG N 658 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 679 " --> pdb=" O ALA N 675 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA N 688 " --> pdb=" O ALA N 684 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU N 689 " --> pdb=" O VAL N 685 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS N 700 " --> pdb=" O ASN N 696 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR N 701 " --> pdb=" O LEU N 697 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU N 702 " --> pdb=" O LYS N 698 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER N 703 " --> pdb=" O ILE N 699 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN N 706 " --> pdb=" O GLU N 702 " (cutoff:3.500A) Processing helix chain 'N' and resid 728 through 763 removed outlier: 4.732A pdb=" N ARG N 734 " --> pdb=" O ALA N 730 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU N 735 " --> pdb=" O ALA N 731 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU N 737 " --> pdb=" O GLU N 733 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN N 738 " --> pdb=" O ARG N 734 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS N 740 " --> pdb=" O GLU N 736 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU N 743 " --> pdb=" O ARG N 739 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN N 745 " --> pdb=" O GLY N 741 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA N 746 " --> pdb=" O ASP N 742 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN N 751 " --> pdb=" O LYS N 747 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU N 752 " --> pdb=" O ILE N 748 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN N 760 " --> pdb=" O LYS N 756 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N THR N 761 " --> pdb=" O ALA N 757 " (cutoff:3.500A) Processing helix chain 'O' and resid 518 through 620 removed outlier: 3.507A pdb=" N LYS O 549 " --> pdb=" O ILE O 545 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE O 567 " --> pdb=" O ASP O 563 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU O 577 " --> pdb=" O ASN O 573 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASP O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA O 584 " --> pdb=" O LYS O 580 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN O 588 " --> pdb=" O ALA O 584 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LYS O 589 " --> pdb=" O ILE O 585 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU O 590 " --> pdb=" O TYR O 586 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER O 604 " --> pdb=" O PHE O 600 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU O 616 " --> pdb=" O GLU O 612 " (cutoff:3.500A) Processing helix chain 'O' and resid 620 through 663 removed outlier: 3.515A pdb=" N LYS O 628 " --> pdb=" O ILE O 624 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU O 629 " --> pdb=" O ASP O 625 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU O 646 " --> pdb=" O GLU O 642 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE O 652 " --> pdb=" O TRP O 648 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN O 653 " --> pdb=" O GLU O 649 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU O 654 " --> pdb=" O ARG O 650 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET O 658 " --> pdb=" O LEU O 654 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA O 661 " --> pdb=" O GLU O 657 " (cutoff:3.500A) Processing helix chain 'O' and resid 670 through 698 removed outlier: 3.668A pdb=" N ASP O 687 " --> pdb=" O LEU O 683 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS O 690 " --> pdb=" O ASP O 686 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS O 691 " --> pdb=" O ASP O 687 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLN O 692 " --> pdb=" O LEU O 688 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU O 693 " --> pdb=" O ARG O 689 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE O 696 " --> pdb=" O GLN O 692 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU O 698 " --> pdb=" O ALA O 694 " (cutoff:3.500A) Processing helix chain 'P' and resid 637 through 647 removed outlier: 3.703A pdb=" N LEU P 641 " --> pdb=" O ASP P 637 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR P 647 " --> pdb=" O ILE P 643 " (cutoff:3.500A) Processing helix chain 'P' and resid 647 through 727 removed outlier: 3.853A pdb=" N ARG P 655 " --> pdb=" O LYS P 651 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS P 660 " --> pdb=" O ASN P 656 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS P 661 " --> pdb=" O GLU P 657 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS P 663 " --> pdb=" O LEU P 659 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS P 665 " --> pdb=" O LYS P 661 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY P 685 " --> pdb=" O GLY P 681 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP P 698 " --> pdb=" O ASN P 694 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN P 699 " --> pdb=" O VAL P 695 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS P 717 " --> pdb=" O LYS P 713 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER P 720 " --> pdb=" O ASP P 716 " (cutoff:3.500A) Processing helix chain 'P' and resid 737 through 777 removed outlier: 3.624A pdb=" N LEU P 744 " --> pdb=" O ASP P 740 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR P 746 " --> pdb=" O ARG P 742 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU P 751 " --> pdb=" O ARG P 747 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU P 753 " --> pdb=" O SER P 749 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS P 756 " --> pdb=" O GLU P 752 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET P 765 " --> pdb=" O LYS P 761 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS P 766 " --> pdb=" O LEU P 762 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 225 removed outlier: 3.710A pdb=" N LYS T 218 " --> pdb=" O ILE T 214 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 220 " --> pdb=" O ASN T 216 