Starting phenix.real_space_refine on Sat May 17 00:07:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.map" model { file = "/net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tek_41189/05_2025/8tek_41189.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.32, per 1000 atoms: 0.68 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: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.44 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: 4.03 Time building geometry restraints manager: 4.26 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: 6.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 35.180 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.870 ------------------------------------------------------------------------------- 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 : 14.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (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 TRP 0.014 0.002 TRP A 676 HIS 0.034 0.001 HIS B 289 PHE 0.012 0.001 PHE D 330 TYR 0.055 0.002 TYR A 295 ARG 0.012 0.001 ARG O 689 Details of bonding type rmsd hydrogen bonds : bond 0.30060 ( 1015) hydrogen bonds : angle 8.36172 ( 3021) covalent geometry : bond 0.01501 (15422) covalent geometry : angle 0.64695 (20583) *********************** 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 : 2.089 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: A 341 MET cc_start: 0.4753 (mmm) cc_final: 0.4502 (tpt) REVERT: B 473 MET cc_start: -0.0776 (ttt) cc_final: -0.1598 (ttt) REVERT: M 233 SER cc_start: 0.6987 (p) cc_final: 0.6757 (t) REVERT: M 258 TYR cc_start: 0.3359 (p90) cc_final: 0.3043 (t80) REVERT: M 322 ASN cc_start: 0.5994 (p0) cc_final: 0.5666 (p0) REVERT: N 703 SER cc_start: 0.5755 (m) cc_final: 0.5395 (t) REVERT: N 726 TYR cc_start: 0.4467 (m-10) cc_final: 0.4250 (m-80) REVERT: O 576 ASN cc_start: 0.4512 (p0) cc_final: 0.4152 (p0) REVERT: g 90 GLU cc_start: 0.5922 (tt0) cc_final: 0.4954 (tt0) REVERT: g 95 ASP cc_start: 0.5354 (t0) cc_final: 0.5136 (t0) outliers start: 0 outliers final: 0 residues processed: 564 average time/residue: 0.3672 time to fit residues: 277.2083 Evaluate side-chains 262 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 70 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 306 ASN B 310 ASN B 442 GLN D 345 GLN D 442 HIS ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 401 GLN E 411 ASN E 416 ASN M 207 GLN M 289 GLN N 599 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN O 543 GLN O 644 GLN P 710 GLN T 249 GLN g 159 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.126811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.110650 restraints weight = 68294.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.110626 restraints weight = 55191.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.110912 restraints weight = 47456.569| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4484 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= 0.635 Angle : 0.808 16.429 20583 Z= 0.447 Chirality : 0.046 0.229 2269 Planarity : 0.005 0.078 2643 Dihedral : 5.357 42.157 1960 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.15 % Favored : 95.73 % Rotamer: Outliers : 2.53 % Allowed : 15.41 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.19), residues: 1781 helix: 0.15 (0.14), residues: 1289 sheet: -0.31 (0.68), residues: 53 loop : -2.13 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 676 HIS 0.032 0.003 HIS B 289 PHE 0.027 0.003 PHE O 606 TYR 0.055 0.003 TYR A 295 ARG 0.009 0.001 ARG B 309 Details of bonding type rmsd hydrogen bonds : bond 0.08075 ( 1015) hydrogen bonds : angle 5.22875 ( 3021) covalent geometry : bond 0.01549 (15422) covalent geometry : angle 0.80755 (20583) *********************** 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 316 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 663 LYS cc_start: 0.7298 (mttt) cc_final: 0.6974 (mttt) REVERT: A 720 LYS cc_start: 0.5543 (tptt) cc_final: 0.5110 (tttt) REVERT: B 473 MET cc_start: -0.1094 (ttt) cc_final: -0.1411 (ttt) REVERT: E 300 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6710 (t70) REVERT: E 342 LEU cc_start: 0.5316 (tp) cc_final: 0.5089 (tt) REVERT: E 401 GLN cc_start: 0.7714 (mt0) cc_final: 0.6700 (tp40) REVERT: M 236 MET cc_start: 0.7797 (ppp) cc_final: 0.7183 (mmm) REVERT: M 258 TYR cc_start: 0.3725 (p90) cc_final: 0.2103 (t80) REVERT: M 263 HIS cc_start: 0.7255 (m90) cc_final: 0.6917 (m90) REVERT: M 287 MET cc_start: 0.5565 (mmm) cc_final: 0.5132 (mmp) REVERT: N 692 ASN cc_start: 0.8388 (t0) cc_final: 0.8027 (t0) REVERT: N 695 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7461 (tttp) REVERT: O 586 TYR cc_start: 0.7248 (t80) cc_final: 0.6458 (m-80) outliers start: 43 outliers final: 24 residues processed: 306 average time/residue: 0.3496 time to fit residues: 145.3037 Evaluate side-chains 220 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 452 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 346 TYR Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 249 ASP Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 633 SER 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 702 ASP Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 290 GLU Chi-restraints excluded: chain g residue 26 ASP Chi-restraints excluded: chain g residue 89 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 77 optimal weight: 0.0980 chunk 106 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS A 342 ASN B 433 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 252 ASN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 519 GLN ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.125910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.109989 restraints weight = 68401.