Starting phenix.real_space_refine on Thu Feb 5 03:51:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tek_41189/02_2026/8tek_41189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tek_41189/02_2026/8tek_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_41189/02_2026/8tek_41189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tek_41189/02_2026/8tek_41189.map" model { file = "/net/cci-nas-00/data/ceres_data/8tek_41189/02_2026/8tek_41189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tek_41189/02_2026/8tek_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.14, per 1000 atoms: 0.21 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: 1.13 Conformation dependent library (CDL) restraints added in 516.7 milliseconds 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: 0.42 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: 2.40 Time building geometry restraints manager: 1.56 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: 17.990 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.490 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- 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 are 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 : 0.599 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: 0.5756 (m) cc_final: 0.5396 (t) REVERT: N 726 TYR cc_start: 0.4467 (m-10) cc_final: 0.4253 (m-80) REVERT: O 576 ASN cc_start: 0.4512 (p0) cc_final: 0.4149 (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: 0.5133 (t0) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.1472 time to fit residues: 112.0038 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 : 0.584 ------------------------------------------------------------------------------- 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 are 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 : 0.427 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: 0.7605 (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 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: 0.1342 time to fit residues: 60.9719 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 : 0.395 ------------------------------------------------------------------------------- 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.128073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.112029 restraints weight = 69202.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.112181 restraints weight = 54620.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.112578 restraints weight = 43684.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.113023 restraints weight = 34635.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.113062 restraints weight = 33041.851| |-----------------------------------------------------------------------------| r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.5116 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= 0.622 Angle : 0.719 16.523 20583 Z= 0.404 Chirality : 0.043 0.224 2269 Planarity : 0.005 0.081 2643 Dihedral : 5.037 42.265 1960 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 3.35 % Allowed : 17.18 % Favored : 79.47 % 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 are 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 0.026 0.002 PHE O 606 TRP 0.037 0.003 TRP A 661 HIS 0.035 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01525 (15422) covalent geometry : angle 0.71939 (20583) hydrogen bonds : bond 0.06937 ( 1015) hydrogen bonds : angle 4.76376 ( 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 289 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 232 time to evaluate : 0.550 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: 0.6376 (OUTLIER) cc_final: 0.5820 (t80) REVERT: A 682 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8075 (tppt) REVERT: A 692 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7393 (p0) REVERT: A 720 LYS cc_start: 0.5816 (tptt) cc_final: 0.5369 (tttt) REVERT: B 434 GLN cc_start: 0.7268 (pp30) cc_final: 0.7058 (pp30) REVERT: B 473 MET cc_start: -0.1405 (ttt) cc_final: -0.1855 (ttt) REVERT: D 348 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7142 (tm-30) REVERT: E 307 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7254 (mp) REVERT: M 258 TYR cc_start: 0.3571 (p90) cc_final: 0.2218 (t80) REVERT: M 263 HIS cc_start: 0.7146 (m90) cc_final: 0.6835 (m90) REVERT: M 287 MET cc_start: 0.5044 (mmm) cc_final: 0.4757 (mmp) REVERT: N 732 GLN cc_start: 0.6218 (mm110) cc_final: 0.6012 (tp-100) REVERT: O 606 PHE cc_start: 0.5716 (t80) cc_final: 0.5338 (t80) REVERT: O 681 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.4946 (tpp) REVERT: P 696 ARG cc_start: 0.6898 (pmt-80) cc_final: 0.6566 (pmt-80) REVERT: T 247 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6128 (tt0) REVERT: T 294 LYS cc_start: 0.6936 (mmtt) cc_final: 0.6383 (mmtt) REVERT: g 95 ASP cc_start: 0.6101 (t0) cc_final: 0.5809 (t0) outliers start: 57 outliers final: 31 residues processed: 272 average time/residue: 0.1265 time to fit residues: 48.6997 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 : 0.425 ------------------------------------------------------------------------------- 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: 6.9990 chunk 135 optimal weight: 40.0000 chunk 159 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 167 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN B 433 ASN B 466 HIS D 342 GLN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.125093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.109831 restraints weight = 69548.