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS T 221 " --> pdb=" O LYS T 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP T 225 " --> pdb=" O LYS T 221 " (cutoff:3.500A) Processing helix chain 'T' and resid 228 through 233 Processing helix chain 'T' and resid 235 through 302 removed outlier: 3.647A pdb=" N ARG T 239 " --> pdb=" O ILE T 235 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER T 241 " --> pdb=" O THR T 237 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER T 263 " --> pdb=" O LYS T 259 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN T 264 " --> pdb=" O GLU T 260 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS T 288 " --> pdb=" O LYS T 284 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG T 293 " --> pdb=" O LEU T 289 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS T 294 " --> pdb=" O GLU T 290 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE T 302 " --> pdb=" O LYS T 298 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 339 removed outlier: 3.695A pdb=" N GLN T 325 " --> pdb=" O LYS T 321 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN T 333 " --> pdb=" O TYR T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 355 removed outlier: 3.668A pdb=" N SER T 354 " --> pdb=" O ARG T 350 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 137 through 145 removed outlier: 3.547A pdb=" N ARG g 141 " --> pdb=" O SER g 137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 462 through 464 removed outlier: 3.509A pdb=" N VAL B 463 " --> pdb=" O GLN g 133 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG g 164 " --> pdb=" O ILE g 79 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LYS g 81 " --> pdb=" O ILE g 162 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE g 162 " --> pdb=" O LYS g 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'g' and resid 28 through 29 removed outlier: 4.116A pdb=" N GLU g 150 " --> pdb=" O LEU g 94 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLN g 92 " --> pdb=" O LEU g 152 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL g 154 " --> pdb=" O GLU g 90 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU g 90 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N CYS g 119 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG g 102 " --> pdb=" O CYS g 119 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N MET g 121 " --> pdb=" O ARG g 102 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ARG g 104 " --> pdb=" O MET g 121 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'g' and resid 32 through 38 removed outlier: 3.710A pdb=" N HIS g 33 " --> pdb=" O MET g 50 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 3021 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: 1.56 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.45: 6276 1.45 - 1.69: 9068 1.69 - 1.92: 74 1.92 - 2.15: 2 2.15 - 2.38: 2 Bond restraints: 15422 Sorted by residual: bond pdb=" CD2 TYR A 295 " pdb=" CE2 TYR A 295 " ideal model delta sigma weight residual 1.382 2.382 -1.000 3.00e-02 1.11e+03 1.11e+03 bond pdb=" CD1 TYR A 295 " pdb=" CE1 TYR A 295 " ideal model delta sigma weight residual 1.382 2.370 -0.988 3.00e-02 1.11e+03 1.08e+03 bond pdb=" CB HIS B 289 " pdb=" CG HIS B 289 " ideal model delta sigma weight residual 1.497 1.913 -0.416 1.40e-02 5.10e+03 8.81e+02 bond pdb=" CE2 TYR A 295 " pdb=" CZ TYR A 295 " ideal model delta sigma weight residual 1.378 2.010 -0.632 2.40e-02 1.74e+03 6.94e+02 bond pdb=" CE1 TYR A 295 " pdb=" CZ TYR A 295 " ideal model delta sigma weight residual 1.378 1.988 -0.610 2.40e-02 1.74e+03 6.47e+02 ... (remaining 15417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 20476 3.37 - 6.74: 102 6.74 - 10.11: 3 10.11 - 13.49: 1 13.49 - 16.86: 1 Bond angle restraints: 20583 Sorted by residual: angle pdb=" CA HIS B 289 " pdb=" CB HIS B 289 " pdb=" CG HIS B 289 " ideal model delta sigma weight residual 113.80 130.66 -16.86 1.00e+00 1.00e+00 2.84e+02 angle pdb=" ND1 HIS B 289 " pdb=" CG HIS B 289 " pdb=" CD2 HIS B 289 " ideal model delta sigma weight residual 106.10 98.56 7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" C GLU D 308 " pdb=" N GLN D 309 " pdb=" CA GLN D 309 " ideal model delta sigma weight residual 122.61 128.43 -5.82 1.56e+00 4.11e-01 1.39e+01 angle pdb=" CG HIS B 289 " pdb=" CD2 HIS B 289 " pdb=" NE2 HIS B 289 " ideal model delta sigma weight residual 107.20 110.73 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" C LYS B 275 " pdb=" N LYS B 276 " pdb=" CA LYS B 276 " ideal model delta sigma weight residual 120.90 125.88 -4.98 1.41e+00 5.03e-01 1.25e+01 ... (remaining 20578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8603 17.97 - 35.94: 1016 35.94 - 53.91: 152 53.91 - 71.88: 29 71.88 - 89.85: 31 Dihedral angle restraints: 9831 sinusoidal: 4407 harmonic: 5424 Sorted by residual: dihedral pdb=" CA ALA g 61 " pdb=" C ALA g 61 " pdb=" N PRO g 62 " pdb=" CA PRO g 62 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA GLU D 307 " pdb=" C GLU D 307 " pdb=" N GLU D 308 " pdb=" CA GLU D 308 " ideal model delta harmonic sigma weight residual 180.00 147.83 32.17 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA LYS E 289 " pdb=" C LYS E 289 " pdb=" N LEU E 290 " pdb=" CA LEU E 290 " ideal model delta harmonic sigma weight residual -180.00 -150.29 -29.71 0 5.00e+00 4.00e-02 3.53e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1502 0.034 - 0.068: 595 0.068 - 0.102: 121 0.102 - 0.137: 41 0.137 - 0.171: 10 Chirality restraints: 2269 Sorted by residual: chirality pdb=" CA ILE B 279 " pdb=" N ILE B 279 " pdb=" C ILE B 279 " pdb=" CB ILE B 279 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CG LEU E 307 " pdb=" CB LEU E 307 " pdb=" CD1 LEU E 307 " pdb=" CD2 LEU E 307 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA ILE E 444 " pdb=" N ILE E 444 " pdb=" C ILE E 444 " pdb=" CB ILE E 444 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.61e-01 ... (remaining 2266 not shown) Planarity restraints: 2643 