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.110579 restraints weight = 50788.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.110489 restraints weight = 48564.861| |-----------------------------------------------------------------------------| r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.012 15422 Z= 0.625 Angle : 0.733 16.570 20583 Z= 0.410 Chirality : 0.044 0.231 2269 Planarity : 0.005 0.075 2643 Dihedral : 5.219 43.642 1960 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.82 % Favored : 96.07 % Rotamer: Outliers : 3.53 % Allowed : 18.71 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 1781 helix: 0.37 (0.14), residues: 1290 sheet: -0.60 (0.67), residues: 55 loop : -2.21 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 661 HIS 0.035 0.003 HIS B 289 PHE 0.021 0.002 PHE O 606 TYR 0.056 0.003 TYR A 295 ARG 0.009 0.001 ARG M 298 Details of bonding type rmsd hydrogen bonds : bond 0.07184 ( 1015) hydrogen bonds : angle 4.89964 ( 3021) covalent geometry : bond 0.01533 (15422) covalent geometry : angle 0.73288 (20583) *********************** 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 273 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 213 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5437 (OUTLIER) cc_final: 0.4938 (pm20) REVERT: A 692 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7600 (p0) REVERT: B 318 MET cc_start: 0.6413 (ttp) cc_final: 0.6132 (tpp) REVERT: B 423 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.6053 (tm-30) REVERT: B 473 MET cc_start: -0.1077 (ttt) cc_final: -0.1406 (ttt) REVERT: D 380 VAL cc_start: 0.5523 (OUTLIER) cc_final: 0.5253 (t) REVERT: D 442 HIS cc_start: 0.6186 (m-70) cc_final: 0.5888 (m170) REVERT: E 300 HIS cc_start: 0.7373 (OUTLIER) cc_final: 0.6011 (t70) REVERT: E 307 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7426 (mp) REVERT: E 401 GLN cc_start: 0.7615 (mt0) cc_final: 0.6613 (tp40) REVERT: M 258 TYR cc_start: 0.3912 (p90) cc_final: 0.2315 (t80) REVERT: M 287 MET cc_start: 0.5475 (mmm) cc_final: 0.5132 (mmp) REVERT: N 568 ASP cc_start: 0.5659 (OUTLIER) cc_final: 0.4970 (m-30) REVERT: N 670 MET cc_start: 0.7763 (mtp) cc_final: 0.7400 (mtm) REVERT: N 695 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7512 (pptt) REVERT: P 696 ARG cc_start: 0.7008 (pmt-80) cc_final: 0.6730 (pmt-80) REVERT: T 247 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6154 (tt0) REVERT: g 48 GLU cc_start: 0.8077 (tt0) cc_final: 0.7846 (tt0) outliers start: 60 outliers final: 32 residues processed: 255 average time/residue: 0.3179 time to fit residues: 113.5070 Evaluate side-chains 223 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 680 PHE Chi-restraints excluded: chain A residue 689 ILE 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 333 SER Chi-restraints excluded: chain B residue 365 THR 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 380 VAL Chi-restraints excluded: chain E residue 300 HIS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 364 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 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 623 MET Chi-restraints excluded: chain N residue 633 SER 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 O residue 583 ASP 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 708 LEU Chi-restraints excluded: chain P residue 765 MET Chi-restraints excluded: chain T residue 290 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 97 LYS Chi-restraints excluded: chain g residue 121 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 28 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 288 GLN B 433 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 416 ASN ** M 289 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** ** O 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 666 ASN P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.124793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.109763 restraints weight = 68367.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.109389 restraints weight = 59930.