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.109515 restraints weight = 58225.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.109745 restraints weight = 53508.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.109711 restraints weight = 44461.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.110052 restraints weight = 37848.660| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.074 15422 Z= 0.634 Angle : 0.744 16.479 20583 Z= 0.415 Chirality : 0.044 0.268 2269 Planarity : 0.005 0.081 2643 Dihedral : 5.273 46.322 1960 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 4.24 % Allowed : 19.65 % Favored : 76.12 % 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 are not related in a simple way. whole: -0.38 (0.19), residues: 1781 helix: 0.47 (0.14), residues: 1298 sheet: -0.57 (0.70), residues: 55 loop : -2.29 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 337 TYR 0.058 0.003 TYR A 295 PHE 0.021 0.003 PHE O 606 TRP 0.045 0.004 TRP A 661 HIS 0.023 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01574 (15422) covalent geometry : angle 0.74369 (20583) hydrogen bonds : bond 0.06773 ( 1015) hydrogen bonds : angle 4.76607 ( 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 285 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 213 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5524 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: A 324 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: A 663 LYS cc_start: 0.7453 (mttt) cc_final: 0.7172 (pttt) REVERT: A 682 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8219 (tppt) REVERT: A 692 ASN cc_start: 0.7820 (OUTLIER) cc_final: 0.7619 (p0) REVERT: B 319 GLN cc_start: 0.7207 (mm110) cc_final: 0.6928 (mm110) REVERT: B 423 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6008 (tm-30) REVERT: B 473 MET cc_start: -0.1573 (ttt) cc_final: -0.1876 (ttt) REVERT: E 300 HIS cc_start: 0.6861 (OUTLIER) cc_final: 0.5260 (t-90) REVERT: M 258 TYR cc_start: 0.4222 (p90) cc_final: 0.2253 (t80) REVERT: M 266 LEU cc_start: 0.2377 (OUTLIER) cc_final: 0.2087 (mm) REVERT: M 287 MET cc_start: 0.5494 (mmm) cc_final: 0.5152 (mmp) REVERT: N 568 ASP cc_start: 0.5240 (OUTLIER) cc_final: 0.4744 (m-30) REVERT: O 590 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: O 681 MET cc_start: 0.5729 (OUTLIER) cc_final: 0.5125 (tpp) REVERT: P 653 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7431 (tm-30) REVERT: P 684 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: T 247 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6141 (tt0) REVERT: T 294 LYS cc_start: 0.6780 (mmtt) cc_final: 0.6220 (mmtt) REVERT: T 301 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.3146 (mt-10) outliers start: 72 outliers final: 38 residues processed: 263 average time/residue: 0.1222 time to fit residues: 45.9753 Evaluate side-chains 229 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 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 356 THR 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 236 MET 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 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 583 ASP 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 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 130 ASN 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: 1.9990 chunk 53 optimal weight: 8.9990 chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 153 optimal weight: 0.0980 chunk 58 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 466 HIS ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 710 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.126643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.110867 restraints weight = 69313.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.110627 restraints weight = 53374.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.110723 restraints weight = 51840.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.111145 restraints weight = 38608.