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 295 " -0.009 2.00e-02 2.50e+03 3.16e-02 2.00e+01 pdb=" CG TYR A 295 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 295 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 295 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR A 295 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR A 295 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 295 " -0.047 2.00e-02 2.50e+03 pdb=" OH TYR A 295 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA g 61 " -0.055 5.00e-02 4.00e+02 8.36e-02 1.12e+01 pdb=" N PRO g 62 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO g 62 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO g 62 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 289 " 0.016 2.00e-02 2.50e+03 2.67e-02 1.07e+01 pdb=" CG HIS B 289 " -0.056 2.00e-02 2.50e+03 pdb=" ND1 HIS B 289 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 HIS B 289 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS B 289 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 289 " -0.001 2.00e-02 2.50e+03 ... (remaining 2640 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 197 2.63 - 3.20: 14541 3.20 - 3.77: 23225 3.77 - 4.33: 31270 4.33 - 4.90: 48364 Nonbonded interactions: 117597 Sorted by model distance: nonbonded pdb=" CZ TYR A 295 " pdb=" ND1 HIS B 289 " model vdw 2.065 3.340 nonbonded pdb=" CD2 TYR A 295 " pdb=" CB HIS B 289 " model vdw 2.135 3.740 nonbonded pdb=" CE2 TYR A 295 " pdb=" CB HIS B 289 " model vdw 2.160 3.740 nonbonded pdb=" CE1 TYR A 295 " pdb=" CG HIS B 289 " model vdw 2.163 3.560 nonbonded pdb=" OH TYR N 701 " pdb=" O TRP O 648 " model vdw 2.171 3.040 ... (remaining 117592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 16.300 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: 0.020 Extract box with map and model: 0.210 Check model and map are aligned: 0.060 Set scattering table: 0.020 Process input model: 11.690 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 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 : 0.015 1.000 15422 Z= 0.609 Angle : 0.647 16.857 20583 Z= 0.374 Chirality : 0.039 0.171 2269 Planarity : 0.004 0.084 2643 Dihedral : 15.857 89.849 6267 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.20), residues: 1781 helix: -0.30 (0.15), residues: 1256 sheet: -0.14 (0.69), residues: 55 loop : -1.90 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O 689 TYR 0.055 0.002 TYR A 295 PHE 0.012 0.001 PHE D 330 TRP 0.014 0.002 TRP A 676 HIS 0.034 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01501 (15422) covalent geometry : angle 0.64695 (20583) hydrogen bonds : bond 0.30060 ( 1015) hydrogen bonds : angle 8.36172 ( 3021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 MET cc_start: 0.4753 (mmm) cc_final: 0.4437 (tpt) REVERT: B 473 MET cc_start: -0.0776 (ttt) cc_final: -0.1597 (ttt) REVERT: M 233 SER cc_start: 0.6987 (p) cc_final: 0.6749 (t) REVERT: M 258 TYR cc_start: 0.3359 (p90) cc_final: 0.3042 (t80) REVERT: M 322 ASN cc_start: 0.5994 (p0) cc_final: 0.5665 (p0) REVERT: N 703 SER cc_start: 0.5755 (m) cc_final: 0.5396 (t) REVERT: N 726 TYR cc_start: 0.4467 (m-10) cc_final: 0.4254 (m-80) REVERT: O 576 ASN cc_start: 0.4512 (p0) cc_final: 0.4150 (p0) REVERT: g 90 GLU cc_start: 0.5922 (tt0) cc_final: 0.4953 (tt0) REVERT: g 95 ASP cc_start: 0.5354 (t0) cc_final: 0.5134 (t0) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1500 time to fit residues: 114.1777 Evaluate side-chains 263 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 310 ASN B 442 GLN D 342 GLN D 442 HIS E 300 HIS E 416 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 207 GLN M 273 ASN M 289 GLN N 599 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN O 543 GLN ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 707 GLN P 710 GLN T 249 GLN g 135 ASN g 159 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.129420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.113330 restraints weight = 68591.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.112908 restraints weight = 49861.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.113156 restraints weight = 46257.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.113286 restraints weight = 35965.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.113499 restraints weight = 34347.040| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.998 15422 Z= 0.624 Angle : 0.748 16.363 20583 Z= 0.417 Chirality : 0.044 0.219 2269 Planarity : 0.005 0.077 2643 Dihedral : 5.065 39.393 1960 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 2.41 % Allowed : 14.12 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.19), residues: 1781 helix: 0.31 (0.14), residues: 1301 sheet: -0.31 (0.69), residues: 55 loop : -2.25 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 309 TYR 0.056 0.002 TYR A 295 PHE 0.025 0.002 PHE O 606 TRP 0.013 0.001 TRP A 676 HIS 0.033 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01520 (15422) covalent geometry : angle 0.74820 (20583) hydrogen bonds : bond 0.08054 ( 1015) hydrogen bonds : angle 5.12715 ( 3021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 295 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 HIS cc_start: 0.6145 (t-170) cc_final: 0.5929 (t-170) REVERT: A 720 LYS cc_start: 0.5392 (tptt) cc_final: 0.5159 (tttt) REVERT: B 332 LEU cc_start: 0.7160 (mp) cc_final: 0.6777 (tt) REVERT: B 473 MET cc_start: -0.1518 (ttt) cc_final: -0.1901 (ttt) REVERT: D 348 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7121 (tm-30) REVERT: D 434 LYS cc_start: 0.7143 (tptp) cc_final: 0.6617 (ptpt) REVERT: D 442 HIS cc_start: 0.6327 (m-70) cc_final: 0.6112 (m170) REVERT: M 236 MET cc_start: 0.7606 (ppp) cc_final: 0.7353 (ppp) REVERT: M 258 TYR cc_start: 0.3531 (p90) cc_final: 0.2289 (t80) REVERT: M 263 HIS cc_start: 0.7120 (m90) cc_final: 0.6833 (m90) REVERT: M 287 MET cc_start: 0.5321 (mmm) cc_final: 0.5041 (mmp) REVERT: N 623 MET cc_start: 0.7061 (tpt) cc_final: 0.6860 (tpt) REVERT: N 692 ASN cc_start: 