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.109628 restraints weight = 51867.944| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.5949 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= 0.625 Angle : 0.724 16.814 20583 Z= 0.404 Chirality : 0.044 0.179 2269 Planarity : 0.005 0.076 2643 Dihedral : 5.244 45.116 1960 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 4.47 % Allowed : 21.06 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1781 helix: 0.43 (0.14), residues: 1301 sheet: -0.73 (0.68), residues: 55 loop : -2.23 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 661 HIS 0.031 0.002 HIS B 289 PHE 0.027 0.002 PHE O 606 TYR 0.053 0.003 TYR A 295 ARG 0.013 0.001 ARG E 337 Details of bonding type rmsd hydrogen bonds : bond 0.06711 ( 1015) hydrogen bonds : angle 4.77523 ( 3021) covalent geometry : bond 0.01538 (15422) covalent geometry : angle 0.72407 (20583) *********************** 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: 76 poor density : 209 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.5164 (pm20) REVERT: A 663 LYS cc_start: 0.7380 (mttp) cc_final: 0.6835 (pttm) REVERT: A 686 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6966 (tp30) REVERT: A 692 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7593 (p0) REVERT: A 728 MET cc_start: 0.7108 (pmm) cc_final: 0.6822 (pmm) REVERT: B 473 MET cc_start: -0.1073 (ttt) cc_final: -0.1376 (ttt) REVERT: D 380 VAL cc_start: 0.5969 (OUTLIER) cc_final: 0.5641 (t) REVERT: D 442 HIS cc_start: 0.6242 (m-70) cc_final: 0.5954 (m170) REVERT: E 300 HIS cc_start: 0.6921 (OUTLIER) cc_final: 0.5253 (t-90) REVERT: E 401 GLN cc_start: 0.7503 (mt0) cc_final: 0.6449 (tp40) REVERT: M 225 LYS cc_start: 0.7449 (tppt) cc_final: 0.6693 (tppt) REVERT: M 258 TYR cc_start: 0.4202 (p90) cc_final: 0.2296 (t80) REVERT: M 266 LEU cc_start: 0.2455 (OUTLIER) cc_final: 0.2042 (mm) REVERT: M 287 MET cc_start: 0.4628 (mmm) cc_final: 0.4202 (mmp) REVERT: N 568 ASP cc_start: 0.5476 (OUTLIER) cc_final: 0.4780 (m-30) REVERT: O 578 MET cc_start: 0.7583 (mmm) cc_final: 0.7288 (mmm) REVERT: O 590 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: O 606 PHE cc_start: 0.5691 (t80) cc_final: 0.5316 (t80) REVERT: P 653 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7431 (tm-30) REVERT: P 657 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7873 (mt-10) REVERT: P 684 GLN cc_start: 0.6429 (OUTLIER) cc_final: 0.5827 (mp10) REVERT: T 247 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6104 (tt0) REVERT: T 294 LYS cc_start: 0.6969 (mmtt) cc_final: 0.6483 (mmtt) REVERT: T 301 GLU cc_start: 0.3428 (OUTLIER) cc_final: 0.3161 (mt-10) REVERT: g 90 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7400 (tt0) outliers start: 76 outliers final: 39 residues processed: 268 average time/residue: 0.3371 time to fit residues: 130.0033 Evaluate side-chains 231 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 181 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 686 GLU 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 442 GLN 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 380 VAL 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 E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 610 ILE Chi-restraints excluded: chain N residue 627 ILE Chi-restraints excluded: chain N residue 633 SER Chi-restraints excluded: chain N residue 661 GLU 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 590 GLU Chi-restraints excluded: chain O residue 658 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 708 LEU 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 90 GLU Chi-restraints excluded: chain g residue 97 LYS Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 169 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 62 optimal weight: 0.0370 chunk 76 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 12 optimal weight: 0.0970 chunk 96 optimal weight: 0.4980 chunk 63 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 overall best weight: 1.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 335 ASN ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS M 289 GLN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN O 679 HIS ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.126289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.110806 restraints weight = 69782.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.111137 restraints weight = 55577.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.111382 restraints weight = 50099.604| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.009 15422 Z= 0.613 Angle : 0.670 16.729 20583 Z= 0.376 Chirality : 0.042 0.297 2269 Planarity : 0.004 0.077 2643 Dihedral : 4.910 43.436 1960 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 3.71 % Allowed : 22.06 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.20), residues: 1781 helix: 0.73 (0.14), residues: 1314 sheet: -0.50 (0.73), residues: 53 loop : -2.27 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 661 HIS 0.034 0.002 HIS B 289 PHE 0.022 0.002 PHE A 685 TYR 0.056 0.002 TYR A 295 ARG 0.009 0.000 ARG D 437 Details of bonding type rmsd hydrogen bonds : bond 0.06070 ( 1015) hydrogen bonds : angle 4.52123 ( 3021) covalent geometry : bond 0.01510 (15422) covalent geometry : angle 0.66988 (20583) *********************** 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 277 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 214 