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.111188 restraints weight = 37206.859| |-----------------------------------------------------------------------------| r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.6054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.101 15422 Z= 0.615 Angle : 0.681 16.405 20583 Z= 0.380 Chirality : 0.042 0.347 2269 Planarity : 0.004 0.085 2643 Dihedral : 4.956 44.929 1960 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.31 % Favored : 96.57 % Rotamer: Outliers : 3.53 % Allowed : 21.53 % Favored : 74.94 % 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 are not related in a simple way. whole: 0.03 (0.20), residues: 1781 helix: 0.78 (0.14), residues: 1305 sheet: -0.58 (0.68), residues: 60 loop : -2.22 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 284 TYR 0.051 0.002 TYR A 295 PHE 0.023 0.002 PHE O 606 TRP 0.044 0.003 TRP A 661 HIS 0.018 0.001 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01538 (15422) covalent geometry : angle 0.68100 (20583) hydrogen bonds : bond 0.06132 ( 1015) hydrogen bonds : angle 4.49419 ( 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 270 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.6352 (OUTLIER) cc_final: 0.6045 (m-80) REVERT: A 663 LYS cc_start: 0.7498 (mttt) cc_final: 0.7165 (pttt) REVERT: A 682 LYS cc_start: 0.8560 (mmmt) cc_final: 0.8348 (tppt) REVERT: A 692 ASN cc_start: 0.7835 (OUTLIER) cc_final: 0.7563 (p0) REVERT: A 720 LYS cc_start: 0.5889 (tptt) cc_final: 0.5635 (tppt) REVERT: A 728 MET cc_start: 0.7107 (pmm) cc_final: 0.6898 (pmm) REVERT: B 319 GLN cc_start: 0.7165 (mm110) cc_final: 0.6866 (mm110) REVERT: B 442 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8166 (tm-30) REVERT: B 473 MET cc_start: -0.1605 (ttt) cc_final: -0.1911 (ttt) REVERT: E 300 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.4801 (t-90) REVERT: M 258 TYR cc_start: 0.3660 (p90) cc_final: 0.2261 (t80) REVERT: M 287 MET cc_start: 0.5474 (mmm) cc_final: 0.5177 (mmp) REVERT: N 568 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5355 (m-30) REVERT: N 695 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7507 (pptt) REVERT: O 590 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7652 (pm20) REVERT: O 606 PHE cc_start: 0.5659 (t80) cc_final: 0.5040 (t80) REVERT: O 681 MET cc_start: 0.5545 (OUTLIER) cc_final: 0.4975 (tpp) REVERT: P 696 ARG cc_start: 0.6755 (pmt-80) cc_final: 0.6406 (pmt-80) REVERT: T 247 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6291 (tt0) REVERT: T 294 LYS cc_start: 0.6652 (mmtt) cc_final: 0.6328 (mmtt) outliers start: 60 outliers final: 29 residues processed: 255 average time/residue: 0.1171 time to fit residues: 42.6706 Evaluate side-chains 231 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 312 HIS 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 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 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 623 MET Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 695 LYS 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 672 ILE Chi-restraints excluded: chain P residue 684 GLN Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 89 PHE 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: 7.9990 chunk 147 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** E 288 ASN ** 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** ** O 569 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.123779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.108833 restraints weight = 69215.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.108212 restraints weight = 58880.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.108476 restraints weight = 51619.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.108867 restraints weight = 38713.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109112 restraints weight = 36166.450| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.035 15422 Z= 0.626 Angle : 0.735 17.175 20583 Z= 0.409 Chirality : 0.044 0.265 2269 Planarity : 0.005 0.089 2643 Dihedral : 5.226 46.567 1960 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 4.65 % Allowed : 22.41 % Favored : 72.94 % 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 are not related in a simple way. whole: -0.21 (0.20), residues: 1781 helix: 0.57 (0.14), residues: 1320 sheet: -0.69 (0.69), residues: 55 loop : -2.26 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 284 TYR 0.060 0.003 TYR A 295 PHE 0.022 0.002 PHE g 139 TRP 0.050 0.003 TRP A 661 HIS 0.025 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01549 (15422) covalent geometry : angle 0.73501 (20583) hydrogen bonds : bond 0.06429 ( 1015) hydrogen bonds : angle 4.65152 ( 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 278 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 199 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5505 (OUTLIER) cc_final: 0.5253 (pm20) REVERT: A 324 PHE cc_start: 0.6295 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: A 339 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: A 663 LYS cc_start: 0.7458 (mttt) cc_final: 0.7186 (pttt) REVERT: A 686 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: A 688 GLN cc_start: 0.7181 (tm-30) cc_final: 0.6959 (tm-30) REVERT: A 727 LYS cc_start: 0.7189 (mppt) cc_final: 0.6768 (mmmt) REVERT: B 319 GLN cc_start: 0.7261 (mm110) cc_final: 0.6961 (mm110) REVERT: B 473 MET cc_start: -0.1108 (ttt) cc_final: -0.1364 (ttt) REVERT: E 300 HIS cc_start: 0.6635 (OUTLIER) cc_final: 0.5058 (t-90) REVERT: M 258 TYR cc_start: 0.4044 (p90) cc_final: 0.2287 (t80) REVERT: M 266 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2497 (mm) REVERT: M 298 ARG cc_start: 0.5059 (ptm160) cc_final: 0.4841 (ptm-80) REVERT: N 568 ASP cc_start: 0.5180 (OUTLIER) cc_final: 0.4679 (m-30) REVERT: O 525 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: O 590 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: O 609 LYS cc_start: 0.8301 (tppp) cc_final: 0.8100 (pttp) REVERT: O 681 MET cc_start: 0.5567 (OUTLIER) cc_final: 0.5000 (tpp) REVERT: P 705 ARG cc_start: 0.7802 (tpm170) cc_final: 0.7516 (mmp80) REVERT: T 247 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6195 (tt0) REVERT: T 294 LYS cc_start: 0.6907 (mmtt) cc_final: 0.6569 (mmtt) REVERT: T 301 GLU cc_start: 0.3973 (OUTLIER) cc_final: 0.3707 (mt-10) outliers start: 79 outliers final: 48 residues processed: 258 average time/residue: 0.1075 time to fit residues: 40.3201 Evaluate side-chains 237 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 178 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 339 GLN 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 293 PHE 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 313 ILE Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER 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 236 MET Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 300 PHE 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 623 MET Chi-restraints excluded: chain N residue 627 ILE 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 586 TYR 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: 0.9980 chunk 103 optimal weight: 9.9990 chunk 126 optimal weight: 0.0030 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 overall best weight: 2.9996 ------------------------------------------------------------------------------- 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** M 332 GLN ** 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** ** O 568 GLN ** 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 = 0.4319 r_free = 0.4319 target = 0.124751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.109125 restraints weight = 69004.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.109052 restraints weight = 55313.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.109531 restraints weight = 44387.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.109893 restraints weight = 35060.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.110026 restraints weight = 33444.894| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.039 15422 Z= 0.614 Angle : 0.686 16.645 20583 Z= 0.382 Chirality : 0.043 0.280 2269 Planarity : 0.004 0.082 2643 Dihedral : 5.025 46.331 1960 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer: Outliers : 3.88 % Allowed : 23.82 % Favored : 72.29 % 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 are not related in a simple way. whole: 0.08 (0.20), residues: 1781 helix: 0.77 (0.14), residues: 1320 sheet: -0.36 (0.78), residues: 48 loop : -2.11 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 284 TYR 0.058 0.002 TYR A 295 PHE 0.020 0.002 PHE A 685 TRP 0.052 0.003 TRP A 661 HIS 0.027 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01520 (15422) covalent geometry : angle 0.68627 (20583) hydrogen bonds : bond 0.06004 ( 1015) hydrogen bonds : angle 4.49301 ( 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 268 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 202 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6076 (m-10) REVERT: A 663 LYS cc_start: 0.7447 (mttt) cc_final: 0.7163 (pttt) REVERT: A 686 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6796 (tp30) REVERT: A 720 LYS cc_start: 0.5895 (tptt) cc_final: 0.5654 (tppt) REVERT: A 727 LYS cc_start: 0.7509 (mppt) cc_final: 0.7039 (mmmt) REVERT: B 473 MET cc_start: -0.1100 (ttt) cc_final: -0.1408 (ttt) REVERT: E 300 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.4922 (t-90) REVERT: M 258 TYR cc_start: 0.4161 (p90) cc_final: 0.2741 (t80) REVERT: M 298 ARG cc_start: 0.5043 (ptm160) cc_final: 0.4836 (ptm-80) REVERT: N 568 ASP cc_start: 0.5323 (OUTLIER) cc_final: 0.4712 (m-30) REVERT: O 525 GLN cc_start: 0.7992 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: O 590 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7610 (pm20) REVERT: O 678 ILE cc_start: 0.7310 (tp) cc_final: 0.7060 (tp) REVERT: O 681 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.4923 (tpp) REVERT: P 684 GLN cc_start: 0.6562 (OUTLIER) cc_final: 0.6148 (mp10) REVERT: P 696 ARG cc_start: 