0.8121 (t0) cc_final: 0.7798 (t0) REVERT: N 695 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7360 (tptm) REVERT: O 586 TYR cc_start: 0.7406 (t80) cc_final: 0.6570 (m-80) REVERT: P 704 MET cc_start: 0.6994 (ttp) cc_final: 0.6736 (ttt) REVERT: P 707 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.6820 (pp30) REVERT: T 247 GLU cc_start: 0.6848 (tm-30) cc_final: 0.6101 (tt0) REVERT: T 291 LYS cc_start: 0.7120 (ptmt) cc_final: 0.6916 (ptmt) REVERT: g 95 ASP cc_start: 0.5996 (t0) cc_final: 0.5552 (t0) outliers start: 41 outliers final: 20 residues processed: 329 average time/residue: 0.1566 time to fit residues: 70.8189 Evaluate side-chains 249 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 298 ARG Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 695 LYS Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 707 GLN Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 0.0970 chunk 125 optimal weight: 5.9990 chunk 108 optimal weight: 20.0000 chunk 135 optimal weight: 40.0000 chunk 76 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 150 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 ASN D 342 GLN D 345 GLN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS E 300 HIS ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 411 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 273 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN P 666 ASN P 710 GLN g 135 ASN g 159 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.128088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.112023 restraints weight = 69544.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.112305 restraints weight = 52426.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.112638 restraints weight = 44682.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.112918 restraints weight = 34944.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.112999 restraints weight = 33373.450| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.011 15422 Z= 0.621 Angle : 0.719 16.524 20583 Z= 0.403 Chirality : 0.043 0.223 2269 Planarity : 0.005 0.081 2643 Dihedral : 5.041 42.279 1960 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 3.41 % Allowed : 17.24 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1781 helix: 0.46 (0.14), residues: 1322 sheet: -0.53 (0.66), residues: 60 loop : -2.29 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 437 TYR 0.056 0.002 TYR A 295 PHE 0.025 0.002 PHE O 606 TRP 0.040 0.003 TRP A 661 HIS 0.035 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01523 (15422) covalent geometry : angle 0.71934 (20583) hydrogen bonds : bond 0.06929 ( 1015) hydrogen bonds : angle 4.75351 ( 3021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 232 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5824 (t80) REVERT: A 682 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8066 (tppt) REVERT: A 692 ASN cc_start: 0.7647 (OUTLIER) cc_final: 0.7383 (p0) REVERT: A 720 LYS cc_start: 0.5816 (tptt) cc_final: 0.5371 (tttt) REVERT: B 473 MET cc_start: -0.1402 (ttt) cc_final: -0.1830 (ttt) REVERT: D 348 GLU cc_start: 0.7363 (tm-30) cc_final: 0.7134 (tm-30) REVERT: E 307 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7250 (mp) REVERT: M 258 TYR cc_start: 0.3583 (p90) cc_final: 0.2218 (t80) REVERT: M 263 HIS cc_start: 0.7132 (m90) cc_final: 0.6818 (m90) REVERT: M 287 MET cc_start: 0.5072 (mmm) cc_final: 0.4774 (mmp) REVERT: N 732 GLN cc_start: 0.6195 (mm110) cc_final: 0.5993 (tp-100) REVERT: O 606 PHE cc_start: 0.5701 (t80) cc_final: 0.5119 (t80) REVERT: O 681 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.4990 (tpp) REVERT: P 696 ARG cc_start: 0.6935 (pmt-80) cc_final: 0.6618 (pmt-80) REVERT: T 247 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6143 (tt0) REVERT: T 294 LYS cc_start: 0.6887 (mmtt) cc_final: 0.6343 (mmtt) REVERT: g 95 ASP cc_start: 0.6113 (t0) cc_final: 0.5835 (t0) outliers start: 58 outliers final: 31 residues processed: 273 average time/residue: 0.1406 time to fit residues: 54.2677 Evaluate side-chains 231 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 317 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain O residue 545 ILE Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 583 ASP Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 95 optimal weight: 7.9990 chunk 135 optimal weight: 40.0000 chunk 159 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN B 433 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.125739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.110031 restraints weight = 69228.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.110409 restraints weight = 54359.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.110772 restraints weight = 45245.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.111006 restraints weight = 35464.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.111096 restraints weight = 33702.955| |-----------------------------------------------------------------------------| r_work (final): 0.4060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.067 15422 Z= 0.623 Angle : 0.712 17.044 20583 Z= 0.401 Chirality : 0.043 0.263 2269 Planarity : 0.005 0.081 2643 Dihedral : 5.157 45.716 1960 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.04 % Favored : 95.85 % Rotamer: Outliers : 3.76 % Allowed : 19.65 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.20), residues: 1781 helix: 0.59 (0.14), residues: 1302 sheet: -0.52 (0.71), residues: 55 loop : -2.25 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 337 TYR 0.057 0.002 TYR A 295 PHE 0.021 0.002 PHE O 606 TRP 0.052 0.004 TRP A 661 HIS 0.020 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01550 (15422) covalent geometry : angle 0.71249 (20583) hydrogen bonds : bond 0.06583 ( 1015) hydrogen bonds : angle 4.66026 ( 3021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 212 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7211 (mttt) cc_final: 0.6972 (pttt) REVERT: A 682 LYS cc_start: 0.8659 (mmmt) cc_final: 0.8406 (tppt) REVERT: A 692 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7625 (p0) REVERT: B 319 GLN cc_start: 0.7188 (mm110) cc_final: 0.6894 (mm110) REVERT: B 423 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6126 (tm-30) REVERT: B 473 MET cc_start: -0.1023 (ttt) cc_final: -0.1444 (ttt) REVERT: E 300 HIS cc_start: 0.6618 (OUTLIER) cc_final: 0.5075 (t-90) REVERT: M 258 TYR cc_start: 0.4162 (p90) cc_final: 0.2214 (t80) REVERT: M 266 LEU cc_start: 0.1891 (OUTLIER) cc_final: 0.1661 (mm) REVERT: M 287 MET cc_start: 0.5427 (mmm) cc_final: 0.5158 (mmp) REVERT: N 568 ASP cc_start: 0.5689 (OUTLIER) cc_final: 0.5081 (m-30) REVERT: O 590 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7528 (pm20) REVERT: O 606 PHE cc_start: 0.5708 (t80) cc_final: 0.5079 (t80) REVERT: O 681 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5048 (tpp) REVERT: P 653 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7323 (tm-30) REVERT: P 684 GLN cc_start: 0.6419 (OUTLIER) cc_final: 0.5828 (mp10) REVERT: T 247 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6104 (tt0) REVERT: T 294 LYS cc_start: 0.6664 (mmtt) cc_final: 0.6161 (mmtt) REVERT: T 301 GLU cc_start: 0.3509 (OUTLIER) cc_final: 0.3149 (mt-10) outliers start: 64 outliers final: 32 residues processed: 259 average time/residue: 0.1337 time to fit residues: 49.2563 Evaluate side-chains 222 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 423 GLU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 443 MET Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 155 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** D 442 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.125096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.109907 restraints weight = 69188.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109402 restraints weight = 58768.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109736 restraints weight = 53471.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.110224 restraints weight = 38535.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.110285 restraints weight = 37632.694| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.6238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.094 15422 Z= 0.623 Angle : 0.721 16.432 20583 Z= 0.402 Chirality : 0.043 0.195 2269 Planarity : 0.005 0.087 2643 Dihedral : 5.153 45.829 1960 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 4.29 % Allowed : 21.47 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1781 helix: 0.56 (0.14), residues: 1322 sheet: -0.35 (0.77), residues: 48 loop : -2.25 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 351 TYR 0.053 0.002 TYR A 295 PHE 0.020 0.002 PHE O 606 TRP 0.048 0.003 TRP A 661 HIS 0.019 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01558 (15422) covalent geometry : angle 0.72097 (20583) hydrogen bonds : bond 0.06417 ( 1015) hydrogen bonds : angle 4.61882 ( 3021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 208 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7318 (mttt) cc_final: 0.7051 (pttt) REVERT: A 682 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8179 (tppt) REVERT: A 686 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7160 (tp30) REVERT: A 720 LYS cc_start: 0.6030 (tptt) cc_final: 0.5777 (tppt) REVERT: A 728 MET cc_start: 0.7112 (pmm) cc_final: 0.6734 (pmm) REVERT: B 319 GLN cc_start: 0.7365 (mm110) cc_final: 0.7108 (mm110) REVERT: B 434 GLN cc_start: 0.7226 (pp30) cc_final: 0.6876 (pp30) REVERT: B 473 MET cc_start: -0.1064 (ttt) cc_final: -0.1361 (ttt) REVERT: E 300 HIS cc_start: 0.6867 (OUTLIER) cc_final: 0.5206 (t-90) REVERT: M 258 TYR cc_start: 0.4021 (p90) cc_final: 0.2317 (t80) REVERT: N 568 ASP cc_start: 0.5178 (OUTLIER) cc_final: 0.4642 (m-30) REVERT: O 590 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: O 681 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.4982 (tpp) REVERT: T 247 GLU cc_start: 0.6890 (tm-30) cc_final: 0.6155 (tt0) REVERT: T 294 LYS cc_start: 0.6883 (mmtt) cc_final: 0.6515 (mmtt) REVERT: T 301 GLU cc_start: 0.3377 (OUTLIER) cc_final: 0.3027 (mt-10) outliers start: 73 outliers final: 41 residues processed: 261 average time/residue: 0.1250 time to fit residues: 47.1862 Evaluate side-chains 227 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 586 TYR Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 29 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 708 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 130 ASN g 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.124192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.109008 restraints weight = 69023.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.108623 restraints weight = 55368.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.108933 restraints weight = 49591.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.109167 restraints weight = 37244.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.109337 restraints weight = 36379.488| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.012 15422 Z= 0.622 Angle : 0.721 16.961 20583 Z= 0.402 Chirality : 0.044 0.283 2269 Planarity : 0.005 0.083 2643 Dihedral : 5.168 47.133 1960 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.87 % Favored : 96.01 % Rotamer: Outliers : 4.59 % Allowed : 22.59 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.20), residues: 1781 helix: 0.58 (0.14), residues: 1324 sheet: -0.57 (0.77), residues: 48 loop : -2.19 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 284 TYR 0.056 0.003 TYR A 295 PHE 0.025 0.002 PHE O 606 TRP 0.051 0.003 TRP A 661 HIS 0.029 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01532 (15422) covalent geometry : angle 0.72135 (20583) hydrogen bonds : bond 0.06340 ( 1015) hydrogen bonds : angle 4.61558 ( 3021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 209 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8239 (tttp) cc_final: 0.8019 (ttpp) REVERT: A 686 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6855 (tp30) REVERT: A 728 MET cc_start: 0.7561 (pmm) cc_final: 0.7237 (pmm) REVERT: B 319 GLN cc_start: 0.7328 (mm110) cc_final: 0.7085 (mm110) REVERT: B 434 GLN cc_start: 0.7116 (pp30) cc_final: 0.6867 (pp30) REVERT: B 473 MET cc_start: -0.1108 (ttt) cc_final: -0.1371 (ttt) REVERT: E 300 HIS cc_start: 0.6620 (OUTLIER) cc_final: 0.5125 (t-90) REVERT: M 258 TYR cc_start: 0.4287 (p90) cc_final: 0.2630 (t80) REVERT: M 266 LEU cc_start: 0.2706 (OUTLIER) cc_final: 0.2376 (mm) REVERT: M 298 ARG cc_start: 0.5218 (ptt180) cc_final: 0.4661 (ptm-80) REVERT: N 568 ASP cc_start: 0.5246 (OUTLIER) cc_final: 0.4740 (m-30) REVERT: O 525 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: O 590 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: O 606 PHE cc_start: 0.5699 (t80) cc_final: 0.5115 (t80) REVERT: O 681 MET cc_start: 0.5572 (OUTLIER) cc_final: 0.4998 (tpp) REVERT: P 684 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6172 (mp10) REVERT: T 247 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6169 (tt0) REVERT: T 280 LYS cc_start: 0.7295 (mmtm) cc_final: 0.7052 (mmtm) REVERT: T 294 LYS cc_start: 0.6896 (mmtt) cc_final: 0.6561 (mmtt) REVERT: T 301 GLU cc_start: 0.3343 (OUTLIER) cc_final: 0.3022 (mt-10) REVERT: g 124 ARG cc_start: 0.6636 (tpp-160) cc_final: 0.6229 (mmt-90) REVERT: g 138 ASP cc_start: 0.7245 (m-30) cc_final: 0.6946 (m-30) outliers start: 78 outliers final: 43 residues processed: 269 average time/residue: 0.1242 time to fit residues: 48.6335 Evaluate side-chains 237 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 185 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 689 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 171 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 142 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.124173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.109263 restraints weight = 68380.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.109208 restraints weight = 57002.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.109469 restraints weight = 51729.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.109950 restraints weight = 36311.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.110023 restraints weight = 34274.889| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.6858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.012 15422 Z= 0.618 Angle : 0.704 16.590 20583 Z= 0.392 Chirality : 0.043 0.262 2269 Planarity : 0.004 0.084 2643 Dihedral : 5.079 46.598 1960 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.12 % Allowed : 23.71 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.20), residues: 1781 helix: 0.69 (0.14), residues: 1324 sheet: -0.56 (0.78), residues: 48 loop : -2.17 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 284 TYR 0.059 0.002 TYR A 295 PHE 0.021 0.002 PHE D 454 TRP 0.014 0.002 TRP A 700 HIS 0.032 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01525 (15422) covalent geometry : angle 0.70375 (20583) hydrogen bonds : bond 0.06159 ( 1015) hydrogen bonds : angle 4.56857 ( 3021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 203 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7001 (tp30) REVERT: A 720 LYS cc_start: 0.5699 (tptt) cc_final: 0.5320 (tppt) REVERT: A 728 MET cc_start: 0.7568 (pmm) cc_final: 0.7191 (pmm) REVERT: B 319 GLN cc_start: 0.7345 (mm110) cc_final: 0.7094 (mm110) REVERT: B 434 GLN cc_start: 0.7093 (pp30) cc_final: 0.6870 (pp30) REVERT: B 473 MET cc_start: -0.1129 (ttt) cc_final: -0.1429 (ttt) REVERT: E 264 LYS cc_start: 0.7208 (tttt) cc_final: 0.6766 (mmmt) REVERT: E 300 HIS cc_start: 0.6516 (OUTLIER) cc_final: 0.5135 (t-90) REVERT: M 258 TYR cc_start: 0.4341 (p90) cc_final: 0.2766 (t80) REVERT: M 266 LEU cc_start: 0.2954 (OUTLIER) cc_final: 0.2679 (mm) REVERT: M 298 ARG cc_start: 0.4920 (ptt180) cc_final: 0.4427 (ptm-80) REVERT: N 568 ASP cc_start: 0.5474 (OUTLIER) cc_final: 0.4943 (m-30) REVERT: O 525 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7297 (mp10) REVERT: O 590 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: O 606 PHE cc_start: 0.5566 (t80) cc_final: 0.5007 (t80) REVERT: O 678 ILE cc_start: 0.7313 (tp) cc_final: 0.7060 (tp) REVERT: O 681 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.4880 (tpp) REVERT: P 684 GLN cc_start: 0.6471 (OUTLIER) cc_final: 0.6009 (mp10) REVERT: T 247 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6226 (tt0) REVERT: T 280 LYS cc_start: 0.7233 (mmtm) cc_final: 0.7013 (mmtm) REVERT: T 294 LYS cc_start: 0.6953 (mmtt) cc_final: 0.6566 (mmtt) REVERT: T 301 GLU cc_start: 0.3295 (OUTLIER) cc_final: 0.2977 (mp0) REVERT: g 124 ARG cc_start: 0.6703 (tpp-160) cc_final: 0.6330 (mmt-90) REVERT: g 138 ASP cc_start: 0.7300 (m-30) cc_final: 0.7054 (m-30) outliers start: 70 outliers final: 47 residues processed: 255 average time/residue: 0.1188 time to fit residues: 43.7240 Evaluate side-chains 237 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 689 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 710 GLN Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 32 optimal weight: 0.7980 chunk 170 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.124155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.109346 restraints weight = 69517.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.108828 restraints weight = 57496.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.109085 restraints weight = 51717.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.109479 restraints weight = 38221.