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7601 (pt0) REVERT: A 663 LYS cc_start: 0.7265 (mttp) cc_final: 0.6832 (pttm) REVERT: A 692 ASN cc_start: 0.7663 (OUTLIER) cc_final: 0.7438 (p0) REVERT: A 728 MET cc_start: 0.7186 (pmm) cc_final: 0.6919 (pmm) REVERT: B 434 GLN cc_start: 0.7341 (pp30) cc_final: 0.7037 (pp30) REVERT: B 473 MET cc_start: -0.1115 (ttt) cc_final: -0.1451 (ttt) REVERT: D 292 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3702 (mt) REVERT: D 380 VAL cc_start: 0.5885 (OUTLIER) cc_final: 0.5627 (t) REVERT: D 442 HIS cc_start: 0.6499 (m-70) cc_final: 0.6289 (m170) REVERT: E 401 GLN cc_start: 0.7254 (mt0) cc_final: 0.6299 (tp40) REVERT: M 225 LYS cc_start: 0.7375 (tppt) cc_final: 0.6693 (tppt) REVERT: M 258 TYR cc_start: 0.3813 (p90) cc_final: 0.2415 (t80) REVERT: M 266 LEU cc_start: 0.2483 (OUTLIER) cc_final: 0.2128 (mm) REVERT: N 568 ASP cc_start: 0.5493 (OUTLIER) cc_final: 0.4788 (m-30) REVERT: N 623 MET cc_start: 0.6835 (tpt) cc_final: 0.6525 (tpt) REVERT: O 590 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: O 606 PHE cc_start: 0.5595 (t80) cc_final: 0.5107 (t80) REVERT: O 681 MET cc_start: 0.5425 (tpt) cc_final: 0.5202 (tpp) REVERT: P 684 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.5807 (mp10) REVERT: P 696 ARG cc_start: 0.6809 (pmt-80) cc_final: 0.6504 (pmt-80) REVERT: T 265 MET cc_start: 0.5178 (ptp) cc_final: 0.4854 (ptm) REVERT: T 301 GLU cc_start: 0.3419 (OUTLIER) cc_final: 0.3101 (mt-10) outliers start: 63 outliers final: 27 residues processed: 266 average time/residue: 0.3056 time to fit residues: 115.7007 Evaluate side-chains 226 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 694 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 464 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 219 ILE Chi-restraints excluded: chain M residue 266 LEU Chi-restraints excluded: chain M residue 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 661 GLU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 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 590 GLU Chi-restraints excluded: chain O residue 644 GLN Chi-restraints excluded: chain O residue 679 HIS 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 708 LEU Chi-restraints excluded: chain T residue 301 GLU Chi-restraints excluded: chain g residue 98 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 96 optimal weight: 20.0000 chunk 90 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 50 optimal weight: 0.1980 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 300 HIS M 332 GLN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 644 GLN O 679 HIS P 710 GLN ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.126083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.110784 restraints weight = 69434.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.110947 restraints weight = 56807.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.111218 restraints weight = 51924.096| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.6466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.074 15422 Z= 0.614 Angle : 0.670 16.720 20583 Z= 0.376 Chirality : 0.042 0.253 2269 Planarity : 0.004 0.082 2643 Dihedral : 4.837 42.813 1960 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.54 % Favored : 96.35 % Rotamer: Outliers : 3.35 % Allowed : 24.41 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.20), residues: 1781 helix: 0.82 (0.14), residues: 1322 sheet: -0.43 (0.73), residues: 53 loop : -2.21 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 661 HIS 0.020 0.002 HIS B 289 PHE 0.023 0.002 PHE M 300 TYR 0.058 0.002 TYR A 295 ARG 0.009 0.001 ARG O 676 Details of bonding type rmsd hydrogen bonds : bond 0.05878 ( 1015) hydrogen bonds : angle 4.48104 ( 3021) covalent geometry : bond 0.01528 (15422) covalent geometry : angle 0.67028 (20583) *********************** 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 261 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6803 (mp10) REVERT: A 661 TRP cc_start: 0.5110 (m-90) cc_final: 0.4743 (m100) REVERT: A 662 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7615 (pt0) REVERT: A 663 LYS cc_start: 0.7248 (mttp) cc_final: 0.6851 (pttm) REVERT: A 692 ASN cc_start: 0.7694 (OUTLIER) cc_final: 0.7416 (p0) REVERT: A 728 MET cc_start: 0.7210 (pmm) cc_final: 0.6941 (pmm) REVERT: B 434 GLN cc_start: 0.7257 (pp30) cc_final: 0.7020 (pp30) REVERT: B 473 MET cc_start: -0.1114 (ttt) cc_final: -0.1439 (ttt) REVERT: D 292 LEU cc_start: 0.4038 (OUTLIER) cc_final: 0.3655 (mt) REVERT: D 380 VAL cc_start: 0.6051 (OUTLIER) cc_final: 0.5781 (t) REVERT: D 442 HIS cc_start: 0.6304 (m-70) cc_final: 0.6080 (m170) REVERT: E 401 GLN cc_start: 0.7336 (mt0) cc_final: 0.6296 (tp40) REVERT: M 225 LYS cc_start: 0.7413 (tppt) cc_final: 0.6696 (tppt) REVERT: M 258 TYR cc_start: 0.3861 (p90) cc_final: 0.2447 (t80) REVERT: M 266 LEU cc_start: 0.2447 (OUTLIER) cc_final: 0.2103 (mm) REVERT: M 287 MET cc_start: 0.3535 (mmp) cc_final: 0.2519 (mmm) REVERT: M 327 GLU cc_start: 0.6824 (tm-30) cc_final: 0.6116 (mp0) REVERT: N 568 ASP cc_start: 0.5453 (OUTLIER) cc_final: 0.4735 (m-30) REVERT: O 525 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: O 590 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: O 606 PHE cc_start: 0.5545 (t80) cc_final: 0.5042 (t80) REVERT: P 653 GLU cc_start: 0.7694 (tm-30) cc_final: 0.7380 (tm-30) REVERT: P 657 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7863 (mt-10) REVERT: P 705 ARG cc_start: 0.7885 (tpm170) cc_final: 0.7621 (mmp80) REVERT: T 247 GLU cc_start: 0.6791 (tm-30) cc_final: 0.6299 (tt0) REVERT: T 265 MET cc_start: 0.5055 (ptp) cc_final: 0.4803 (ptm) REVERT: T 294 LYS cc_start: 0.6832 (mmtt) cc_final: 0.6362 (mmtt) REVERT: T 301 GLU cc_start: 0.3369 (OUTLIER) cc_final: 0.3052 (mt-10) REVERT: g 90 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7337 (tt0) outliers start: 57 outliers final: 29 residues processed: 251 average time/residue: 0.2986 time to fit residues: 106.4661 Evaluate side-chains 221 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 694 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 464 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU 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 661 GLU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 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 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 g residue 90 GLU Chi-restraints excluded: chain g residue 98 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 0.4980 chunk 174 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 40.0000 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 300 HIS ** M 332 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 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 = 0.4332 r_free = 0.4332 target = 0.125598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.110196 restraints weight = 69737.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.110103 restraints weight = 56120.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.110564 restraints weight = 46365.257| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.085 15422 Z= 0.615 Angle : 0.683 16.518 20583 Z= 0.382 Chirality : 0.042 0.215 2269 Planarity : 0.004 0.080 2643 Dihedral : 4.829 42.960 1960 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.71 % Favored : 96.18 % Rotamer: Outliers : 3.41 % Allowed : 24.71 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1781 helix: 0.83 (0.14), residues: 1322 sheet: -0.37 (0.77), residues: 48 loop : -2.15 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP A 661 HIS 0.020 0.001 HIS B 289 PHE 0.024 0.002 PHE M 300 TYR 0.056 0.002 TYR A 295 ARG 0.007 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.05839 ( 1015) hydrogen bonds : angle 4.49456 ( 3021) covalent geometry : bond 0.01536 (15422) covalent geometry : angle 0.68299 (20583) *********************** 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 261 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 203 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 LYS cc_start: 0.8088 (tttp) cc_final: 0.7705 (ttpp) REVERT: A 661 TRP cc_start: 0.5207 (OUTLIER) cc_final: 0.4900 (m100) REVERT: A 662 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7669 (pt0) REVERT: A 663 LYS cc_start: 0.7347 (mttp) cc_final: 0.6909 (pttm) REVERT: A 686 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7204 (tp30) REVERT: A 688 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6622 (tm-30) REVERT: A 692 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7529 (p0) REVERT: A 728 MET cc_start: 0.7237 (pmm) cc_final: 0.6915 (pmm) REVERT: B 434 GLN cc_start: 0.7355 (pp30) cc_final: 0.7148 (pp30) REVERT: B 473 MET cc_start: -0.1093 (ttt) cc_final: -0.1404 (ttt) REVERT: D 292 LEU cc_start: 0.3997 (OUTLIER) cc_final: 0.3662 (mt) REVERT: D 330 PHE cc_start: 0.5523 (m-10) cc_final: 0.5313 (m-10) REVERT: D 380 VAL cc_start: 0.6140 (OUTLIER) cc_final: 0.5826 (t) REVERT: E 401 GLN cc_start: 0.7363 (mt0) cc_final: 0.6279 (tp40) REVERT: M 225 LYS cc_start: 0.7504 (tppt) cc_final: 0.6742 (tppt) REVERT: M 258 TYR cc_start: 0.4203 (p90) cc_final: 0.2688 (t80) REVERT: M 266 LEU cc_start: 0.2529 (OUTLIER) cc_final: 0.2178 (mm) REVERT: N 568 ASP cc_start: 0.5576 (OUTLIER) cc_final: 0.4802 (m-30) REVERT: O 525 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: O 590 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: O 606 PHE cc_start: 0.5582 (t80) cc_final: 0.5086 (t80) REVERT: P 705 ARG cc_start: 0.7844 (tpm170) cc_final: 0.7550 (mmp80) REVERT: T 247 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6247 (tt0) REVERT: T 280 LYS cc_start: 0.7255 (mmtm) cc_final: 0.6947 (mmtm) REVERT: T 294 LYS cc_start: 0.7002 (mmtt) cc_final: 0.6454 (mmtt) REVERT: T 301 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.3066 (mt-10) REVERT: g 90 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7384 (tt0) outliers start: 58 outliers final: 37 residues processed: 247 average time/residue: 0.3119 time to fit residues: 108.9296 Evaluate side-chains 236 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 661 TRP Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 