0.6605 (pmt-80) cc_final: 0.6280 (pmt-80) REVERT: T 247 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6262 (tt0) REVERT: T 280 LYS cc_start: 0.7319 (mmtm) cc_final: 0.7103 (mmtm) REVERT: T 294 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6552 (mmtt) REVERT: T 301 GLU cc_start: 0.3959 (OUTLIER) cc_final: 0.3690 (mt-10) REVERT: g 124 ARG cc_start: 0.6823 (tpp-160) cc_final: 0.6416 (mmt-90) outliers start: 66 outliers final: 35 residues processed: 255 average time/residue: 0.1105 time to fit residues: 41.0155 Evaluate side-chains 220 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 324 PHE 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 D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER 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 247 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 610 ILE 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 679 HIS Chi-restraints excluded: chain O residue 681 MET Chi-restraints excluded: chain P residue 643 ILE 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 T residue 301 GLU Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 89 PHE 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: 7.9990 chunk 170 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 406 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 = 0.4290 r_free = 0.4290 target = 0.122871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.108020 restraints weight = 69776.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.107420 restraints weight = 62637.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.107703 restraints weight = 53222.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.107972 restraints weight = 39766.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.108450 restraints weight = 37336.998| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.042 15422 Z= 0.628 Angle : 0.765 16.648 20583 Z= 0.423 Chirality : 0.045 0.186 2269 Planarity : 0.005 0.092 2643 Dihedral : 5.283 47.657 1960 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer: Outliers : 3.82 % Allowed : 24.65 % Favored : 71.53 % 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 are not related in a simple way. whole: -0.16 (0.20), residues: 1781 helix: 0.60 (0.14), residues: 1315 sheet: -1.15 (0.72), residues: 55 loop : -2.09 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 284 TYR 0.061 0.003 TYR A 295 PHE 0.017 0.002 PHE D 454 TRP 0.055 0.003 TRP A 661 HIS 0.025 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01553 (15422) covalent geometry : angle 0.76457 (20583) hydrogen bonds : bond 0.06403 ( 1015) hydrogen bonds : angle 4.69744 ( 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 252 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5431 (OUTLIER) cc_final: 0.5207 (pm20) REVERT: A 324 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5814 (m-10) REVERT: A 686 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6942 (tp30) REVERT: A 727 LYS cc_start: 0.7645 (mppt) cc_final: 0.7247 (mmmt) REVERT: B 473 MET cc_start: -0.1205 (ttt) cc_final: -0.1438 (ttt) REVERT: D 380 VAL cc_start: 0.5855 (m) cc_final: 0.5435 (t) REVERT: E 264 LYS cc_start: 0.7192 (tttt) cc_final: 0.6763 (mmmt) REVERT: E 300 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.5465 (t-90) REVERT: M 258 TYR cc_start: 0.4455 (p90) cc_final: 0.2849 (t80) REVERT: N 568 ASP cc_start: 0.5235 (OUTLIER) cc_final: 0.4763 (m-30) REVERT: O 525 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: O 590 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: O 609 LYS cc_start: 0.8508 (tppp) cc_final: 0.8209 (pttp) REVERT: O 678 ILE cc_start: 0.7312 (tp) cc_final: 0.7070 (tp) REVERT: O 681 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4940 (tpp) REVERT: P 684 GLN cc_start: 0.6618 (OUTLIER) cc_final: 0.6031 (mp10) REVERT: T 247 GLU cc_start: 0.6866 (tm-30) cc_final: 0.6179 (tt0) REVERT: T 280 LYS cc_start: 0.7273 (mmtm) cc_final: 0.7026 (mmtm) REVERT: T 294 LYS cc_start: 0.6952 (mmtt) cc_final: 0.6595 (mmtt) REVERT: T 301 GLU cc_start: 0.4740 (OUTLIER) cc_final: 0.4463 (mp0) REVERT: g 124 ARG cc_start: 0.6811 (tpp-160) cc_final: 0.6397 (mmt-90) outliers start: 65 outliers final: 44 residues processed: 234 average time/residue: 0.1202 time to fit residues: 41.0012 Evaluate side-chains 232 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 178 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 324 PHE 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 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 D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 437 ARG 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 236 MET Chi-restraints excluded: chain M residue 247 ILE 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 689 GLU 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 586 TYR 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 672 ILE Chi-restraints excluded: chain P residue 684 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 89 PHE 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: 40.0000 chunk 99 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** 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** O 568 GLN ** 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 = 0.4293 r_free = 0.4293 target = 0.122907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.108142 restraints weight = 69077.