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109598 restraints weight = 36293.832| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.065 15422 Z= 0.617 Angle : 0.717 17.119 20583 Z= 0.399 Chirality : 0.044 0.262 2269 Planarity : 0.005 0.084 2643 Dihedral : 5.065 46.497 1960 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 4.41 % Allowed : 24.71 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.20), residues: 1781 helix: 0.77 (0.14), residues: 1310 sheet: -0.55 (0.77), residues: 48 loop : -2.12 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 284 TYR 0.062 0.002 TYR A 295 PHE 0.019 0.002 PHE O 606 TRP 0.042 0.003 TRP A 661 HIS 0.023 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01537 (15422) covalent geometry : angle 0.71699 (20583) hydrogen bonds : bond 0.06087 ( 1015) hydrogen bonds : angle 4.53687 ( 3021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 198 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 682 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8306 (tppt) REVERT: A 686 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6782 (tp30) REVERT: A 688 GLN cc_start: 0.6894 (tm-30) cc_final: 0.6679 (tm-30) REVERT: A 720 LYS cc_start: 0.5916 (tptt) cc_final: 0.5518 (tppt) REVERT: A 728 MET cc_start: 0.7612 (pmm) cc_final: 0.7295 (pmm) REVERT: B 319 GLN cc_start: 0.7357 (mm110) cc_final: 0.7104 (mm110) REVERT: B 434 GLN cc_start: 0.7118 (pp30) cc_final: 0.6911 (pp30) REVERT: B 473 MET cc_start: -0.1380 (ttt) cc_final: -0.1592 (ttt) REVERT: E 264 LYS cc_start: 0.7188 (tttt) cc_final: 0.6757 (mmmt) REVERT: E 300 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.5432 (t-90) REVERT: M 258 TYR cc_start: 0.4240 (p90) cc_final: 0.2758 (t80) REVERT: M 266 LEU cc_start: 0.3066 (OUTLIER) cc_final: 0.2786 (mm) REVERT: M 298 ARG cc_start: 0.4915 (ptt180) cc_final: 0.4420 (ptm-80) REVERT: N 568 ASP cc_start: 0.5358 (OUTLIER) cc_final: 0.4830 (m-30) REVERT: O 525 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7289 (mp10) REVERT: O 590 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7515 (pm20) REVERT: O 606 PHE cc_start: 0.5702 (t80) cc_final: 0.5160 (t80) REVERT: O 678 ILE cc_start: 0.7291 (tp) cc_final: 0.7051 (tp) REVERT: O 681 MET cc_start: 0.5493 (OUTLIER) cc_final: 0.4916 (tpp) REVERT: P 684 GLN cc_start: 0.6475 (OUTLIER) cc_final: 0.6001 (mp10) REVERT: T 247 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6262 (tt0) REVERT: T 280 LYS cc_start: 0.7255 (mmtm) cc_final: 0.7028 (mmtm) REVERT: T 294 LYS cc_start: 0.6935 (mmtt) cc_final: 0.6585 (mmtt) REVERT: T 301 GLU cc_start: 0.4068 (OUTLIER) cc_final: 0.3644 (mp0) REVERT: g 124 ARG cc_start: 0.6718 (tpp-160) cc_final: 0.6353 (mmt-90) outliers start: 75 outliers final: 53 residues processed: 249 average time/residue: 0.1072 time to fit residues: 38.8204 Evaluate side-chains 245 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 183 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 442 HIS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 247 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 597 LEU Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 689 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 79 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 145 optimal weight: 0.0970 chunk 72 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.124093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.106064 restraints weight = 68720.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.106606 restraints weight = 43481.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.106436 restraints weight = 35839.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.106644 restraints weight = 33233.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.106708 restraints weight = 30995.423| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.7227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.071 15422 Z= 0.618 Angle : 0.722 16.770 20583 Z= 0.401 Chirality : 0.044 0.265 2269 Planarity : 0.005 0.084 2643 Dihedral : 5.065 46.251 1960 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 4.12 % Allowed : 24.94 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.11 (0.20), residues: 1781 helix: 0.82 (0.14), residues: 1307 sheet: -0.50 (0.84), residues: 43 loop : -2.10 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 284 TYR 0.061 0.002 TYR A 295 PHE 0.020 0.002 PHE D 454 TRP 0.055 0.003 TRP A 661 HIS 0.023 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01541 (15422) covalent geometry : angle 0.72191 (20583) hydrogen bonds : bond 0.06032 ( 1015) hydrogen bonds : angle 4.52233 ( 3021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 195 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 686 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6506 (tm-30) REVERT: A 700 TRP cc_start: 0.6197 (t60) cc_final: 0.5846 (t60) REVERT: A 728 MET cc_start: 0.7566 (pmm) cc_final: 0.7277 (pmm) REVERT: B 282 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.1976 (ptp) REVERT: B 319 GLN cc_start: 0.7357 (mm110) cc_final: 0.7120 (mm110) REVERT: B 473 MET cc_start: -0.1414 (ttt) cc_final: -0.1621 (ttt) REVERT: D 289 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.6006 (t0) REVERT: E 264 LYS cc_start: 0.7148 (tttt) cc_final: 0.6770 (mmmt) REVERT: E 300 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.5204 (t-90) REVERT: M 258 TYR cc_start: 0.3881 (p90) cc_final: 0.2456 (t80) REVERT: M 266 LEU cc_start: 0.2852 (OUTLIER) cc_final: 0.2605 (mm) REVERT: M 298 ARG cc_start: 0.5118 (ptt180) cc_final: 0.4712 (ptm-80) REVERT: N 568 ASP cc_start: 0.5835 (OUTLIER) cc_final: 0.5215 (m-30) REVERT: O 525 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7254 (mp10) REVERT: O 590 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: O 606 PHE cc_start: 0.5813 (t80) cc_final: 0.5283 (t80) REVERT: O 681 MET cc_start: 0.5509 (OUTLIER) cc_final: 0.4957 (tpp) REVERT: P 684 GLN cc_start: 0.6576 (OUTLIER) cc_final: 0.6016 (mp10) REVERT: T 280 LYS cc_start: 0.7309 (mmtm) cc_final: 0.7061 (mmtm) REVERT: T 294 LYS cc_start: 0.6794 (mmtt) cc_final: 0.6517 (mmtt) REVERT: T 301 GLU cc_start: 0.4709 (OUTLIER) cc_final: 0.4243 (mp0) REVERT: g 124 ARG cc_start: 0.6940 (tpp-160) cc_final: 0.6551 (mmt-90) REVERT: g 138 ASP cc_start: 0.7187 (m-30) cc_final: 0.6770 (m-30) outliers start: 70 outliers final: 50 residues processed: 244 average time/residue: 0.1014 time to fit residues: 36.4262 Evaluate side-chains 248 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 187 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 442 HIS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 689 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain P residue 710 GLN Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 117 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 111 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.123971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.109650 restraints weight = 69404.