694 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 464 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 314 LEU 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 187 ILE Chi-restraints excluded: chain M residue 190 GLU 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 661 GLU Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain 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 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 90 GLU Chi-restraints excluded: chain g residue 98 ASN Chi-restraints excluded: chain g residue 138 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 136 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS B 335 ASN B 406 ASN D 289 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 HIS E 300 HIS ** 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** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.121869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.106874 restraints weight = 69251.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.106539 restraints weight = 57427.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.106473 restraints weight = 62962.416| |-----------------------------------------------------------------------------| r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.025 15422 Z= 0.634 Angle : 0.800 17.299 20583 Z= 0.440 Chirality : 0.046 0.200 2269 Planarity : 0.005 0.087 2643 Dihedral : 5.344 46.197 1960 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.56 % Rotamer: Outliers : 3.71 % Allowed : 24.94 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1781 helix: 0.54 (0.14), residues: 1309 sheet: -0.55 (0.77), residues: 44 loop : -2.27 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A 661 HIS 0.026 0.002 HIS B 289 PHE 0.024 0.003 PHE M 300 TYR 0.067 0.003 TYR A 295 ARG 0.009 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06528 ( 1015) hydrogen bonds : angle 4.82747 ( 3021) covalent geometry : bond 0.01566 (15422) covalent geometry : angle 0.80016 (20583) *********************** 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 257 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 194 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.4890 (OUTLIER) cc_final: 0.4606 (pm20) REVERT: A 686 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: A 728 MET cc_start: 0.7342 (pmm) cc_final: 0.7004 (pmm) REVERT: B 319 GLN cc_start: 0.7317 (mm110) cc_final: 0.7084 (mm110) REVERT: B 332 LEU cc_start: 0.7045 (mp) cc_final: 0.6373 (tt) REVERT: D 289 ASN cc_start: 0.5548 (t0) cc_final: 0.4834 (m110) REVERT: D 380 VAL cc_start: 0.6247 (OUTLIER) cc_final: 0.5825 (t) REVERT: E 264 LYS cc_start: 0.7220 (tttt) cc_final: 0.6824 (mmmt) REVERT: E 401 GLN cc_start: 0.7279 (mt0) cc_final: 0.5756 (tp40) REVERT: M 225 LYS cc_start: 0.7514 (tppt) cc_final: 0.6771 (tppt) REVERT: M 258 TYR cc_start: 0.4466 (p90) cc_final: 0.2825 (t80) REVERT: N 568 ASP cc_start: 0.5266 (OUTLIER) cc_final: 0.4790 (m-30) REVERT: O 525 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7383 (mp10) REVERT: O 590 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: O 606 PHE cc_start: 0.5652 (t80) cc_final: 0.5215 (t80) REVERT: P 684 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6193 (mp10) REVERT: T 247 GLU cc_start: 0.6816 (tm-30) cc_final: 0.6134 (tt0) REVERT: T 301 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.4538 (mp0) REVERT: T 343 LEU cc_start: 0.7294 (mp) cc_final: 0.6708 (mp) REVERT: g 124 ARG cc_start: 0.6825 (tpp-160) cc_final: 0.6418 (mmt-90) REVERT: g 126 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8134 (t0) outliers start: 63 outliers final: 37 residues processed: 239 average time/residue: 0.2940 time to fit residues: 100.6196 Evaluate side-chains 227 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 GLU 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 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 D residue 339 VAL Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL 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 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 236 MET Chi-restraints excluded: chain M residue 302 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 603 TYR Chi-restraints excluded: chain N residue 605 ASP Chi-restraints excluded: chain N residue 640 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain O residue 679 HIS Chi-restraints excluded: chain 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 290 GLU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 119 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 88 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 104 optimal weight: 7.9990 chunk 94 optimal weight: 0.3980 chunk 101 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 60 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 692 ASN B 335 ASN ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS M 289 GLN ** 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** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 135 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.124202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.108995 restraints weight = 69079.