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.108136 restraints weight = 59670.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.108306 restraints weight = 56131.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.108392 restraints weight = 41385.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.108783 restraints weight = 36156.063| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.7262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.032 15422 Z= 0.622 Angle : 0.739 17.245 20583 Z= 0.411 Chirality : 0.044 0.190 2269 Planarity : 0.005 0.084 2643 Dihedral : 5.210 47.820 1960 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 3.94 % Allowed : 24.29 % Favored : 71.76 % 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 are not related in a simple way. whole: -0.10 (0.20), residues: 1781 helix: 0.64 (0.14), residues: 1323 sheet: -0.52 (0.84), residues: 43 loop : -2.19 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 284 TYR 0.064 0.003 TYR A 295 PHE 0.021 0.002 PHE D 454 TRP 0.059 0.004 TRP A 661 HIS 0.026 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01539 (15422) covalent geometry : angle 0.73914 (20583) hydrogen bonds : bond 0.06216 ( 1015) hydrogen bonds : angle 4.64166 ( 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 260 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 193 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: A 324 PHE cc_start: 0.6419 (OUTLIER) cc_final: 0.5751 (m-10) REVERT: A 686 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6981 (tp30) REVERT: A 727 LYS cc_start: 0.7670 (mppt) cc_final: 0.7273 (mmmt) REVERT: B 473 MET cc_start: -0.0624 (ttt) cc_final: -0.0956 (ttt) REVERT: E 264 LYS cc_start: 0.7266 (tttt) cc_final: 0.6898 (mmmt) REVERT: E 300 HIS cc_start: 0.6754 (OUTLIER) cc_final: 0.5415 (t-90) REVERT: E 402 ARG cc_start: 0.8292 (tpt170) cc_final: 0.7706 (ptm-80) REVERT: M 258 TYR cc_start: 0.3849 (p90) cc_final: 0.2552 (t80) REVERT: N 568 ASP cc_start: 0.5540 (OUTLIER) cc_final: 0.4955 (m-30) REVERT: O 525 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7321 (mp10) REVERT: O 590 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: O 678 ILE cc_start: 0.7293 (tp) cc_final: 0.7046 (tp) REVERT: O 681 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4742 (tpp) REVERT: P 684 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.6045 (mp10) REVERT: P 705 ARG cc_start: 0.6900 (mmp80) cc_final: 0.6668 (mmp80) REVERT: T 247 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6215 (tt0) REVERT: T 294 LYS cc_start: 0.6828 (mmtt) cc_final: 0.6546 (mmtt) REVERT: T 301 GLU cc_start: 0.4967 (OUTLIER) cc_final: 0.4608 (mp0) REVERT: g 124 ARG cc_start: 0.6989 (tpp-160) cc_final: 0.6545 (mmt-90) REVERT: g 126 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8115 (t0) outliers start: 67 outliers final: 46 residues processed: 239 average time/residue: 0.1105 time to fit residues: 38.2032 Evaluate side-chains 238 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 324 PHE 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 D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER 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 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 610 ILE Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 689 GLU 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 586 TYR 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 702 ASP Chi-restraints excluded: chain P residue 704 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 98 ASN Chi-restraints excluded: chain g residue 126 ASP 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: 6.9990 chunk 100 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 138 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 115 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 ASN ** M 175 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.122108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.107346 restraints weight = 69386.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.106872 restraints weight = 58966.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.107087 restraints weight = 51801.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.107486 restraints weight = 38249.