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109077 restraints weight = 63284.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.109590 restraints weight = 50463.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.109811 restraints weight = 38220.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.110127 restraints weight = 36154.716| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.074 15422 Z= 0.619 Angle : 0.741 16.719 20583 Z= 0.412 Chirality : 0.044 0.254 2269 Planarity : 0.005 0.083 2643 Dihedral : 5.069 46.135 1960 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.76 % Favored : 96.13 % Rotamer: Outliers : 3.71 % Allowed : 25.41 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.20), residues: 1781 helix: 0.82 (0.14), residues: 1306 sheet: -0.53 (0.84), residues: 43 loop : -2.10 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.060 0.003 TYR A 295 PHE 0.024 0.002 PHE D 454 TRP 0.043 0.003 TRP A 661 HIS 0.022 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01543 (15422) covalent geometry : angle 0.74133 (20583) hydrogen bonds : bond 0.06024 ( 1015) hydrogen bonds : angle 4.54003 ( 3021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3562 Ramachandran restraints generated. 1781 Oldfield, 0 Emsley, 1781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 661 TRP cc_start: 0.5025 (m-90) cc_final: 0.4334 (m100) REVERT: A 682 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8321 (tppt) REVERT: A 686 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6840 (tp30) REVERT: A 700 TRP cc_start: 0.6145 (t60) cc_final: 0.5873 (t60) REVERT: A 720 LYS cc_start: 0.5627 (tptt) cc_final: 0.5222 (tppt) REVERT: A 728 MET cc_start: 0.7813 (pmm) cc_final: 0.7385 (pmm) REVERT: B 282 MET cc_start: 0.2371 (OUTLIER) cc_final: 0.2140 (ptp) REVERT: B 319 GLN cc_start: 0.7348 (mm110) cc_final: 0.7097 (mm110) REVERT: E 264 LYS cc_start: 0.7157 (tttt) cc_final: 0.6764 (mmmt) REVERT: E 300 HIS cc_start: 0.6820 (OUTLIER) cc_final: 0.5630 (t-90) REVERT: M 258 TYR cc_start: 0.3756 (p90) cc_final: 0.2499 (t80) REVERT: M 266 LEU cc_start: 0.2898 (OUTLIER) cc_final: 0.2647 (mm) REVERT: M 298 ARG cc_start: 0.4777 (ptt180) cc_final: 0.4380 (ptm-80) REVERT: M 345 GLN cc_start: 0.4177 (OUTLIER) cc_final: 0.3879 (pm20) REVERT: N 568 ASP cc_start: 0.5345 (OUTLIER) cc_final: 0.4789 (m-30) REVERT: O 525 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: O 590 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: O 606 PHE cc_start: 0.5619 (t80) cc_final: 0.5108 (t80) REVERT: O 681 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4870 (tpp) REVERT: P 684 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6012 (mp10) REVERT: P 705 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7068 (mmp80) REVERT: T 280 LYS cc_start: 0.7182 (mmtm) cc_final: 0.6961 (mmtm) REVERT: T 294 LYS cc_start: 0.6689 (mmtt) cc_final: 0.6427 (mmtt) REVERT: T 301 GLU cc_start: 0.5034 (OUTLIER) cc_final: 0.4619 (mp0) REVERT: g 124 ARG cc_start: 0.7022 (tpp-160) cc_final: 0.6622 (mmt-90) REVERT: g 138 ASP cc_start: 0.7126 (m-30) cc_final: 0.6685 (m-30) outliers start: 63 outliers final: 49 residues processed: 238 average time/residue: 0.1148 time to fit residues: 39.6276 Evaluate side-chains 241 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain B residue 312 HIS Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 442 HIS Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain M residue 324 HIS Chi-restraints excluded: chain M residue 345 GLN Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 689 GLU Chi-restraints excluded: chain N residue 704 LEU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 604 SER Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE Chi-restraints excluded: chain P residue 656 ASN Chi-restraints excluded: chain P residue 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain P residue 704 MET Chi-restraints excluded: chain P residue 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 6 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 37 optimal weight: 0.4980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** M 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.124167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.108655 restraints weight = 68457.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.108972 restraints weight = 50775.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109148 restraints weight = 45952.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.109276 restraints weight = 36110.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109689 restraints weight = 32101.691| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.076 15422 Z= 0.617 Angle : 0.726 16.682 20583 Z= 0.403 Chirality : 0.043 0.248 2269 Planarity : 0.004 0.083 2643 Dihedral : 5.036 45.719 1960 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.41 % Rotamer: Outliers : 3.88 % Allowed : 25.41 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.20), residues: 1781 helix: 0.86 (0.14), residues: 1307 sheet: -0.53 (0.84), residues: 43 loop : -2.13 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.059 0.002 TYR A 295 PHE 0.024 0.002 PHE D 454 TRP 0.033 0.003 TRP A 661 HIS 0.022 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01539 (15422) covalent geometry : angle 0.72566 (20583) hydrogen bonds : bond 0.05905 ( 1015) hydrogen bonds : angle 4.49436 ( 3021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3610.78 seconds wall clock time: 62 minutes 44.98 seconds (3764.98 seconds total)