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.108928 restraints weight = 57269.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.109409 restraints weight = 48319.860| |-----------------------------------------------------------------------------| r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6634 moved from start: 0.7177 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= 0.614 Angle : 0.715 16.816 20583 Z= 0.395 Chirality : 0.043 0.191 2269 Planarity : 0.004 0.078 2643 Dihedral : 4.975 44.646 1960 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 25.88 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1781 helix: 0.78 (0.14), residues: 1316 sheet: -0.52 (0.77), residues: 48 loop : -2.23 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 661 HIS 0.028 0.002 HIS B 289 PHE 0.024 0.002 PHE g 184 TYR 0.059 0.002 TYR A 295 ARG 0.010 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.05981 ( 1015) hydrogen bonds : angle 4.54853 ( 3021) covalent geometry : bond 0.01518 (15422) covalent geometry : angle 0.71536 (20583) *********************** 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 248 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 686 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6864 (tp30) REVERT: A 728 MET cc_start: 0.7526 (pmm) cc_final: 0.7200 (pmm) REVERT: B 319 GLN cc_start: 0.7138 (mm110) cc_final: 0.6861 (mm110) REVERT: B 332 LEU cc_start: 0.6828 (mp) cc_final: 0.6378 (tt) REVERT: B 432 ASP cc_start: 0.8301 (t0) cc_final: 0.8052 (t0) REVERT: D 289 ASN cc_start: 0.6032 (t0) cc_final: 0.5435 (m110) REVERT: D 380 VAL cc_start: 0.5793 (OUTLIER) cc_final: 0.5267 (t) REVERT: E 264 LYS cc_start: 0.7132 (tttt) cc_final: 0.6764 (mmmt) REVERT: E 401 GLN cc_start: 0.7112 (mt0) cc_final: 0.6713 (mt0) REVERT: E 461 MET cc_start: 0.4480 (tpt) cc_final: 0.4256 (tpt) REVERT: M 225 LYS cc_start: 0.7363 (tppt) cc_final: 0.6663 (tppt) REVERT: M 258 TYR cc_start: 0.4191 (p90) cc_final: 0.2765 (t80) REVERT: N 568 ASP cc_start: 0.5674 (OUTLIER) cc_final: 0.5064 (m-30) REVERT: O 525 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7262 (mp10) REVERT: O 590 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7599 (pm20) REVERT: O 606 PHE cc_start: 0.5644 (t80) cc_final: 0.5090 (t80) REVERT: P 684 GLN cc_start: 0.6428 (OUTLIER) cc_final: 0.5969 (mp10) REVERT: P 689 GLU cc_start: 0.5759 (tm-30) cc_final: 0.5338 (mm-30) REVERT: T 247 GLU cc_start: 0.6741 (tm-30) cc_final: 0.6281 (tt0) REVERT: T 294 LYS cc_start: 0.6870 (mmtt) cc_final: 0.6506 (mmtt) REVERT: T 301 GLU cc_start: 0.4590 (OUTLIER) cc_final: 0.4129 (mp0) REVERT: T 343 LEU cc_start: 0.7281 (mp) cc_final: 0.6582 (mt) REVERT: g 124 ARG cc_start: 0.7072 (tpp-160) cc_final: 0.6628 (mmt-90) outliers start: 47 outliers final: 33 residues processed: 234 average time/residue: 0.3185 time to fit residues: 105.5322 Evaluate side-chains 232 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 290 CYS 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 D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL 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 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 268 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 640 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 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 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 290 GLU 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 98 ASN Chi-restraints excluded: chain g residue 121 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 109 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 156 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** A 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 434 GLN ** 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 300 HIS ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 GLN ** 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** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.122732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.107822 restraints weight = 69072.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.107160 restraints weight = 58333.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.107481 restraints weight = 50816.736| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.7353 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= 0.625 Angle : 0.770 16.785 20583 Z= 0.421 Chirality : 0.045 0.185 2269 Planarity : 0.005 0.086 2643 Dihedral : 5.156 45.305 1960 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer: Outliers : 3.00 % Allowed : 25.76 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1781 helix: 0.65 (0.14), residues: 1311 sheet: -0.57 (0.81), residues: 44 loop : -2.22 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP A 661 HIS 0.027 0.002 HIS B 289 PHE 0.024 0.002 PHE M 300 TYR 0.062 0.002 TYR A 295 ARG 0.012 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.06221 ( 1015) hydrogen bonds : angle 4.67967 ( 3021) covalent geometry : bond 0.01546 (15422) covalent geometry : angle 0.76986 (20583) ********************** 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 247 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 1.