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.107725 restraints weight = 35653.325| |-----------------------------------------------------------------------------| r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.7465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.025 15422 Z= 0.626 Angle : 0.771 17.013 20583 Z= 0.427 Chirality : 0.045 0.236 2269 Planarity : 0.005 0.088 2643 Dihedral : 5.301 48.057 1960 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 3.94 % Allowed : 24.65 % Favored : 71.41 % 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 are not related in a simple way. whole: -0.19 (0.20), residues: 1781 helix: 0.59 (0.14), residues: 1314 sheet: -1.37 (0.74), residues: 51 loop : -2.10 (0.31), residues: 416 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 M 300 TRP 0.035 0.003 TRP A 661 HIS 0.028 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01547 (15422) covalent geometry : angle 0.77117 (20583) hydrogen bonds : bond 0.06323 ( 1015) hydrogen bonds : angle 4.69068 ( 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: 67 poor density : 191 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5275 (OUTLIER) cc_final: 0.5007 (pm20) REVERT: A 324 PHE cc_start: 0.6469 (OUTLIER) cc_final: 0.5801 (m-10) REVERT: A 686 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.6968 (tp30) REVERT: A 727 LYS cc_start: 0.7594 (mppt) cc_final: 0.7232 (mmmt) REVERT: E 264 LYS cc_start: 0.7284 (tttt) cc_final: 0.6911 (mmmt) REVERT: E 300 HIS cc_start: 0.6828 (OUTLIER) cc_final: 0.5730 (t-90) REVERT: M 258 TYR cc_start: 0.3854 (p90) cc_final: 0.2748 (t80) REVERT: N 568 ASP cc_start: 0.5580 (OUTLIER) cc_final: 0.4905 (m-30) REVERT: O 525 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: O 590 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: O 609 LYS cc_start: 0.8514 (tppp) cc_final: 0.8113 (mmmt) REVERT: O 678 ILE cc_start: 0.7069 (tp) cc_final: 0.6852 (tp) REVERT: O 681 MET cc_start: 0.5562 (OUTLIER) cc_final: 0.4959 (tpp) REVERT: P 684 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.6002 (mp10) REVERT: T 247 GLU cc_start: 0.6860 (tm-30) cc_final: 0.6272 (tt0) REVERT: T 280 LYS cc_start: 0.7027 (mmtm) cc_final: 0.6697 (mmtm) REVERT: T 294 LYS cc_start: 0.6927 (mmtt) cc_final: 0.6604 (mmtt) REVERT: g 124 ARG cc_start: 0.7006 (tpp-160) cc_final: 0.6589 (mmt-90) outliers start: 67 outliers final: 48 residues processed: 239 average time/residue: 0.1116 time to fit residues: 38.7817 Evaluate side-chains 239 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 182 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 365 LEU 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 D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain E residue 300 HIS 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 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 627 ILE Chi-restraints excluded: chain N residue 661 GLU Chi-restraints excluded: chain N residue 689 GLU 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 586 TYR 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 702 ASP Chi-restraints excluded: chain T residue 323 LYS Chi-restraints excluded: chain g residue 64 ASP Chi-restraints excluded: chain g residue 89 PHE Chi-restraints excluded: chain g residue 98 ASN Chi-restraints excluded: chain g residue 126 ASP 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: 0.7980 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 37 optimal weight: 6.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 175 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** ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.122397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.107691 restraints weight = 68922.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.107165 restraints weight = 61703.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.107634 restraints weight = 50909.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.107934 restraints weight = 37917.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.108201 restraints weight = 36372.840| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.7605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.027 15422 Z= 0.622 Angle : 0.762 16.969 20583 Z= 0.424 Chirality : 0.044 0.190 2269 Planarity : 0.005 0.084 2643 Dihedral : 5.250 47.747 1960 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 3.65 % Allowed : 24.65 % Favored : 71.71 % 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 are not related in a simple way. whole: -0.11 (0.20), residues: 1781 helix: 0.62 (0.14), residues: 1322 sheet: -0.60 (0.87), residues: 39 loop : -2.11 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 284 TYR 0.060 0.003 TYR A 295 PHE 0.025 0.002 PHE D 454 TRP 0.054 0.003 TRP A 661 HIS 0.028 0.002 HIS B 289 Details of bonding type rmsd covalent geometry : bond 0.01537 (15422) covalent geometry : angle 0.76185 (20583) hydrogen bonds : bond 0.06200 ( 1015) hydrogen bonds : angle 4.66672 ( 3021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3463.28 seconds wall clock time: 60 minutes 21.40 seconds (3621.40 seconds total)