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 320 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6902 (tp) REVERT: A 339 GLN cc_start: 0.6923 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: A 663 LYS cc_start: 0.7524 (mttp) cc_final: 0.7175 (pttt) REVERT: A 686 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7092 (tp30) REVERT: A 728 MET cc_start: 0.7439 (pmm) cc_final: 0.7168 (pmm) REVERT: B 319 GLN cc_start: 0.7211 (mm110) cc_final: 0.6985 (mm110) REVERT: B 332 LEU cc_start: 0.6915 (mp) cc_final: 0.6186 (tt) REVERT: D 337 TYR cc_start: 0.6217 (m-80) cc_final: 0.5964 (m-80) REVERT: D 380 VAL cc_start: 0.6021 (OUTLIER) cc_final: 0.5488 (t) REVERT: E 264 LYS cc_start: 0.7264 (tttt) cc_final: 0.6905 (mmmt) REVERT: E 401 GLN cc_start: 0.6868 (mt0) cc_final: 0.6628 (mt0) REVERT: M 225 LYS cc_start: 0.7451 (tppt) cc_final: 0.6721 (tppt) REVERT: M 258 TYR cc_start: 0.3773 (p90) cc_final: 0.2717 (t80) REVERT: N 568 ASP cc_start: 0.5422 (OUTLIER) cc_final: 0.4844 (m-30) REVERT: O 525 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7336 (mp10) REVERT: O 590 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: O 606 PHE cc_start: 0.5582 (t80) cc_final: 0.5096 (t80) REVERT: P 684 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6024 (mp10) REVERT: T 247 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6290 (tt0) REVERT: T 280 LYS cc_start: 0.7005 (mmtm) cc_final: 0.6645 (mmtm) REVERT: T 294 LYS cc_start: 0.6915 (mmtt) cc_final: 0.6539 (mmtt) REVERT: T 301 GLU cc_start: 0.5071 (OUTLIER) cc_final: 0.4716 (mp0) REVERT: T 343 LEU cc_start: 0.7293 (mp) cc_final: 0.6591 (mt) REVERT: g 124 ARG cc_start: 0.6974 (tpp-160) cc_final: 0.6540 (mmt-90) REVERT: g 126 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.8104 (t0) outliers start: 51 outliers final: 31 residues processed: 231 average time/residue: 0.3055 time to fit residues: 100.4959 Evaluate side-chains 231 residues out of total 1700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 190 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 339 GLN 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 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 D residue 369 SER Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain E residue 364 LEU Chi-restraints excluded: chain E residue 458 THR Chi-restraints excluded: chain M residue 174 PHE Chi-restraints excluded: chain M residue 187 ILE Chi-restraints excluded: chain M residue 190 GLU Chi-restraints excluded: chain M residue 268 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 640 LYS Chi-restraints excluded: chain N residue 727 VAL Chi-restraints excluded: chain N residue 728 ILE Chi-restraints excluded: chain N residue 759 ASP Chi-restraints excluded: chain O residue 525 GLN Chi-restraints excluded: chain O residue 550 LYS Chi-restraints excluded: chain O residue 551 LEU Chi-restraints excluded: chain O residue 571 LEU Chi-restraints excluded: chain O residue 590 GLU Chi-restraints excluded: chain O residue 658 MET Chi-restraints excluded: chain 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 290 GLU 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 98 ASN Chi-restraints excluded: chain g residue 121 MET Chi-restraints excluded: chain g residue 126 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 89 optimal weight: 20.0000 chunk 171 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 HIS ** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS ** M 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 289 GLN ** N 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 691 ASN ** P 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.123431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.108383 restraints weight = 69201.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.108502 restraints weight = 57897.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.108578 restraints weight = 51210.251| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.7472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 1.031 15422 Z= 0.616 Angle : 0.733 16.747 20583 Z= 0.403 Chirality : 0.043 0.184 2269 Planarity : 0.005 0.079 2643 Dihedral : 5.027 44.804 1960 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 25.88 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.20), residues: 1781 helix: 0.75 (0.14), residues: 1313 sheet: -0.45 (0.85), residues: 43 loop : -2.20 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP A 661 HIS 0.028 0.002 HIS B 289 PHE 0.023 0.002 PHE M 300 TYR 0.060 0.002 TYR A 295 ARG 0.011 0.001 ARG E 284 Details of bonding type rmsd hydrogen bonds : bond 0.05956 ( 1015) hydrogen bonds : angle 4.56100 ( 3021) covalent geometry : bond 0.01525 (15422) covalent geometry : angle 0.73264 (20583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6843.15 seconds wall clock time: 120 minutes 13.23 seconds (7213.23 seconds total)